From noreply at r-forge.r-project.org Tue Jun 19 18:43:06 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 19 Jun 2018 18:43:06 +0200 (CEST) Subject: [R-gregmisc-commits] r2173 - in pkg/gtools: R man Message-ID: <20180619164306.1BE4118109D@r-forge.r-project.org> Author: warnes Date: 2018-06-19 18:43:05 +0200 (Tue, 19 Jun 2018) New Revision: 2173 Modified: pkg/gtools/R/baseOf.R pkg/gtools/man/baseOf.Rd Log: Improvements to baseOf() function. Modified: pkg/gtools/R/baseOf.R =================================================================== --- pkg/gtools/R/baseOf.R 2017-08-23 23:03:36 UTC (rev 2172) +++ pkg/gtools/R/baseOf.R 2018-06-19 16:43:05 UTC (rev 2173) @@ -1,32 +1,73 @@ +# Transform integer to array of digits in specified +baseOf <- function(v, + b=10, + l=1) +{ + if (is.null(v)) + stop("v is null") + if(length(v)==0) + return(integer(0)) -# transform base -# -# This function rewrites regular integer numbers as an array of its digits. -# The base of the numbering scheme may be changed away from 10, -# which defines our decimal system, to any other integer value. For -# b=2, the number is returned in the dual system. The least significant -# digit has the highest index in the array, i.e. it appears on the right. -# -# v = value of base 10 to be transformed -# b = new base -# l = minimal length of returned array (default is 1) -# return value: array of factors, highest exponent first -baseOf<-function(v,b=10,l=1) { - remainder<-v - i<-l - ret<-NULL - while(remainder>0 || i>0) { - #print(paste("i=",i," remainder=",remainder)) - m<-remainder%%b - if (is.null(ret)) { - ret<-m - } - else { - ret<-c(m,ret) - } - remainder <- remainder %/% b - i<-i-1 - } - return(ret) + if(any(as.integer(v) != v)) + stop("non-integer value(s) provided for v.") + + if (length(v) > 1) + { + # this returns a list which may have vectors of varying lenths + val.list <- lapply(X=v, FUN=baseOf.inner, b=b, l=l) + longest <- max(sapply(val.list, length)) + + # call again, forcing all elements to have the same lenth + retval <- t(sapply(X=v, FUN=baseOf.inner, b=b, l=longest)) + + # add informative row and column names + rownames(retval) <- paste0('v.', v) + colnames(retval) <- paste0('b.', c(0, b^(1: (longest- 1) ) ) ) + + retval + } + else + retval <- baseOf.inner(v=v, b=b, l=l) + + retval } - + + +# Transform integer to array of digits in specified +baseOf.inner <- function(v, + b=10, + l=1) +{ + if (is.na(v)) + return(rep(NA, l)) + + if(v==0) + return(rep(0, l)) + + remainder <- v + i <- l + ret <- NULL + while(remainder > 0 || i >0) + { + #print(paste("i=",i," remainder=",remainder)) + m <- remainder%%b + if (is.null(ret)) + { + ret <- m + } + else + { + ret <- c(m,ret) + } + remainder <- remainder %/% b + i <- i-1 + } + + if(length(ret)>1) + names(ret) <- c(0, b^( 1:(length(ret)- 1 ) ) ) + + return(ret) +} + + + Modified: pkg/gtools/man/baseOf.Rd =================================================================== --- pkg/gtools/man/baseOf.Rd 2017-08-23 23:03:36 UTC (rev 2172) +++ pkg/gtools/man/baseOf.Rd 2018-06-19 16:43:05 UTC (rev 2173) @@ -1,11 +1,11 @@ \name{baseOf} \alias{baseOf} -\title{Transform integer to new base} +\title{Transform an integer to an array of base-n digits} \description{ -Transforms a given base-10 integer to an array of digits of another base. +Transform an integer to an array of base-n digits } \usage{ -baseOf(v,b=10,l=1) +baseOf(v, base=10, len=1) } \arguments{ \item{v}{ @@ -19,12 +19,33 @@ } } \details{ - This function rewrites regular integer numbers as an array of its digits. + This function converts the elements of an integer vector as an array of its digits. The base of the numbering scheme may be changed away from 10, which defines our decimal system, to any other integer value. For b=2, the number is returned in the dual system. The least significant digit has the highest index in the array, i.e. it appears on the right. The highest exponent is at position 1, i.e. left. + + To write decimal values in another base is very common in computer science. + In particular at the basis 2 the then possible values 0 and 1 are often + interpreted as logical false or true. And at the very interface to + electrical engineering, it is indicacted as an absence or presence of + voltage. When several bit values are transported synchronously, then + it is common to give every lane of such a data bus a unique 2^x value + and interpret it as a number in the dual system. To distinguish 256 + characters one once needed 8 bit ("byte"). It is the common + unit in which larger non-printable data is presented. + Because of the many non-printable characters and the difficulty for most humans to + memorize an even longer alphabet, it is presented as two half bytes ("nibble") + of 4 bit in a hexadecimal presentation. Example code is shown below. + + For statisticians, it is more likely to use bit representations for + hashing. A bit set to 1 (TRUE) at e.g. position 2, 9 or 17 is interpreted + as the presence of a particular feature combination of a sample. + With baseOf, you can refer to the bit combination as a number, which + is more easily and more efficiently dealt with than with an array of + binary values. The example code presents a counter of combinations of + features which may be interpreted as a Venn diagram. } \author{Steffen Moeller \email{moeller at debian.org} } \examples{ @@ -42,6 +63,21 @@ paste(c(0:9,LETTERS)[baseOf(123,16)],collapse="") # decimal representation but filling leading zeroes baseOf(123,l=5) +# and converting that back +sum(2^(4:0)*baseOf(123,l=5)) +# hashing and a tabular venn diagram derived from it +m<-matrix(sample(c(FALSE,TRUE),replace=TRUE,size=300),ncol=4) +colnames(m)<-c("strong","colorful","nice","humorous") +names(dimnames(m)) <- c("samples","features") +head(m) +m.val <- apply(m,1,function(X){return(sum(2^((ncol(m)-1):0)*X))}) +m.val.rle <- rle(sort(m.val)) +m.counts <- cbind(t(baseOf(m.val.rle$value,b=2,l=ncol(m))), + m.val.rle$length) +colnames(m.counts)<- c(colnames(m),"num") +rownames(m.counts)<- apply(m.counts[,1:ncol(m)],1,paste,collapse="") +m.counts[1==m.counts[,"nice"]&1==m.counts[,"humorous"],,drop=F] +m.counts[,"num",drop=T] } \keyword{base} From noreply at r-forge.r-project.org Tue Jun 19 18:43:56 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 19 Jun 2018 18:43:56 +0200 (CEST) Subject: [R-gregmisc-commits] r2174 - in pkg/gtools: R man Message-ID: <20180619164356.EE9CE18004D@r-forge.r-project.org> Author: warnes Date: 2018-06-19 18:43:55 +0200 (Tue, 19 Jun 2018) New Revision: 2174 Added: pkg/gtools/R/split_path.R pkg/gtools/man/split_path.Rd Log: Add spit_path() function. Added: pkg/gtools/R/split_path.R =================================================================== --- pkg/gtools/R/split_path.R (rev 0) +++ pkg/gtools/R/split_path.R 2018-06-19 16:43:55 UTC (rev 2174) @@ -0,0 +1,29 @@ +#' Split a File Path into Components +#' +#' @description This function converts a character scalar containing a +#' \emph{valid} file path into a character vector of path components +#' (e.g. directories). +#' +#' @param character scalar. Path to be processed. +#' @param depth_firs logical. Should path be returned depth first? Defaults +#' to \code{TRUE}. +#' +#' @return Character vector of path components, depth first. +#' +#' @export +#' +split_path <- function(x, depth_first=TRUE) +{ + if(length(x)>1) warning("This function is not vectorized.", + "Only processing the first element of x.") + retval <- split_path_inner(x) + if(!depth_first) + retval <- rev(retval) + retval[retval>""] +} + + +split_path_inner <- function(path) { + if (dirname(path) %in% c(".", path)) return(basename(path)) + return(c(basename(path), split_path_inner(dirname(path)))) +} Added: pkg/gtools/man/split_path.Rd =================================================================== --- pkg/gtools/man/split_path.Rd (rev 0) +++ pkg/gtools/man/split_path.Rd 2018-06-19 16:43:55 UTC (rev 2174) @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/split_path.R +\name{split_path} +\alias{split_path} +\title{Split a File Path into Components} +\usage{ +split_path(x, depth_first = TRUE) +} +\arguments{ +\item{character}{scalar. Path to be processed.} + +\item{depth_firs}{logical. Should path be returned depth first? Defaults +to \code{TRUE}.} +} +\value{ +Character vector of path components, depth first. +} +\description{ +This function converts a character scalar containing a + \emph{valid} file path into a character vector of path components + (e.g. directories). +} From noreply at r-forge.r-project.org Tue Jun 19 18:48:57 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 19 Jun 2018 18:48:57 +0200 (CEST) Subject: [R-gregmisc-commits] r2175 - pkg/gtools Message-ID: <20180619164857.67A52186FC5@r-forge.r-project.org> Author: warnes Date: 2018-06-19 18:48:56 +0200 (Tue, 19 Jun 2018) New Revision: 2175 Modified: pkg/gtools/DESCRIPTION pkg/gtools/NAMESPACE Log: Update DESCRIPTION and NAMESPACE for gtools 3.8.0. Modified: pkg/gtools/DESCRIPTION =================================================================== --- pkg/gtools/DESCRIPTION 2018-06-19 16:43:55 UTC (rev 2174) +++ pkg/gtools/DESCRIPTION 2018-06-19 16:48:56 UTC (rev 2175) @@ -21,11 +21,12 @@ - modify the TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - - convert characters to/from ASCII codes. -Version: 3.7.0 -Date: 2017-06-14 + - convert characters to/from ASCII codes ('asc', 'chr'). + - convert character vector to ASCII representation ('ASCIIfy') +Version: 3.8.0 +Date: 2018-06-19 Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley Maintainer: Gregory R. Warnes License: GPL-2 Depends: methods, stats, utils - +NeedsCompilation: yes Modified: pkg/gtools/NAMESPACE =================================================================== --- pkg/gtools/NAMESPACE 2018-06-19 16:43:55 UTC (rev 2174) +++ pkg/gtools/NAMESPACE 2018-06-19 16:48:56 UTC (rev 2175) @@ -7,6 +7,7 @@ ask, assert, assignEdgewise, + baseOf, binsearch, capture, capwords, @@ -39,6 +40,7 @@ scat, setTCPNoDelay, smartbind, + split_path, sprint, stars.pval, strmacro, From noreply at r-forge.r-project.org Wed Jun 20 17:28:10 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 17:28:10 +0200 (CEST) Subject: [R-gregmisc-commits] r2176 - in pkg/gtools: R man Message-ID: <20180620152810.21A0B180457@r-forge.r-project.org> Author: warnes Date: 2018-06-20 17:28:09 +0200 (Wed, 20 Jun 2018) New Revision: 2176 Modified: pkg/gtools/R/baseOf.R pkg/gtools/man/baseOf.Rd Log: Revert argument names for baseOf() to 'base' and 'len' instead of 'b' and 'l'. Modified: pkg/gtools/R/baseOf.R =================================================================== --- pkg/gtools/R/baseOf.R 2018-06-19 16:48:56 UTC (rev 2175) +++ pkg/gtools/R/baseOf.R 2018-06-20 15:28:09 UTC (rev 2176) @@ -1,7 +1,7 @@ -# Transform integer to array of digits in specified +# Transform integer to array of digits in specified base baseOf <- function(v, - b=10, - l=1) + base=10, + len=1) { if (is.null(v)) stop("v is null") @@ -14,20 +14,20 @@ if (length(v) > 1) { # this returns a list which may have vectors of varying lenths - val.list <- lapply(X=v, FUN=baseOf.inner, b=b, l=l) + val.list <- lapply(X=v, FUN=baseOf.inner, base=base, len=len) longest <- max(sapply(val.list, length)) # call again, forcing all elements to have the same lenth - retval <- t(sapply(X=v, FUN=baseOf.inner, b=b, l=longest)) + retval <- t(sapply(X=v, FUN=baseOf.inner, base=base, len=longest)) # add informative row and column names rownames(retval) <- paste0('v.', v) - colnames(retval) <- paste0('b.', c(0, b^(1: (longest- 1) ) ) ) + colnames(retval) <- paste0('b.', c(0, base^(1: (longest- 1) ) ) ) retval } else - retval <- baseOf.inner(v=v, b=b, l=l) + retval <- baseOf.inner(v=v, base=base, len=len) retval } @@ -35,22 +35,22 @@ # Transform integer to array of digits in specified baseOf.inner <- function(v, - b=10, - l=1) + base=10, + len=1) { if (is.na(v)) - return(rep(NA, l)) + return(rep(NA, len)) if(v==0) - return(rep(0, l)) + return(rep(0, len)) remainder <- v - i <- l + i <- len ret <- NULL while(remainder > 0 || i >0) { #print(paste("i=",i," remainder=",remainder)) - m <- remainder%%b + m <- remainder%%base if (is.null(ret)) { ret <- m @@ -59,12 +59,12 @@ { ret <- c(m,ret) } - remainder <- remainder %/% b + remainder <- remainder %/% base i <- i-1 } if(length(ret)>1) - names(ret) <- c(0, b^( 1:(length(ret)- 1 ) ) ) + names(ret) <- c(0, base^( 1:(length(ret)- 1 ) ) ) return(ret) } Modified: pkg/gtools/man/baseOf.Rd =================================================================== --- pkg/gtools/man/baseOf.Rd 2018-06-19 16:48:56 UTC (rev 2175) +++ pkg/gtools/man/baseOf.Rd 2018-06-20 15:28:09 UTC (rev 2176) @@ -11,10 +11,10 @@ \item{v}{ A single integer value to be transformed. } - \item{b}{ + \item{base}{ The base to which to transform to. } - \item{l}{ + \item{len}{ The minimal length of the returned array. } } @@ -22,7 +22,7 @@ This function converts the elements of an integer vector as an array of its digits. The base of the numbering scheme may be changed away from 10, which defines our decimal system, to any other integer value. For - b=2, the number is returned in the dual system. The least significant + base=2, the number is returned in the dual system. The least significant digit has the highest index in the array, i.e. it appears on the right. The highest exponent is at position 1, i.e. left. @@ -51,32 +51,41 @@ \examples{ # decimal representation baseOf(123) + # dual representation -baseOf(123,b=2) +baseOf(123,base=2) + # octal representation -baseOf(123,b=8) +baseOf(123,base=8) + # hexadecimal representation -baseOf(123,b=16) +baseOf(123,base=16) + # hexadecimal with more typical letter-notation c(0:9,LETTERS)[baseOf(123,16)] + # hexadecimal again, now showing a single string paste(c(0:9,LETTERS)[baseOf(123,16)],collapse="") + # decimal representation but filling leading zeroes -baseOf(123,l=5) +baseOf(123,len=5) + # and converting that back -sum(2^(4:0)*baseOf(123,l=5)) +sum(2^(4:0)*baseOf(123,len=5)) + # hashing and a tabular venn diagram derived from it m<-matrix(sample(c(FALSE,TRUE),replace=TRUE,size=300),ncol=4) colnames(m)<-c("strong","colorful","nice","humorous") names(dimnames(m)) <- c("samples","features") head(m) + m.val <- apply(m,1,function(X){return(sum(2^((ncol(m)-1):0)*X))}) m.val.rle <- rle(sort(m.val)) -m.counts <- cbind(t(baseOf(m.val.rle$value,b=2,l=ncol(m))), - m.val.rle$length) +m.counts <- cbind(baseOf(m.val.rle$value,base=2,len=ncol(m)), + m.val.rle$lengths) colnames(m.counts)<- c(colnames(m),"num") rownames(m.counts)<- apply(m.counts[,1:ncol(m)],1,paste,collapse="") -m.counts[1==m.counts[,"nice"]&1==m.counts[,"humorous"],,drop=F] +m.counts[1==m.counts[,"nice"]&1==m.counts[,"humorous"],,drop=FALSE] m.counts[,"num",drop=T] } \keyword{base} From noreply at r-forge.r-project.org Wed Jun 20 17:28:48 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 17:28:48 +0200 (CEST) Subject: [R-gregmisc-commits] r2177 - pkg/gtools/man Message-ID: <20180620152848.A2F1B180457@r-forge.r-project.org> Author: warnes Date: 2018-06-20 17:28:48 +0200 (Wed, 20 Jun 2018) New Revision: 2177 Modified: pkg/gtools/man/baseOf.Rd Log: Use 'TRUE' instead of 'T' in example. Modified: pkg/gtools/man/baseOf.Rd =================================================================== --- pkg/gtools/man/baseOf.Rd 2018-06-20 15:28:09 UTC (rev 2176) +++ pkg/gtools/man/baseOf.Rd 2018-06-20 15:28:48 UTC (rev 2177) @@ -86,7 +86,7 @@ colnames(m.counts)<- c(colnames(m),"num") rownames(m.counts)<- apply(m.counts[,1:ncol(m)],1,paste,collapse="") m.counts[1==m.counts[,"nice"]&1==m.counts[,"humorous"],,drop=FALSE] -m.counts[,"num",drop=T] +m.counts[,"num",drop=TRUE] } \keyword{base} From noreply at r-forge.r-project.org Wed Jun 20 17:29:34 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 17:29:34 +0200 (CEST) Subject: [R-gregmisc-commits] r2178 - in pkg/gtools: R man Message-ID: <20180620152934.EB174180457@r-forge.r-project.org> Author: warnes Date: 2018-06-20 17:29:34 +0200 (Wed, 20 Jun 2018) New Revision: 2178 Modified: pkg/gtools/R/split_path.R pkg/gtools/man/split_path.Rd Log: Fix function argument documenation for 'split_path()' Modified: pkg/gtools/R/split_path.R =================================================================== --- pkg/gtools/R/split_path.R 2018-06-20 15:28:48 UTC (rev 2177) +++ pkg/gtools/R/split_path.R 2018-06-20 15:29:34 UTC (rev 2178) @@ -4,8 +4,8 @@ #' \emph{valid} file path into a character vector of path components #' (e.g. directories). #' -#' @param character scalar. Path to be processed. -#' @param depth_firs logical. Should path be returned depth first? Defaults +#' @param x character scalar. Path to be processed. +#' @param depth_first logical. Should path be returned depth first? Defaults #' to \code{TRUE}. #' #' @return Character vector of path components, depth first. Modified: pkg/gtools/man/split_path.Rd =================================================================== --- pkg/gtools/man/split_path.Rd 2018-06-20 15:28:48 UTC (rev 2177) +++ pkg/gtools/man/split_path.Rd 2018-06-20 15:29:34 UTC (rev 2178) @@ -7,9 +7,9 @@ split_path(x, depth_first = TRUE) } \arguments{ -\item{character}{scalar. Path to be processed.} +\item{x}{character scalar. Path to be processed.} -\item{depth_firs}{logical. Should path be returned depth first? Defaults +\item{depth_first}{logical. Should path be returned depth first? Defaults to \code{TRUE}.} } \value{ From noreply at r-forge.r-project.org Wed Jun 20 17:30:39 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 17:30:39 +0200 (CEST) Subject: [R-gregmisc-commits] r2179 - pkg/gtools Message-ID: <20180620153039.1B05D180457@r-forge.r-project.org> Author: warnes Date: 2018-06-20 17:30:38 +0200 (Wed, 20 Jun 2018) New Revision: 2179 Modified: pkg/gtools/DESCRIPTION Log: Add asc(), chr(), and ASCIIfy() to package summary text. Modified: pkg/gtools/DESCRIPTION =================================================================== --- pkg/gtools/DESCRIPTION 2018-06-20 15:29:34 UTC (rev 2178) +++ pkg/gtools/DESCRIPTION 2018-06-20 15:30:38 UTC (rev 2179) @@ -21,8 +21,8 @@ - modify the TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - - convert characters to/from ASCII codes ('asc', 'chr'). - - convert character vector to ASCII representation ('ASCIIfy') + - convert characters to/from ASCII codes ('asc', 'chr'), + - convert character vector to ASCII representation ('ASCIIfy'). Version: 3.8.0 Date: 2018-06-19 Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley From noreply at r-forge.r-project.org Wed Jun 20 17:31:19 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 17:31:19 +0200 (CEST) Subject: [R-gregmisc-commits] r2180 - pkg/gtools/R Message-ID: <20180620153119.46D70180457@r-forge.r-project.org> Author: warnes Date: 2018-06-20 17:31:18 +0200 (Wed, 20 Jun 2018) New Revision: 2180 Modified: pkg/gtools/R/smartbind.R Log: Add parenthesis for clarity (should have no functional difference). Modified: pkg/gtools/R/smartbind.R =================================================================== --- pkg/gtools/R/smartbind.R 2018-06-20 15:30:38 UTC (rev 2179) +++ pkg/gtools/R/smartbind.R 2018-06-20 15:31:18 UTC (rev 2180) @@ -9,9 +9,9 @@ { data <- modifyList(list, data) } - data <- data[!sapply(data, function(l) is.null(l) | ncol(l)==0 | nrow(l)==0)] - + data <- data[!sapply(data, function(l) is.null(l) | (ncol(l)==0) | (nrow(l)==0) )] + defaultNames <- seq.int(length(data)) if(is.null(names(data))) @@ -28,7 +28,7 @@ else data.frame(as.list(x), check.names=FALSE) ) - + #retval <- new.env() retval <- base::list() rowLens <- unlist(lapply(data, nrow)) From noreply at r-forge.r-project.org Wed Jun 20 22:35:54 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 22:35:54 +0200 (CEST) Subject: [R-gregmisc-commits] r2181 - pkg/gmodels Message-ID: <20180620203554.BE54C18124A@r-forge.r-project.org> Author: warnes Date: 2018-06-20 22:35:54 +0200 (Wed, 20 Jun 2018) New Revision: 2181 Removed: pkg/gmodels/test/ Log: Remove duplicated/incorrect 'test' directory. From noreply at r-forge.r-project.org Wed Jun 20 22:40:23 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 22:40:23 +0200 (CEST) Subject: [R-gregmisc-commits] r2182 - pkg/gmodels/R Message-ID: <20180620204024.06A1E180B49@r-forge.r-project.org> Author: warnes Date: 2018-06-20 22:40:23 +0200 (Wed, 20 Jun 2018) New Revision: 2182 Modified: pkg/gmodels/R/est_p_ci.R Log: Use base::trimws() instead of gdata::trim() Modified: pkg/gmodels/R/est_p_ci.R =================================================================== --- pkg/gmodels/R/est_p_ci.R 2018-06-20 20:35:54 UTC (rev 2181) +++ pkg/gmodels/R/est_p_ci.R 2018-06-20 20:40:23 UTC (rev 2182) @@ -7,7 +7,7 @@ if(is.character(term) && !(term %in% rownames(info))) stop(term, " is not a coefficient in model.") info <- info[term,] - info.ci <- trim(format( round(mult * info[1:3], digits=digits) )) + info.ci <- trimws(format( round(mult * info[1:3], digits=digits) )) if(mult < 0) names(info.ci) <- rev(names(info.ci)) paste("Est=", info.ci[1], @@ -26,11 +26,11 @@ { if( !all(c("lower CI", "upper CI") %in% colnames(model) ) ) stop("object does not contain confidence interval information.") - - if(is.character(term) && !(term %in% rownames(info))) + + if(is.character(term) && !(term %in% rownames(model))) stop(term, " is not a coefficient in model.") - - info.ci <- trim(format( round(mult * model[term, c("lower CI", "upper CI")], + + info.ci <- trimws(format( round(mult * model[term, c("lower CI", "upper CI")], digits=digits) ) ) if(mult < 0) names(info.ci) <- rev(names(info.ci)) From noreply at r-forge.r-project.org Wed Jun 20 22:42:47 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 22:42:47 +0200 (CEST) Subject: [R-gregmisc-commits] r2183 - pkg/gmodels/R Message-ID: <20180620204248.43BB9180B49@r-forge.r-project.org> Author: warnes Date: 2018-06-20 22:42:45 +0200 (Wed, 20 Jun 2018) New Revision: 2183 Modified: pkg/gmodels/R/ci.R Log: Remove trailing whitespace Modified: pkg/gmodels/R/ci.R =================================================================== --- pkg/gmodels/R/ci.R 2018-06-20 20:40:23 UTC (rev 2182) +++ pkg/gmodels/R/ci.R 2018-06-20 20:42:45 UTC (rev 2183) @@ -116,12 +116,12 @@ } -ci.fit_contrast <- function (x, confidence = 0.95, alpha = 1 - confidence, ...) +ci.fit_contrast <- function (x, confidence = 0.95, alpha = 1 - confidence, ...) { if( !all(c("lower CI", "upper CI") %in% colnames(x) ) ) stop("object does not contain confidence interval information.") - colnames(x) <- c("Estimate", "Std. Error", "Delete", - "p-value", + colnames(x) <- c("Estimate", "Std. Error", "Delete", + "p-value", "CI lower", "CI upper") x[, c(1, 5:6, 2, 4), drop=FALSE] } From noreply at r-forge.r-project.org Wed Jun 20 22:46:34 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 22:46:34 +0200 (CEST) Subject: [R-gregmisc-commits] r2184 - in pkg/gmodels: R man Message-ID: <20180620204635.02AF3184F14@r-forge.r-project.org> Author: warnes Date: 2018-06-20 22:46:34 +0200 (Wed, 20 Jun 2018) New Revision: 2184 Modified: pkg/gmodels/R/fit.contrast.R pkg/gmodels/man/ci.Rd pkg/gmodels/man/estimable.Rd pkg/gmodels/man/fit.contrast.Rd Log: Fix R CMD check issues. Modified: pkg/gmodels/R/fit.contrast.R =================================================================== --- pkg/gmodels/R/fit.contrast.R 2018-06-20 20:42:45 UTC (rev 2183) +++ pkg/gmodels/R/fit.contrast.R 2018-06-20 20:46:34 UTC (rev 2184) @@ -1,8 +1,8 @@ # $Id$ fit.contrast.lm <- function(model, varname, coeff, showall=FALSE, - conf.int, - df=FALSE, + conf.int=NULL, + df=FALSE, ...) { # check class of model @@ -102,10 +102,10 @@ if(!df) retval <- retval[,-5,drop=FALSE] - + class(retval) <- "fit_contrast" - - retval + + retval } # fit.contrast.lme and fit.contrast.mer are necessary because Modified: pkg/gmodels/man/ci.Rd =================================================================== --- pkg/gmodels/man/ci.Rd 2018-06-20 20:42:45 UTC (rev 2183) +++ pkg/gmodels/man/ci.Rd 2018-06-20 20:46:34 UTC (rev 2184) @@ -2,11 +2,11 @@ % \name{ci} \alias{ci} -\alias{ci.default} +\alias{ci.numeric} \alias{ci.binom} \alias{ci.lm} \alias{ci.lme} -\alias{ci.mer} +%%\alias{ci.mer} \alias{ci.estimable} \alias{ci.fit_contrast} \title{Compute Confidence Intervals} @@ -17,13 +17,13 @@ provided. } \usage{ ci(x, confidence=0.95, alpha=1 - confidence, ...) - \method{ci}{default}(x, confidence=0.95, alpha=1-confidence, na.rm=FALSE, ...) + \method{ci}{numeric}(x, confidence=0.95, alpha=1-confidence, na.rm=FALSE, ...) \method{ci}{binom}(x, confidence=0.95, alpha=1-confidence, ...) \method{ci}{lm}(x, confidence=0.95, alpha=1-confidence, ...) \method{ci}{lme}(x, confidence=0.95, alpha=1-confidence, ...) - \method{ci}{mer}(x, confidence=0.95, alpha=1-confidence, n.sim=10000, ...) - \method{ci}{estimable}(x, confidence=0.95, alpha=1-confidence, ...) - \method{ci}{fit_contrast}(x, confidence=0.95, alpha=1-confidence, ...) +%%\method{ci}{mer}(x, confidence=0.95, alpha=1-confidence, n.sim=10000, ...) + \method{ci}{estimable}(x, confidence=0.95, alpha=1-confidence, ...) + \method{ci}{fit_contrast}(x, confidence=0.95, alpha=1-confidence, ...) } \arguments{ \item{x}{ object from which to compute confidence intervals. } @@ -32,7 +32,7 @@ \item{na.rm}{boolean indicating whether missing values should be removed. Defaults to \code{FALSE}.} \item{\dots}{Arguments for methods} - \item{n.sim}{Number of samples to take in \code{mcmcsamp}.} +%% \item{n.sim}{Number of samples to take in \code{mcmcsamp}.} } %\details{ % ~~ If necessary, more details than the __description__ above ~~ @@ -52,7 +52,7 @@ \examples{ -# mean and confidence interval +# mean and confidence interval ci( rnorm(10) ) # binomial proportion and exact confidence interval @@ -64,13 +64,13 @@ # confidence intervals for regression parameteres data(state) reg <- lm(Area ~ Population, data=as.data.frame(state.x77)) -ci(reg) +ci(reg) %\dontrun{ -# mer example -library(lme4) -fm2 <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) -ci(fm2) +%# mer example +%library(lme4) +%fm2 <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) +%ci(fm2) %} Modified: pkg/gmodels/man/estimable.Rd =================================================================== --- pkg/gmodels/man/estimable.Rd 2018-06-20 20:42:45 UTC (rev 2183) +++ pkg/gmodels/man/estimable.Rd 2018-06-20 20:46:34 UTC (rev 2184) @@ -3,7 +3,7 @@ \name{estimable} \alias{estimable} \alias{estimable.default} -\alias{estimable.mer} +%%\alias{estimable.mer} \alias{estimable.mlm} %\alias{.wald} %\alias{.to.est} @@ -16,8 +16,8 @@ \usage{ estimable(obj, cm, beta0, conf.int=NULL, show.beta0, ...) \method{estimable}{default} (obj, cm, beta0, conf.int=NULL, show.beta0, joint.test=FALSE, ...) -\method{estimable}{mer}(obj, cm, beta0, conf.int=NULL, - show.beta0, sim.mer=TRUE, n.sim=1000, ...) +%%\method{estimable}{mer}(obj, cm, beta0, conf.int=NULL, +%% show.beta0, sim.mer=TRUE, n.sim=1000, ...) \method{estimable}{mlm}(obj, cm, beta0, conf.int=NULL, show.beta0, ...) %.wald(obj, cm,beta0=rep(0, ifelse(is.null(nrow(cm)), 1, nrow(cm)))) %.to.est(obj, params) @@ -37,12 +37,12 @@ \item{show.beta0}{Logical value. If TRUE a column for beta0 will be included in the output table. Defaults to TRUE when beta0 is specified, FALSE otherwise.} - \item{sim.mer}{Logical value. If TRUE p-values and confidence - intervals will be estimated using \code{mcmcsamp}. - } - \item{n.sim}{Number of MCMC samples to take in - \code{mcmcsamp}. - } +%% \item{sim.mer}{Logical value. If TRUE p-values and confidence +%% intervals will be estimated using \code{mcmcsamp}. +%% } +%% \item{n.sim}{Number of MCMC samples to take in +%% \code{mcmcsamp}. +%% } \item{...}{ignored} } \details{ @@ -61,12 +61,12 @@ subset of) the model parameters, and each row should contain the corresponding coefficient to be applied. Model parameters which are not present in the set of column names of \code{cm} will be set to zero. - + The estimates and their variances are obtained by applying the contrast matrix (generated from) \code{cm} to the model estimates variance-covariance matrix. Degrees of freedom are obtained from the appropriate model terms. - + The user is responsible for ensuring that the specified linear functions are meaningful. @@ -91,10 +91,10 @@ the beta0 value (optional, see \code{show.beta0} above), estimated coefficients, standard errors, t values, degrees of freedom, two-sided p-values, and the lower and upper endpoints of the - 1-alpha confidence intervals. + 1-alpha confidence intervals. } \author{ - BXC (Bendix Carstensen) \email{bxc\@novonordisk.com}, + BXC (Bendix Carstensen) \email{bxc\@novonordisk.com}, Gregory R. Warnes \email{greg at warnes.net}, Soren Hojsgaard \email{sorenh at agrsci.dk}, and Randall C Johnson \email{rjohnson at ncifcrf.gov} @@ -142,11 +142,11 @@ # Sepal.Width by Species interaction terms. data(iris) lm1 <- lm (Sepal.Length ~ Sepal.Width + Species + Sepal.Width:Species, data=iris) -glm1 <- glm(Sepal.Length ~ Sepal.Width + Species + Sepal.Width:Species, data=iris, +glm1 <- glm(Sepal.Length ~ Sepal.Width + Species + Sepal.Width:Species, data=iris, family=quasipoisson("identity")) cm <- rbind( - 'Setosa vs. Versicolor' = c(0, 0, 1, 0, 1, 0), + 'Setosa vs. Versicolor' = c(0, 0, 1, 0, 1, 0), 'Setosa vs. Virginica' = c(0, 0, 0, 1, 0, 1), 'Versicolor vs. Virginica'= c(0, 0, 1,-1, 1,-1) ) Modified: pkg/gmodels/man/fit.contrast.Rd =================================================================== --- pkg/gmodels/man/fit.contrast.Rd 2018-06-20 20:42:45 UTC (rev 2183) +++ pkg/gmodels/man/fit.contrast.Rd 2018-06-20 20:46:34 UTC (rev 2184) @@ -4,7 +4,7 @@ \alias{fit.contrast} \alias{fit.contrast.lm} \alias{fit.contrast.lme} -\alias{fit.contrast.mer} +%%\alias{fit.contrast.mer} \title{Compute and test arbitrary contrasts for regression objects} \description{ Compute and test arbitrary contrasts for regression objects. @@ -15,12 +15,12 @@ conf.int=NULL, df=FALSE, ...) \method{fit.contrast}{lme}(model, varname, coeff, showall=FALSE, conf.int=NULL, df=FALSE, ...) -\method{fit.contrast}{mer}(model, varname, coeff, showall=FALSE, - conf.int=NULL, sim.mer = TRUE, n.sim = 1000, ...) +%% \method{fit.contrast}{mer}(model, varname, coeff, showall=FALSE, +%% conf.int=NULL, sim.mer = TRUE, n.sim = 1000, ...) } \arguments{ \item{model}{regression (lm,glm,aov,lme) object for which the - contrast(s) will be computed.} + contrast(s) will be computed.} \item{varname}{variable name} \item{coeff}{vector or matrix specifying contrasts (one per row).} \item{showall}{return all regression coefficients. If \code{TRUE}, all @@ -34,12 +34,12 @@ \item{df}{boolean indicating whether to return a column containing the degrees of freedom.} \item{\dots}{optional arguments provided by methods.} - \item{sim.mer}{Logical value. If TRUE p-values and confidence - intervals will be estimated using \code{mcmcsamp}. This option only takes effect for mer - objects.} - \item{n.sim}{Number of samples to use in \code{mcmcsamp}.} +%% \item{sim.mer}{Logical value. If TRUE p-values and confidence +%% intervals will be estimated using \code{mcmcsamp}. This option only takes effect for mer +%% objects.} +%% \item{n.sim}{Number of samples to use in \code{mcmcsamp}.} } - + \details{ Computes the specified contrast(s) by re-fitting the model with the appropriate arguments. A contrast of the form \code{c(1,0,0,-1)} @@ -51,7 +51,7 @@ containing the degrees of freedom is included. If \code{conf.int} is specified lower and upper confidence limits are also returned.} \references{Venables & Ripley, Section 6.2} - + \author{ Gregory R. Warnes \email{greg at warnes.net}} \seealso{ \code{\link{lm}}, \code{\link{contrasts}}, @@ -83,7 +83,7 @@ sum(-1/2*gm[1], -1/2*gm[2], 1/2*gm[3], 1/2*gm[4]) # mean of 1st group vs mean of 2nd, 3rd and 4th groups -fit.contrast(reg, x, c( -3/3, 1/3, 1/3, 1/3) ) +fit.contrast(reg, x, c( -3/3, 1/3, 1/3, 1/3) ) # estimate should be equal to: sum(-3/3*gm[1], 1/3*gm[2], 1/3*gm[3], 1/3*gm[4]) @@ -138,10 +138,10 @@ "2 vs 3" = 2 ) ) ) -# example for lme +# example for lme library(nlme) data(Orthodont) -fm1 <- lme(distance ~ Sex, data = Orthodont,random=~1|Subject) +fm1 <- lme(distance ~ Sex, data = Orthodont,random=~1|Subject) # Contrast for sex. This example is equivalent to standard treatment # contrast. From noreply at r-forge.r-project.org Wed Jun 20 22:50:52 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 22:50:52 +0200 (CEST) Subject: [R-gregmisc-commits] r2185 - pkg/gmodels Message-ID: <20180620205052.4C94E1805A8@r-forge.r-project.org> Author: warnes Date: 2018-06-20 22:50:51 +0200 (Wed, 20 Jun 2018) New Revision: 2185 Modified: pkg/gmodels/NAMESPACE Log: Remove obsolete functions. Modified: pkg/gmodels/NAMESPACE =================================================================== --- pkg/gmodels/NAMESPACE 2018-06-20 20:46:34 UTC (rev 2184) +++ pkg/gmodels/NAMESPACE 2018-06-20 20:50:51 UTC (rev 2185) @@ -1,4 +1,3 @@ - export( CrossTable, ci, @@ -14,19 +13,19 @@ summary.glh.test ) -S3method(ci, default) S3method(ci, binom) S3method(ci, lm) S3method(ci, lme) -S3method(ci, mer) +#S3method(ci, mer) +S3method(ci, numeric) S3method(ci, estimable) S3method(fit.contrast, lm) S3method(fit.contrast, lme) -S3method(fit.contrast, mer) +#S3method(fit.contrast, mer) S3method(estimable, default) -S3method(estimable, mer) +#S3method(estimable, mer) S3method(estimable, mlm) S3method(print, glh.test) From noreply at r-forge.r-project.org Wed Jun 20 22:51:40 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 22:51:40 +0200 (CEST) Subject: [R-gregmisc-commits] r2186 - in pkg/gmodels: . inst Message-ID: <20180620205140.CAAFA1805A8@r-forge.r-project.org> Author: warnes Date: 2018-06-20 22:51:40 +0200 (Wed, 20 Jun 2018) New Revision: 2186 Modified: pkg/gmodels/DESCRIPTION pkg/gmodels/inst/ChangeLog Log: Update DESCRIPTION and ChangeLog for gmodels 2.16.1 Modified: pkg/gmodels/DESCRIPTION =================================================================== --- pkg/gmodels/DESCRIPTION 2018-06-20 20:50:51 UTC (rev 2185) +++ pkg/gmodels/DESCRIPTION 2018-06-20 20:51:40 UTC (rev 2186) @@ -1,6 +1,6 @@ Package: gmodels -Version: 2.16.0 -Date: 2014-07-24 +Version: 2.16.1 +Date: 2018-06-20 Title: Various R programming tools for model fitting Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley, and Randall C Johnson. Contributions from Randall C. Johnson are Copyright @@ -8,7 +8,7 @@ Program, of the NIH, National Cancer Institute, Center for Cancer Research under NCI Contract NO1-CO-12400. Maintainer: Gregory R. Warnes -Description: Various R programming tools for model fitting +Description: Various R programming tools for model fitting. Depends: R (>= 1.9.0) Suggests: gplots, gtools, Matrix, nlme, lme4 (>= 0.999999-0) Imports: MASS, gdata, stats Modified: pkg/gmodels/inst/ChangeLog =================================================================== --- pkg/gmodels/inst/ChangeLog 2018-06-20 20:50:51 UTC (rev 2185) +++ pkg/gmodels/inst/ChangeLog 2018-06-20 20:51:40 UTC (rev 2186) @@ -1,194 +1,350 @@ -2014-07-24 warnes +2018-06-20 20:35 warnes - * [r1868] DESCRIPTION, NAMESPACE, R/ci.R, R/estimable.R, man/ci.Rd, - man/estimable.Rd: - Estimable now adds the class 'estimable' to - returned objects. + * test: Remove duplicated/incorrect 'test' directory. + +2017-06-12 23:53 warnes + + * DESCRIPTION: Update imports + +2017-06-12 23:53 warnes + + * NAMESPACE: Add imports for base R packages to NAMESPACE + +2017-06-05 21:27 warnes + + * inst/NEWS: Update NEWS and ChangeLog files for 2.18.0. + +2016-08-15 19:11 warnes + + * test, test/lme-test.R, test/test_estimable_mlm.R: Add tests for + mlm and (obsolete) lme + +2016-08-15 19:05 warnes + + * R/est_p_ci.R: Add est_p_ci generic and lm method + +2016-08-12 17:15 warnes + + * DESCRIPTION, NAMESPACE, R/ci.R, R/fit.contrast.R, inst/ChangeLog, + inst/NEWS, man/ci.Rd, man/estimable.Rd, man/fit.contrast.Rd: + Updates... + +2015-07-22 00:53 warnes + + * DESCRIPTION: Update gmodels DESCRIPTION + +2015-07-22 00:48 warnes + + * test, tests, tests/lme-test.R: Renamed 'test' directory to + 'tests', commented out tests for lme4 which has a changed API + +2015-07-20 23:38 warnes + + * DESCRIPTION, NAMESPACE: Changs to squash new R CMD check warnings + +2015-07-19 03:22 warnes + + * DESCRIPTION, NAMESPACE, R/ci.R, R/est.mer.R, R/estimable.R, + R/fit.contrast.R, R/to.est.R, inst/NEWS, man/ci.Rd, + man/estimable.Rd, man/fit.contrast.Rd: - Removed references to + 'mer' objects, sincel the nlme4 update is not backwards + compatible with my code. + - Removed 'require' calls. + +2015-07-19 02:34 warnes + + * DESCRIPTION, inst/ChangeLog, inst/NEWS: Update DESCRIPTION, + ChangeLog, and NEWS for gmodels 2.16.1 + +2015-07-19 02:30 warnes + + * R/ci.R, man/ci.Rd: ci.binom() was using an incorrect method for + calculating binomial confidence interval. The revised code + calculates the Clopper-Pearson 'exect' interval, which is + *conservative* due to the discrete nature of the binomial + distribution. + +2015-05-02 17:38 warnes + + * Rename 'trunk' to 'pkg' for compatibility with R-forge + +2015-04-06 21:52 warnes + + * Add ChangeLog files to repository + +2014-07-24 15:18 warnes + + * Update NEWS for gmodels 2.16.0 + +2014-07-24 15:14 warnes + + * - Estimable now adds the class 'estimable' to returned objects. - New ci() method for estimable objects. - Minor improvemets to man page formatting. -2013-07-18 warnes +2013-07-18 14:09 warnes - * [r1710] DESCRIPTION, inst/NEWS: Looks like Brian Ripley - repackaged for R 3.0.0 and bumped version number, so change it to - 2.15.5 - * [r1709] DESCRIPTION, inst/NEWS: Update for gmodels 2.15.4 - * [r1708] man/ci.Rd: Update to current Rd syntax - * [r1707] R/estimable.mlm.R, test/test_estimable_mlm.R: Correct bug - in estimable.mlm + * Looks like Brian Ripley repackaged for R 3.0.0 and bumped version + number, so change it to 2.15.5 -2013-07-15 warnes +2013-07-18 13:57 warnes - * [r1706] R/ci.R, man/ci.Rd: Remove unused argument to ci.mer + * Update for gmodels 2.15.4 -2012-06-28 warnes +2013-07-18 13:54 warnes - * [r1577] DESCRIPTION, inst/NEWS: Update for gmodels version - 2.15.3. - * [r1576] R/percentile.R: Move percentile() function to a separate - file. - * [r1575] R/est.lmer.R, R/est.mer.R: Update est.mer() to support - new S4 "mer" class. - * [r1574] man/ci.Rd: Make lme4 example executable. + * Update to current Rd syntax -2012-06-27 warnes +2013-07-18 13:46 warnes - * [r1573] test/lme-test.R: Add test code submitted by - Ariel.Muldoon at oregonstate.edu. + * Correct bug in estimable.mlm -2012-04-19 warnes +2013-07-15 18:13 warnes - * [r1528] inst/NEWS: Update for release 2.15.2 - * [r1527] DESCRIPTION: Update version and date. - * [r1526] man/estimable.Rd: The 'Design' package has been replaced - my 'rms', so update man page references. - * [r1525] R/ci.R, R/est.mer.R: More fixes for support of S4 'mer' - class from lme4 package. - * [r1524] man/coefFrame.Rd: Split long line. - * [r1523] man/ci.Rd, man/glh.test.Rd: Changes to pass R CMD check + * Remove unused argument to ci.mer -2011-12-14 warnes +2012-06-28 00:49 warnes - * [r1521] R/ci.R: Improve formatting of ci.mer(). - * [r1520] R/est.mer.R: Modify est.mer to work with recent lme4 - 'mer' S4 objects. + * Update for gmodels version 2.15.3. -2011-01-16 warnes +2012-06-28 00:47 warnes - * [r1466] DESCRIPTION, inst/NEWS, man/ci.Rd, man/estimable.Rd, - man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd, - man/make.contrasts.Rd: Fix warnings reported by R CMD check. - Update version number to 2.15.1. + * Move percentile() function to a separate file. -2009-05-09 warnes +2012-06-28 00:41 warnes - * [r1337] test, test/lme-test.R: Add tests for lme4 'mer' objects - * [r1336] inst/NEWS: Update for 2.15.0 - * [r1335] DESCRIPTION: Update description for 2.15.0 - * [r1334] R/est.mer.R: Add support for lme4's 'mer' objects - * [r1333] NAMESPACE, R/ci.R, R/est.lmer.R, R/estimable.R, - R/fit.contrast.R, R/to.est.R: Add support for lme4's 'mer' - objects - * [r1332] man/glh.test.Rd: Fix .Rd syntax error - * [r1331] NEWS: Add softlinks for ChangeLog and NEWS to top level - dir for convenience - * [r1330] ChangeLog, NEWS, inst, inst/NEWS: Move ChangeLog and NEWS - files into inst directory - * [r1329] DESCRIPTION, man/ci.Rd, man/estimable.Rd, - man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd, - man/make.contrasts.Rd: Update Greg's email address + * Update est.mer() to support new S4 "mer" class. -2008-04-10 warnes +2012-06-28 00:40 warnes - * [r1255] man/ci.Rd: Improve languages a bit + * Make lme4 example executable. -2008-01-02 warnes +2012-06-27 22:42 warnes - * [r1236] man/CrossTable.Rd: Update Marc's email address + * Add test code submitted by Ariel.Muldoon at oregonstate.edu. -2007-12-12 warnes +2012-04-19 22:09 warnes - * [r1233] DESCRIPTION: Move copyright notice for Randall's - contributions from License section to Author section of the - DESCRIPTION file. + * Update for release 2.15.2 -2007-12-07 warnes +2012-04-19 22:07 warnes - * [r1232] DESCRIPTION, NEWS: Update DESCRIPTION and NEWS for - release 2.14.1 - * [r1231] man/estimable.Rd: Correct minor typos in man page for - estimable() - * [r1230] R/estimable.R: Add support for lme models to estimable() - * [r1229] man/estimable.Rd: Replace non-ascii characters in Soren's - name with (equivalent?) ascii character to avoid character - encoding issues. + * Update version and date. -2007-10-22 warnes +2012-04-19 22:06 warnes - * [r1196] DESCRIPTION: Clarify GPL version + * The 'Design' package has been replaced my 'rms', so update man + page references. -2007-07-26 warnes +2012-04-19 22:05 warnes - * [r1105] DESCRIPTION, NAMESPACE, NEWS, R/estimable.mlm.R, - man/estimable.Rd: Add support for mlm to estimable(). - * [r1104] R/estimable.R, R/estimable.mlm.R: Add estimable method - for mlm objects + * More fixes for support of S4 'mer' class from lme4 package. -2007-03-09 warnes +2012-04-19 21:13 warnes - * [r1079] R/ci.R: Remove stray character - * [r1078] NEWS: Update NEWS file. - * [r1077] DESCRIPTION: Update version number - * [r1076] R/ci.R: Minor code formatting changes - * [r1075] R/est.lmer.R, man/ci.Rd: Flip lower and upper interval in - ci.lmer(). Add example to man page. - * [r1074] man/ci.Rd, man/estimable.Rd: Fix some old email - addressses that got missed + * Split long line. -2006-11-29 warnes +2012-04-19 17:50 warnes - * [r1029] NEWS: Update for 2.13.1 - * [r1028] NAMESPACE: Correct declartion of S3 methods for - estimable() - * [r1027] DESCRIPTION: Add additional suggested packages - * [r1026] R/estimable.R, man/estimable.Rd: - Add generic + * Changes to pass R CMD check + +2011-12-14 18:17 warnes + + * Improve formatting of ci.mer(). + +2011-12-14 18:14 warnes + + * Modify est.mer to work with recent lme4 'mer' S4 objects. + +2011-01-16 22:17 warnes + + * Fix warnings reported by R CMD check. Update version number to + 2.15.1. + +2009-05-09 05:29 warnes + + * Add tests for lme4 'mer' objects + +2009-05-09 05:04 warnes + + * Update for 2.15.0 + +2009-05-09 05:02 warnes + + * Update description for 2.15.0 + +2009-05-09 05:01 warnes + + * Add support for lme4's 'mer' objects + +2009-05-09 05:00 warnes + + * Add support for lme4's 'mer' objects + +2009-05-09 04:53 warnes + + * Fix .Rd syntax error + +2009-05-09 04:37 warnes + + * Add softlinks for ChangeLog and NEWS to top level dir for + convenience + +2009-05-09 04:36 warnes + + * Move ChangeLog and NEWS files into inst directory + +2009-05-09 04:00 warnes + + * Update Greg's email address + +2008-04-10 14:05 warnes + + * Improve languages a bit + +2008-01-02 16:56 warnes + + * Update Marc's email address + +2007-12-12 21:16 warnes + + * Move copyright notice for Randall's contributions from License + section to Author section of the DESCRIPTION file. + +2007-12-07 22:21 warnes + + * Update DESCRIPTION and NEWS for release 2.14.1 + +2007-12-07 22:10 warnes + + * Correct minor typos in man page for estimable() + +2007-12-07 22:09 warnes + + * Add support for lme models to estimable() + +2007-12-07 22:07 warnes + + * Replace non-ascii characters in Soren's name with (equivalent?) + ascii character to avoid character encoding issues. + +2007-10-22 02:24 warnes + + * Clarify GPL version + +2007-07-26 00:20 warnes + + * Add support for mlm to estimable(). + +2007-07-26 00:10 warnes + + * Add estimable method for mlm objects + +2007-03-09 22:35 warnes + + * Remove stray character + +2007-03-09 20:10 warnes + + * Update NEWS file. + +2007-03-09 20:07 warnes + + * Update version number + +2007-03-09 20:06 warnes + + * Minor code formatting changes + +2007-03-09 20:06 warnes + + * Flip lower and upper interval in ci.lmer(). Add example to man + page. + +2007-03-09 19:43 warnes + + * Fix some old email addressses that got missed + +2006-11-29 00:11 warnes + + * Update for 2.13.1 + +2006-11-29 00:05 warnes + + * Correct declartion of S3 methods for estimable() + +2006-11-29 00:05 warnes + + * Add additional suggested packages + +2006-11-29 00:04 warnes + + * - Add generic - Fix code vs. doc inconsistiencies -2006-11-28 warnes +2006-11-28 22:38 warnes - * [r1025] R/ci.R, R/estimable.R, R/fast.prcomp.R: Remove extraneous - comma that causes errors in R 2.5.0 + * Remove extraneous comma that causes errors in R 2.5.0 -2006-11-27 warnes +2006-11-27 20:45 warnes - * [r1016] DESCRIPTION, NEWS: Update for 2.13.1 - * [r1015] DESCRIPTION, NAMESPACE: Add missing export of methods for - estimable() + * Update for 2.13.1 -2006-11-14 ggorjan +2006-11-27 20:36 warnes - * [r1012] R/ci.R, R/fast.prcomp.R, man/ci.Rd: Removed executable - property + * Add missing export of methods for estimable() -2006-08-02 warnes +2006-11-14 22:25 ggorjan - * [r977] man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd, - man/make.contrasts.Rd: Update my email address + * Removed executable property -2006-06-06 nj7w +2006-08-02 22:21 warnes - * [r966] man/ci.Rd, man/estimable.Rd, man/fit.contrast.Rd: Updated - ci, estimable and fit.contrast as per Randall Johnson + * Update my email address -2006-06-05 nj7w +2006-06-06 19:17 nj7w - * [r965] DESCRIPTION: Additions as per Randall C Johnson - * [r964] R/ci.R, R/estimable.R, R/fit.contrast.R, R/to.est.R: - Additions as per Randall C Johnson - * [r963] R/est.lmer.R: - New function to estimate CI's and p-values - using mcmcsamp() from the + * Updated ci, estimable and fit.contrast as per Randall Johnson + +2006-06-05 21:00 nj7w + + * Additions as per Randall C Johnson + +2006-06-05 20:59 nj7w + + * Additions as per Randall C Johnson + +2006-06-05 20:57 nj7w + + * - New function to estimate CI's and p-values using mcmcsamp() + from the Matrix package -2006-05-05 nj7w +2006-05-05 18:29 nj7w - * [r959] R/CrossTable.R, man/CrossTable.Rd: Fixed an error: - According to Marc Schwartz - there was an error when a matrix - without dimnames(or names(dimnames)) was passed as x argument + * Fixed an error: According to Marc Schwartz - there was an error + when a matrix without dimnames(or names(dimnames)) was passed as + x argument -2005-12-13 nj7w +2005-12-13 16:03 nj7w - * [r808] ChangeLog: Removed ChangeLog - * [r807] NEWS: Updated NEWS + * Removed ChangeLog -2005-12-12 nj7w +2005-12-13 16:02 nj7w - * [r796] DESCRIPTION: Updated version number for CRAN + * Updated NEWS -2005-12-04 warnes +2005-12-12 21:57 nj7w - * [r781] NEWS: Update for 2.11.0 - * [r780] DESCRIPTION, NAMESPACE, R/ci.R, R/estimable.R, - R/fit.contrast.R, R/to.est.R, man/ci.Rd, man/estimable.Rd: - Integration of code changes suggested by Randall C Johnson to add + * Updated version number for CRAN + +2005-12-04 06:27 warnes + + * Update for 2.11.0 + +2005-12-04 06:12 warnes + + * Integration of code changes suggested by Randall C Johnson to add support for lmer (lme version 4) objects to ci(), estimable(), and fit.contrast(). @@ -201,69 +357,76 @@ estimable(reg, c( 0, 1, 0, -1) ) which should make estimable much easier to use for large models. -2005-12-01 nj7w +2005-12-01 16:54 nj7w - * [r776] man/ci.Rd, man/coefFrame.Rd, man/estimable.Rd, - man/fit.contrast.Rd, man/make.contrasts.Rd: Updated Greg's email - address + * Updated Greg's email address -2005-10-27 warnes +2005-10-27 11:21 warnes - * [r709] DESCRIPTION: Update version number. Bump minor version - since we added functionality. - * [r708] DESCRIPTION, NAMESPACE: Add ci.binom() to NAMESPACE, bump - version + * Update version number. Bump minor version since we added + functionality. -2005-10-26 warnes +2005-10-27 10:33 warnes - * [r707] R/ci.R, man/ci.Rd: Add ci.binom + * Add ci.binom() to NAMESPACE, bump version -2005-10-25 warnes +2005-10-26 13:39 warnes - * [r706] NAMESPACE: Add gdata::nobs to import list. Needed by ci() + * Add ci.binom -2005-09-12 nj7w +2005-10-25 21:18 warnes - * [r671] man/fast.prcomp.Rd, man/glh.test.Rd: Updated Greg's email + * Add gdata::nobs to import list. Needed by ci() -2005-09-07 nj7w +2005-09-12 15:44 nj7w - * [r667] man/CrossTable.Rd: Fixed man page + * Updated Greg's email -2005-09-06 nj7w +2005-09-07 15:31 nj7w - * [r664] DESCRIPTION: Updated DESCRIPTION - * [r663] NEWS: Added NEWS - * [r662] DESCRIPTION: Fixed the Package name + * Fixed man page -2005-09-02 nj7w +2005-09-06 21:34 nj7w - * [r655] ChangeLog: Added ChangeLog + * Updated DESCRIPTION -2005-08-31 nj7w +2005-09-06 21:34 nj7w - * [r644] DESCRIPTION: Added DESCRIPTION file - * [r643] DESCRIPTION.in: removed DESCRIPTION.in + * Added NEWS -2005-07-11 nj7w +2005-09-06 16:21 nj7w - * [r627] R/CrossTable.R, man/CrossTable.Rd: Revision based on Marc - Schwartz's suggestions: + * Fixed the Package name + +2005-09-02 23:10 nj7w + + * Added ChangeLog + +2005-08-31 16:28 nj7w + + * Added DESCRIPTION file + +2005-08-31 16:27 nj7w + + * removed DESCRIPTION.in + +2005-07-11 21:35 nj7w + + * Revision based on Marc Schwartz's suggestions: 1) Added 'dnn' argument to enable specification of dimnames as per table() 2) Corrected bug in SPSS output for 1d table, where proportions were being printed and not percentages ('%' output) -2005-06-09 nj7w +2005-06-09 14:20 nj7w - * [r625] R/ci.R, R/coefFrame.R, R/estimable.R, R/fast.prcomp.R, - R/fit.contrast.R, R/glh.test.R, R/make.contrasts.R, - man/CrossTable.Rd, man/ci.Rd, man/coefFrame.Rd, man/estimable.Rd, - man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd, - man/make.contrasts.Rd: Updating the version number, and various - help files to synchronize splitting of gregmisc bundle in 4 - individual components. - * [r623] R/CrossTable.R: Updates by Marc Schwartz: + * Updating the version number, and various help files to + synchronize splitting of gregmisc bundle in 4 individual + components. + +2005-06-09 14:13 nj7w + + * Updates by Marc Schwartz: CrossTable: # Revision 2.0 2005/04/27 @@ -271,110 +434,110 @@ # so that large integers do not print in # scientific notation -2005-05-13 nj7w +2005-05-13 18:59 nj7w - * [r621] man/CrossTable.Rd: 1) Using dQuote.ascii function in - read.xls as the new version of dQuote doesn't work proprly with - UTF-8 locale. + * 1) Using dQuote.ascii function in read.xls as the new version of + dQuote doesn't work proprly with UTF-8 locale. 2) Modified CrossTable.Rd usage in gmodels 3) Modified heatmap.2 usage in gplots. -2005-05-11 warnes +2005-05-11 13:51 warnes - * [r620] DESCRIPTION.in, NAMESPACE: Add dependency on - gdata::frameApply. + * Add dependency on gdata::frameApply. -2005-03-31 warnes +2005-03-31 20:32 warnes - * [r593] NAMESPACE: Add ceofFrame function to NAMESPACE - * [r592] man/coefFrame.Rd: coefFrame example needs to properly load - ELISA data from gtools package - * [r588] R/CrossTable.R, man/CrossTable.Rd, man/ci.Rd, - man/estimable.Rd, man/fast.prcomp.Rd, man/fit.contrast.Rd, - man/glh.test.Rd, man/make.contrasts.Rd: Ensure that each file has - $Id$ header, and no $Log$ - * [r587] R/coefFrame.R, man/coefFrame.Rd: Add coefFrame() function - contributed by Jim Rogers + * Add ceofFrame function to NAMESPACE -2005-01-18 warnes +2005-03-31 19:05 warnes - * [r521] R/CrossTable.R: Removed Windows Line Endings + * coefFrame example needs to properly load ELISA data from gtools + package -2005-01-14 nj7w +2005-03-31 18:31 warnes - * [r518] man/CrossTable.Rd: Updated the manual to reflect - prop.chisq change in its R file. + * Ensure that each file has $Id$ header, and no $Log$ -2005-01-14 warnes +2005-03-31 18:30 warnes - * [r517] R/CrossTable.R: Nitin added display of the Chisquare - contribution of each cell, as suggested + * Add coefFrame() function contributed by Jim Rogers + +2005-01-18 19:53 warnes + + * Removed Windows Line Endings + +2005-01-14 21:40 nj7w + + * Updated the manual to reflect prop.chisq change in its R file. + +2005-01-14 19:14 warnes + + * Nitin added display of the Chisquare contribution of each cell, + as suggested by Greg Snow. -2005-01-12 warnes +2005-01-12 20:50 warnes - * [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent - poeple from installing on old + * Add dependency on R 1.9.0+ to prevent poeple from installing on + old versions of R which don't support namespaces. -2004-12-23 nj7w +2004-12-23 19:32 nj7w - * [r507] R/CrossTable.R, man/CrossTable.Rd: Split the function - print.CrossTable.vector in two parts - for SAS behaiour and SPSS - behaviour. Also put the code of printing statistics in a function - 'print.statistics' + * Split the function print.CrossTable.vector in two parts - for SAS + behaiour and SPSS behaviour. Also put the code of printing + statistics in a function 'print.statistics' -2004-12-21 warnes +2004-12-21 22:38 warnes - * [r502] R/CrossTable.R: Added & extended changes made by Nitin to - implement 'SPSS' format, as suggested by + * Added & extended changes made by Nitin to implement 'SPSS' + format, as suggested by Dirk Enzmann . -2004-09-30 warneg +2004-09-30 21:03 warneg - * [r464] man/glh.test.Rd: Fix typos. + * Fix typos. -2004-09-27 warneg +2004-09-27 21:01 warneg - * [r461] DESCRIPTION, DESCRIPTION.in: Updated to pass R CMD check. + * Updated to pass R CMD check. -2004-09-03 warneg +2004-09-03 22:44 warneg - * [r450] man/fit.contrast.Rd: Add explicit package to call to - quantcut in example. - * [r446] DESCRIPTION, NAMESPACE, R/CrossTable.R, R/ci.R, - R/estimable.R, R/fast.prcomp.R, R/fit.contrast.R, R/glh.test.R, - R/make.contrasts.R, man/estimable.Rd, man/fit.contrast.Rd, - man/glh.test.Rd, man/make.contrasts.Rd: initial bundle checkin + * Add explicit package to call to quantcut in example. -2004-09-02 warneg +2004-09-03 17:27 warneg - * [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE: Initial revision + * initial bundle checkin -2004-05-25 warnes +2004-09-02 17:14 warneg - * [r327] R/CrossTable.R, man/CrossTable.Rd: Updates from Mark - Schwartz. + * Initial revision -2004-04-13 warnes +2004-05-25 02:57 warnes - * [r314] man/estimable.Rd: Fix latex warning: it doesn't like - double subscripts. + * Updates from Mark Schwartz. -2004-03-26 warnes +2004-04-13 11:41 warnes - * [r306] man/fast.prcomp.Rd: Reflect movement of code from 'mva' - package to 'stats' in R 1.9.0. + * Fix latex warning: it doesn't like double subscripts. -2004-03-25 warnes +2004-03-26 22:28 warnes - * [r296] R/estimable.R, man/estimable.Rd: - Estimable was reporting - sqrt(X^2) rather than X^2 in the output. + * Reflect movement of code from 'mva' package to 'stats' in R + 1.9.0. + +2004-03-25 20:09 warnes + + * - Estimable was reporting sqrt(X^2) rather than X^2 in the + output. - Provide latex math markup for linear algebra expressions in help text. - Other clarifications in help text - * [r295] R/estimable.R, man/estimable.Rd: Add enhancements to - estimable() provided by S?ren H?jsgaard + +2004-03-25 18:17 warnes + + * Add enhancements to estimable() provided by S?ren H?jsgaard \email{sorenh at agrsci.dk}: I have made a modified version of the function [..] which @@ -382,40 +545,38 @@ 2) can test hypotheses af the forb L * beta = beta0 both as a single Wald test and row-wise for each row in L. -2003-11-17 warnes +2003-11-17 21:40 warnes - * [r221] R/fit.contrast.R: - Fix incorrect handling of glm objects - by fit.contrast, as reported + * - Fix incorrect handling of glm objects by fit.contrast, as + reported by Ulrich Halekoh, Phd . - Add regression test code to for this bug. -2003-08-07 warnes +2003-08-07 03:49 warnes - * [r217] R/ci.R: - Fixed incorrect denominator in standard error - for mean in ci.default. + * - Fixed incorrect denominator in standard error for mean in + ci.default. -2003-04-22 warnes +2003-04-22 17:24 warnes - * [r190] R/fit.contrast.R: - the variable 'df' was used within the - lme code section overwriting + * - the variable 'df' was used within the lme code section + overwriting the argument 'df'. -2003-03-12 warnes +2003-03-12 17:58 warnes - * [r173] man/fit.contrast.Rd: - Fixed a typo in the example + * - Fixed a typo in the example - Added to lme example -2003-03-07 warnes +2003-03-07 15:48 warnes - * [r168] R/fast.prcomp.R: - Minor changes to code to allow the - package to be provided as an + * - Minor changes to code to allow the package to be provided as an S-Plus chapter. -2003-01-30 warnes +2003-01-30 21:53 warnes - * [r160] R/fit.contrast.R, man/fit.contrast.Rd: - Renamed - 'contrast.lm' to 'fit.contrast'. This new name is more + * - Renamed 'contrast.lm' to 'fit.contrast'. This new name is more descriptive and makes it easier to create and use methods for other classes, eg lme. @@ -429,8 +590,11 @@ calls fit.contrast - Updated help text to match changes. - * [r158] R/CrossTable.R, man/CrossTable.Rd: - Removed argument - 'correct' and now print separate corrected values + +2003-01-30 21:41 warnes + + * - Removed argument 'correct' and now print separate corrected + values for 2 x 2 tables. - Added arguments 'prop.r', 'prop.c' and 'prop.t' to toggle printing @@ -444,65 +608,72 @@ table counts, proportions and the results of the appropriate statistical tests. - * [r157] R/make.contrasts.R: - Added explicit check to ensure that - the number of specified + +2003-01-30 14:58 warnes + + * - Added explicit check to ensure that the number of specified contrasts is less than or equal to the ncol - 1. Previously, this failed with an obtuse error message when the contrast matrix had row names, and silently dropped contrasts over ncol-1. -2002-11-04 warnes +2002-11-04 14:13 warnes - * [r142] R/CrossTable.R: - Moved fisher.test() to after table is - printed, so that table is + * - Moved fisher.test() to after table is printed, so that table is still printed in the event that fisher.test() results in errors. -2002-10-29 warnes +2002-10-29 23:06 warnes - * [r138] R/fast.prcomp.R, man/fast.prcomp.Rd: - Fixes to fast.svd - to make it actually work. + * - Fixes to fast.svd to make it actually work. - Updates to man page to fix mistmatches between code and docs and to fix warnings. - * [r137] R/make.contrasts.R, man/make.contrasts.Rd: - Moved - make.contrasts to a separate file. + +2002-10-29 23:00 warnes + + * - Moved make.contrasts to a separate file. - Enhanced make contrasts to better label contrast matrix, to give how.many a default value, and to coerce vectors into row matrixes. - Added help page for make.contrasts. - Added link from contrasts.lm seealso to make.contrasts. - * [r136] R/fast.prcomp.R, man/fast.prcomp.Rd: Initial checkin for - fast.prcomp() and fast.svd(). -2002-09-26 warnes +2002-10-29 19:29 warnes - * [r127] man/glh.test.Rd: - Added note and example code to - illustrate how to properly compute + * Initial checkin for fast.prcomp() and fast.svd(). + +2002-09-26 12:11 warnes + + * - Added note and example code to illustrate how to properly + compute contrasts for the first factor in the model. -2002-09-24 warnes +2002-09-24 19:12 warnes - * [r124] R/glh.test.R: - Fixed a typo. + * - Fixed a typo. -2002-09-23 warnes +2002-09-23 14:27 warnes - * [r119] man/CrossTable.Rd, man/glh.test.Rd: - Fixed syntax errors - in barplot2.Rd and CrossTable.Rd + * - Fixed syntax errors in barplot2.Rd and CrossTable.Rd - Fixed incorrect translation of 'F' (distribution) to 'FALSE' in glh.test.Rd - * [r117] R/ci.R, man/estimable.Rd, man/glh.test.Rd: - Modified all - files to include CVS Id and Log tags. - * [r116] R/CrossTable.R, man/CrossTable.Rd: - Added CrossTable() - and barplot2() code and docs contributed by Marc Schwartz. + +2002-09-23 13:59 warnes + + * - Modified all files to include CVS Id and Log tags. + +2002-09-23 13:38 warnes + + * - Added CrossTable() and barplot2() code and docs contributed by + Marc Schwartz. - Permit combinations() to be used when r>n provided repeat.allowed=TRUE - Bumped up version number -2002-08-01 warnes +2002-08-01 19:37 warnes - * [r114] R/ci.R, man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: - - Corrected documentation mismatch for ci, ci.default. + * - Corrected documentation mismatch for ci, ci.default. - Replaced all occurences of '_' for assignment with '<-'. @@ -512,103 +683,130 @@ - Updaded version number and date. -2002-04-09 warneg +2002-04-09 00:51 warneg - * [r109] R/ci.R, R/estimable.R, R/glh.test.R, man/glh.test.Rd: - Checkin for version 0.5.3 + * Checkin for version 0.5.3 -2002-03-26 warneg +2002-03-26 21:22 warneg - * [r104] R/ci.R, R/glh.test.R, man/ci.Rd, man/glh.test.Rd: - - Changed methods to include '...' to match the generic. + * - Changed methods to include '...' to match the generic. - Updated for version 0.5.1 - * [r99] man/glh.test.Rd: Removed incorrect link to 'contrast' from - seealso. -2002-02-20 warneg +2002-03-26 15:30 warneg - * [r81] man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: Minor - changes, typo and formatting fixes. + * Removed incorrect link to 'contrast' from seealso. -2002-01-17 warneg +2002-02-20 20:09 warneg - * [r70] man/estimable.Rd: - Fixed errror in last example by adding - 'conf.int' parameter to + * Minor changes, typo and formatting fixes. + +2002-01-17 23:51 warneg + + * - Fixed errror in last example by adding 'conf.int' parameter to 'estimable' call. - * [r69] R/glh.test.R: - Fixed typo in code that resulted in an - syntax error. -2002-01-10 warneg +2002-01-17 23:42 warneg - * [r68] R/glh.test.R: - print.glh.test() was using cat() to - printing the call. This didn't work and + * - Fixed typo in code that resulted in an syntax error. + +2002-01-10 17:35 warneg + + * - print.glh.test() was using cat() to printing the call. This + didn't work and generated an error. -2001-12-19 warneg +2001-12-19 20:06 warneg - * [r66] man/glh.test.Rd: - Fixed display of formulae. + * - Fixed display of formulae. - Added description of return value - * [r65] R/glh.test.R: - Removed extra element of return object. -2001-12-18 warneg +2001-12-19 20:05 warneg - * [r64] man/estimable.Rd: - Updated documentation to reflect change - of parameters from 'alpha' + * - Removed extra element of return object. + +2001-12-18 22:14 warneg + + * - Updated documentation to reflect change of parameters from + 'alpha' to 'conf.int', including the new optional status of the confidence intervals. - * [r63] R/estimable.R: - Modified to make confidence intervals - optional. Changed 'alpha' + +2001-12-18 22:12 warneg + + * - Modified to make confidence intervals optional. Changed 'alpha' parameter giving significance level to 'conf.int' giving confidence level. - * [r62] man/glh.test.Rd: - Added summary.glh.test to alias, usage, - and example sections. - * [r61] R/glh.test.R: - Modified to work correctly when obj is of - class 'aov' by specifying + +2001-12-18 21:36 warneg + + * - Added summary.glh.test to alias, usage, and example sections. + +2001-12-18 21:34 warneg + + * - Modified to work correctly when obj is of class 'aov' by + specifying summary.lm instead of summary. This ensures that the summary object has the fields we need. - Moved detailed reporting of results from 'print' to 'summary' function and added a simpler report to 'print' - * [r60] R/estimable.R: - Modified to work correctly when obj is of - class 'aov' by specifying + +2001-12-18 21:27 warneg + + * - Modified to work correctly when obj is of class 'aov' by + specifying summary.lm instead of summary. This ensures that the summary object has the fields we need. - * [r59] R/glh.test.R, man/glh.test.Rd: Initial checkin. -2001-12-17 warneg +2001-12-18 00:45 warneg - * [r56] man/estimable.Rd: - Fixed spelling errors. - * [r55] man/estimable.Rd: - Fixed the link to contrasts.lm. + * Initial checkin. + +2001-12-17 18:59 warneg + + * - Fixed spelling errors. + +2001-12-17 18:52 warneg + + * - Fixed the link to contrasts.lm. - Rephrased title/description to be more clear. -2001-12-10 warneg +2001-12-10 19:35 warneg - * [r49] man/estimable.Rd: Renamed 'contrsts.coeff.Rd' to - 'estimable.Rd' corresponding to function rename. - * [r48] R/estimable.R: renamed from contrast.coeff.R to estimable.R - (incorrectly via contrast.lm.R) + * Renamed 'contrsts.coeff.Rd' to 'estimable.Rd' corresponding to + function rename. -2001-12-07 warneg +2001-12-10 19:26 warneg - * [r37] man/ci.Rd: - Added text noting that lme is now supported. - * [r36] R/ci.R: - Fixed typo: DF column was being filled in with - p-value. - * [r35] R/ci.R: - Added ci.lme method to handle lme objects. + * renamed from contrast.coeff.R to estimable.R (incorrectly via + contrast.lm.R) -2001-10-16 warneg +2001-12-07 19:50 warneg - * [r27] man/ci.Rd: Fixed unbalanced brace. + * - Added text noting that lme is now supported. -2001-08-25 warneg +2001-12-07 19:19 warneg - * [r12] man/ci.Rd: - Added CVS header. + * - Fixed typo: DF column was being filled in with p-value. + +2001-12-07 18:49 warneg + + * - Added ci.lme method to handle lme objects. + +2001-10-16 23:15 warneg + + * Fixed unbalanced brace. + +2001-08-25 05:52 warneg + + * - Added CVS header. - Added my email address. -2001-05-30 warneg +2001-05-30 13:23 warneg - * [r2] ., R, R/ci.R, man, man/ci.Rd: Initial revision + * Initial revision From noreply at r-forge.r-project.org Wed Jun 20 23:02:30 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 23:02:30 +0200 (CEST) Subject: [R-gregmisc-commits] r2187 - pkg/gmodels Message-ID: <20180620210230.553401808E9@r-forge.r-project.org> Author: warnes Date: 2018-06-20 23:02:29 +0200 (Wed, 20 Jun 2018) New Revision: 2187 Modified: pkg/gmodels/NAMESPACE Log: Add imports from stats package. Modified: pkg/gmodels/NAMESPACE =================================================================== --- pkg/gmodels/NAMESPACE 2018-06-20 20:51:40 UTC (rev 2186) +++ pkg/gmodels/NAMESPACE 2018-06-20 21:02:29 UTC (rev 2187) @@ -1,3 +1,4 @@ + export( CrossTable, ci, @@ -13,19 +14,19 @@ summary.glh.test ) +S3method(ci, numeric) S3method(ci, binom) S3method(ci, lm) S3method(ci, lme) -#S3method(ci, mer) -S3method(ci, numeric) +##S3method(ci, mer) S3method(ci, estimable) S3method(fit.contrast, lm) S3method(fit.contrast, lme) -#S3method(fit.contrast, mer) +##S3method(fit.contrast, mer) S3method(estimable, default) -#S3method(estimable, mer) +##S3method(estimable, mer) S3method(estimable, mlm) S3method(print, glh.test) @@ -35,6 +36,16 @@ importFrom(gdata, frameApply) importFrom(gdata, nobs) -importFrom(stats, chisq.test, coef, family, fisher.test, - mcnemar.test, pchisq, pf, pt, qbeta, qt, sd, - summary.glm, summary.lm) +importFrom(stats, "chisq.test") +importFrom(stats, "coef") +importFrom(stats, "family") +importFrom(stats, "fisher.test") +importFrom(stats, "mcnemar.test") +importFrom(stats, "pchisq") +importFrom(stats, "pf") +importFrom(stats, "pt") +importFrom(stats, "qbeta") +importFrom(stats, "qt") +importFrom(stats, "sd") +importFrom(stats, "summary.glm") +importFrom(stats, "summary.lm") From noreply at r-forge.r-project.org Wed Jun 20 23:04:06 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 23:04:06 +0200 (CEST) Subject: [R-gregmisc-commits] r2188 - in pkg/gmodels: . inst Message-ID: <20180620210406.47E561808E9@r-forge.r-project.org> Author: warnes Date: 2018-06-20 23:04:04 +0200 (Wed, 20 Jun 2018) New Revision: 2188 Modified: pkg/gmodels/DESCRIPTION pkg/gmodels/inst/NEWS Log: Update DESCRIPTION and NEWS for gmodels 2.18.0. Modified: pkg/gmodels/DESCRIPTION =================================================================== --- pkg/gmodels/DESCRIPTION 2018-06-20 21:02:29 UTC (rev 2187) +++ pkg/gmodels/DESCRIPTION 2018-06-20 21:04:04 UTC (rev 2188) @@ -1,7 +1,7 @@ Package: gmodels -Version: 2.16.1 -Date: 2018-06-20 -Title: Various R programming tools for model fitting +Version: 2.18.0 +Date: 2018-06-19 +Title: Various R Programming Tools for Model Fitting Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley, and Randall C Johnson. Contributions from Randall C. Johnson are Copyright (2005) SAIC-Frederick, Inc. Funded by the Intramural Research @@ -11,7 +11,6 @@ Description: Various R programming tools for model fitting. Depends: R (>= 1.9.0) Suggests: gplots, gtools, Matrix, nlme, lme4 (>= 0.999999-0) -Imports: MASS, gdata, stats +Imports: MASS, gdata License: GPL-2 -URL: http://www.sf.net/projects/r-gregmisc NeedsCompilation: no Modified: pkg/gmodels/inst/NEWS =================================================================== --- pkg/gmodels/inst/NEWS 2018-06-20 21:02:29 UTC (rev 2187) +++ pkg/gmodels/inst/NEWS 2018-06-20 21:04:04 UTC (rev 2188) @@ -1,25 +1,19 @@ -Version 2.18.0 - 2017-06-05 +Version 2.18.0 - 2018-06-19 --------------------------- -New functions: +Bug fixes: -- Add update.list() function to replace named elements a list. -- Add mv() function to rename an object. -- Add first(), last(), 'first<-'() and 'last<-'() functions to extract - or replace first or last vector/list elements. +- ci.binom() was using an incorrect method for calcuating binomial + conficence intervals. It now calculates the Clopper-Pearson 'exect' + interval, which is *conservative* due to the discrete nature of the + binomial distribution. -New features: +Other Changes: -- Add 'byrow' argument to lowerTriangle()/upperTriangle() functions. +- Support for lme4 objects has been removed due to incompatible + changes to the lme4 package. -Other User-visible Changes: - -- humanReadable() now properly handles a single value for the argument 'justify'. -- Improve logging and error reporting for remove.vars() -- read.xls() now handles latin-1 files properly on MS-Windows. -- write.fwf() now properly handles matrix arguments. - -Version 2.16.0 - 2015-04-22 +Version 2.16.0 - 2014-07-24 --------------------------- New features: From noreply at r-forge.r-project.org Wed Jun 20 23:06:42 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Jun 2018 23:06:42 +0200 (CEST) Subject: [R-gregmisc-commits] r2189 - pkg/gmodels/inst Message-ID: <20180620210642.4D0D3180998@r-forge.r-project.org> Author: warnes Date: 2018-06-20 23:06:41 +0200 (Wed, 20 Jun 2018) New Revision: 2189 Modified: pkg/gmodels/inst/ChangeLog Log: Update ChangeLog for gmodels 2.18.0. Modified: pkg/gmodels/inst/ChangeLog =================================================================== --- pkg/gmodels/inst/ChangeLog 2018-06-20 21:04:04 UTC (rev 2188) +++ pkg/gmodels/inst/ChangeLog 2018-06-20 21:06:41 UTC (rev 2189) @@ -1,3 +1,25 @@ +2018-06-20 20:51 warnes + + * DESCRIPTION, inst/ChangeLog: Update DESCRIPTION and ChangeLog for + gmodels 2.16.1 + +2018-06-20 20:50 warnes + + * NAMESPACE: Remove obsolete functions. + +2018-06-20 20:46 warnes + + * R/fit.contrast.R, man/ci.Rd, man/estimable.Rd, + man/fit.contrast.Rd: Fix R CMD check issues. + +2018-06-20 20:42 warnes + + * R/ci.R: Remove trailing whitespace + +2018-06-20 20:40 warnes + + * R/est_p_ci.R: Use base::trimws() instead of gdata::trim() + 2018-06-20 20:35 warnes * test: Remove duplicated/incorrect 'test' directory. From noreply at r-forge.r-project.org Thu Jun 21 19:09:00 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 21 Jun 2018 19:09:00 +0200 (CEST) Subject: [R-gregmisc-commits] r2190 - pkg/gtools Message-ID: <20180621170900.272071870C7@r-forge.r-project.org> Author: warnes Date: 2018-06-21 19:08:59 +0200 (Thu, 21 Jun 2018) New Revision: 2190 Removed: pkg/gtools/ChangeLog pkg/gtools/NEWS Log: Remove symlinks Deleted: pkg/gtools/ChangeLog =================================================================== --- pkg/gtools/ChangeLog 2018-06-20 21:06:41 UTC (rev 2189) +++ pkg/gtools/ChangeLog 2018-06-21 17:08:59 UTC (rev 2190) @@ -1 +0,0 @@ -link inst/ChangeLog \ No newline at end of file Deleted: pkg/gtools/NEWS =================================================================== --- pkg/gtools/NEWS 2018-06-20 21:06:41 UTC (rev 2189) +++ pkg/gtools/NEWS 2018-06-21 17:08:59 UTC (rev 2190) @@ -1 +0,0 @@ -link inst/NEWS \ No newline at end of file From noreply at r-forge.r-project.org Thu Jun 21 19:09:49 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 21 Jun 2018 19:09:49 +0200 (CEST) Subject: [R-gregmisc-commits] r2191 - in pkg/gtools: . inst Message-ID: <20180621170949.9862618434C@r-forge.r-project.org> Author: warnes Date: 2018-06-21 19:09:49 +0200 (Thu, 21 Jun 2018) New Revision: 2191 Added: pkg/gtools/.Rbuildignore pkg/gtools/ChangeLog pkg/gtools/NEWS Removed: pkg/gtools/inst/ChangeLog pkg/gtools/inst/NEWS Log: Move NEWS and ChangeLog to top level directory Added: pkg/gtools/.Rbuildignore =================================================================== --- pkg/gtools/.Rbuildignore (rev 0) +++ pkg/gtools/.Rbuildignore 2018-06-21 17:09:49 UTC (rev 2191) @@ -0,0 +1,3 @@ +^revdep +^.*\.Rproj$ +^\.Rproj\.user$ Copied: pkg/gtools/ChangeLog (from rev 2190, pkg/gtools/inst/ChangeLog) =================================================================== --- pkg/gtools/ChangeLog (rev 0) +++ pkg/gtools/ChangeLog 2018-06-21 17:09:49 UTC (rev 2191) @@ -0,0 +1,1059 @@ +2017-06-14 warnes + + * [r2169] DESCRIPTION, NAMESPACE, R/checkRVersion.R, + R/newVersionAvailable.R, R/roman2int.R, R/setTCPNoDelay.R, + man/combinations.Rd, man/defmacro.Rd, src/gtools.h[ADD], + src/gtools_load.c[ADD], src/setTCPNoDelay.c, + tests/test_setTCPNoDelay.R: Explicitly register C routines used + by gtools + +2017-06-13 warnes + + * [r2168] man/combinations.Rd, man/defmacro.Rd: Update R News URLS + +2017-06-12 warnes + + * [r2165] man/capwords.Rd: Update link for taxise::taxize_capwords + in gtools::capwords man page + + * [r2164] inst/ChangeLog: Fix typos + + * [r2163] man/capwords.Rd: Update link for taxise::taxize_capwords + in gtools::capwords man page + + * [r2162] DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/NEWS: Update + meta files for gtools 3.7.0 + + * [r2161] tests/smartbind_emptynames.R: Fix test for smartbind with + empty column names + + * [r2160] man/setTCPNoDelay.Rd, tests/test_setTCPNoDelay.R: Add + improved example to man page for setTCPnoDelat() and fix test + function. + + * [r2159] man/ask.Rd: Add 'con' argument to ask() to allow + specification of the connection to query for input. + + * [r2158] R/capwords.R, man/capwords.Rd: Add capwords() function to + apply standard capitalization rules to a scharacter string. + +2017-05-23 warnes + + * [r2145] R/ask.R, R/quantcut.R, R/smartbind.R: - Integrate changes + made by Mango Solutions at + https://github.com/MangoTheCat/SASxport. - Remove functions + duplicated from the Hmisc package. - Minor code cleanup. + +2016-08-24 warnes + + * [r2144] tests/test_setTCPNoDelay.R: Add more testing code. + +2016-08-15 warnes + + * [r2143] inst/ChangeLog: Update ChangeLog + + * [r2142] DESCRIPTION: Update version number and date + + * [r2141] tests/test_setTCPNoDelay.R[ADD]: Add test code for + setTCPNoDelay + + * [r2140] R/setTCPNoDelay.R: Modify setTCPNoDelay to work with + current socket objects + + * [r2139] src/setTCPNoDelay.c: checkStatus() was not correctly + getting the error message. + +2016-04-22 warnes + + * [r2127] NAMESPACE, R/capwords.R[ADD], man/capwords.Rd[ADD]: Add + capwords() function to properly capatilize strings for use in + titles + + * [r2126] R/na.replace.R, man/na.replace.Rd: na.replace() now + accepts a function providing the replcement value. + +2015-11-24 warnes + + * [r2071] R/smartbind.R: Correct error when column types don't + match (reported by + +2015-10-15 warnes + + * [r2069] R/smartbind.R: smartbind() was not properly handling + columsn that were numeric on one df and character in the other + and other similar ctype conflicts. Fixed. + +2015-08-08 warnes + + * [r2067] tests/smartbind_emptynames.R[ADD]: Add half-hearted test + file + + * [r2066] R/smartbind.R: - Improve assignment of default names in + smartbind. - Disambiguate 'list' into an object named 'list' and + the function base::list() in smartbind(). + + * [r2065] DESCRIPTION, man/smartbind.Rd: Add example of using + 'list' argument to smartbind() man page. + + * [r2064] R/smartbind.R, man/smartbind.Rd: - smartbind() gets a new + argument 'list' to pass a list of data frames, instead of/in + addition to data frames as arguments. - Fix bug in smartbind's + handling of factor levels. + +2015-07-14 warnes + + * [r2057] R/loadedPackages.R, man/loadedPackages.Rd: Modify + loadedPackages() to return data silently so that the results + don't get printed twice. + +2015-05-27 warnes + + * [r2049] data/badDend.rda[ADD], man/badDend.Rd[ADD], + man/unByteCode.Rd: Create local dataset to use in the example + code for unByteCode instead of relying on web access. + + * [r2048] R/trimws.R: Fix missing closing paren. + + * [r2047] R/keywords.R, R/roman2int.R, R/trim.R[DEL], + R/trimws.R[ADD]: Two functions in gtools need to use either + gdata::trim() or base::trimws() (added in R 3.2.0). The previous + solution was to include gdata/R/gdata/R/trim.R in gtools using a + symbolic link. + + Unfortunately, Rforge doesn't seem to like the symbolic link when + building packages, and generates an error. + + So, instead, create the file trimws.R, which creates trimws() if + it isn't already available (e.g. via base::trimws), and modify + keywords() and roman2int() to use trimws() instead of + gdata::trim(). + + * [r2046] man/roman2int.Rd[ADD]: Add man page for roman2int(). + + * [r2045] man/mixedsort.Rd: Remove extraneous closing paren. + + * [r2044] NAMESPACE: Add roman2int() to exported function list. + + * [r2043] R/asc.R: Looks like we also lost the change of argument + name to chr(). Fixed. + + * [r2042] R/asc.R: Somehow lost 'simplify=TRUE' argument to asc. + Fixed. + + * [r2041] DESCRIPTION: Update gtools version number to 3.5.0 + + * [r2040] DESCRIPTION, inst/ChangeLog, inst/NEWS: Update + DESCRIPTION, ChangeLog, NEWS + + * [r2039] R/mixedsort.R, man/mixedsort.Rd: Add roman numeral + support to mixedorder() and mixedsort(). + + * [r2037] man/asc.Rd[ADD]: Add asc() and chr() functions for + converting between characters and ASCII codes + + * [r2036] R/roman2int.R: roman2int() now returns NA for invalid + roman numeral strings instead of generating an error. + + * [r2035] NAMESPACE: Add asc(), chr(), assignEdgewise(), + unByteCode(), and unByteCodeAssign() to package NAMESPACE. + + * [r2034] R/asc.R[ADD]: Add asc() and chr() functions for + converting between characters and ASCII codes + +2015-05-26 warnes + + * [r2030] inst/ChangeLog[ADD]: Add changelog to svn repository + +2015-05-25 warnes + + * [r2029] tests/test_ddirichlet.R: Add library call. + + * [r2028] man/unByteCode.Rd: Fix typo and add documentation for + argument 'name'. + + * [r2027] man/mixedsort.Rd: Fix typo. + + * [r2026] man/mixedsort.Rd: Add description of blanklast argument, + fix typo. + + * [r2025] man/quantcut.Rd: Change usage to match actual definition. + + * [r2024] man/mixedsort.Rd: Note characters sorting ignores case. + + * [r2023] man/mixedsort.Rd: Remove '...' from arglist to match + source code. + + * [r2022] man/mixedsort.Rd: Replace unicode quotes with \code{..}. + +2015-05-23 warnes + + * [r2021] tests/test_ddirichlet.R[ADD]: Add regression test + ddirichlet() bug for x[i]=0, alpha[i]=1: ddirichlet(x, alpha) was + returning NA rather than 0. + + * [r2020] R/dirichlet.R: ddirichlet() was incorrectly returning NA + when x[i]=0 and alpha[i]=1. In this case, the one calculation + became (-Inf * 0), which R evaluates to NaN. The correction is to + detect this case and substitute -Inf instead of NaN. + +2015-05-08 warnes + + * [r2019] R/mixedsort.R: Summary: Speed up mixedorder by moving + suppressWarnings outside of lapply loops. (Suggestion by Henrik + Bengtsson.) + +2015-05-02 warnes + + * [r2018] Rename 'trunk' to 'pkg' for compatibility with R-forge + + * [r2017] Minor layout change. + + * [r2016] Remove stray 'svn' that was inserted into the code. + + * [r2015] Add man page for unByteCode(), assignEdgeWise(), and + unByteCodeAssign() + +2015-04-28 warnes + + * [r1976] Changes to mixedsort(): - Hands off objects that are not + character vectors to the default sort. - Add 'decreasing', + 'na.last', and 'blank.last' arguments. + + * [r1975] Add private function 'checkReverseDependencies'. + +2015-04-23 warnes + + * [r1950] Update NEWS and ChangeLog + + * [r1949] - The 'q' argument to quantcut()'s 'q' now accept an + integer indicating the number of equally spaced quantile groups + to create. (Suggestion and patch submitted by Ryan C. Thompson.) + + * [r1946] Revers accidental text deletion: + + * [r1945] Update for gtools 3.4.3 + + * [r1944] Remove debugging code and stray browser() call + +2015-04-14 warnes + + * [r1923] Fix typo + +2015-04-09 warnes + + * [r1921] Update gtools ChangeLog + + * [r1920] Move first()/last()/left()/right() to gdata. Add new + functions na.replace() and loadedPackages(). Add more text to + package description. + +2015-04-08 warnes + + * [r1919] Move first/last/left/right to from gtools to gdata + +2015-04-06 warnes + + * [r1918] Correct URL + + * [r1917] Update NEWS and ChangeLog for gtools 3.5.0 + + * [r1916] Add ChangeLog files to repository + + * [r1915] Implement fix to keywords() needed for R-3.4.1, as + suggested by Kurt Hornik. + + * [r1914] - Export S3 methods for first(), last(), left() and + right(). - Ensure code matches man page for first(), last(), + left(), and right(). + +2014-10-09 warnes + + * [r1897] Update for 3.5.0 release of gtools + + * [r1896] Make right() and left() S3 methods for classes data.frame + and matrix + +2014-08-27 warnes + + * [r1872] Fix man page + + * [r1871] Finish adding first(), last(), left(), and right(). + + * [r1870] Add functions first(), last(), left(), and right(). + +2014-05-28 warnes + + * [r1816] Update for gtools 3.4.1 + + * [r1815] Add test to ensure smartbind() properly handles Date + columns. + + * [r1814] smartbind: Convert non-native type columns (except + factor) to character. + +2014-04-18 arnima + + * [r1813] Main arg is 'x' like showNonASCII(x), preformatted notes + instead of verb + +2014-04-17 warnes + + * [r1810] Update ASCIIfy man page to match source code and add + keywords + + * [r1809] Update NEWS for gtools 3.4.0 + + * [r1808] Add ASCIIfy function posted to RDevel by Arni Magnusson + +2014-03-01 warnes + + * [r1776] Fix cut-and-paste error. + + * [r1775] Update files for gtools 3.3.1 release + + * [r1774] Fix bug in gtools::mixedorder regular expression for + regognizing numbers. (Periods weren't escaped). + +2014-02-11 warnes + + * [r1773] Create and use locate copy of tools:::.split_op_version. + + * [r1772] Update for gtools 3.3.0. + + * [r1771] Fix arguments + + * [r1770] Update arguments to match code. + + * [r1769] Add getDependencies() function to return a list of + package dependencies. + +2014-01-14 warnes + + * [r1768] Update for bug-fix release + + * [r1767] Add test file for binsearch() function. + + * [r1766] Fixed bug where binsearch() returned the wrong endpoint & + value when the found value was at the upper endpoint. + +2014-01-13 warnes + + * [r1765] Fix typo + +2014-01-11 warnes + + * [r1764] Update for gtools release 3.2.0 + + * [r1763] fixes for R CMD check + + * [r1762] Fixes for gtools release 3.2.0 + +2013-12-23 warnes + + * [r1761] Extend the keywords() function to return keywords + associated with a specified topic via 'keywords(topic)'. + + * [r1760] Add keyword. + + * [r1759] Add stars.pval() function to convert p-values into + significance symbols. + +2013-11-26 warnes + + * [r1748] mixedorder() was failing to correctly handle numbers + including decimals due to a faulty regular expression. Prior to + the fix: + + > drr [1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg" > + gtools::mixedsort(drr) [1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 + mg" After the fix: + + > drr [1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg" > + mixedsort(drr) [1] "Dose 0.04 mg" "Dose 0.3 mg" "Dose 0.5 mg" + + In addition, an optimization was added that checked if the input + vector was numeric. If so, simply use the existing base::order + function. + +2013-11-18 warnes + + * [r1747] Use ".Deprecated" instead of warning. + +2013-11-06 warnes + + * [r1746] Update files for gtools 3.1.1 + + * [r1745] Fix problem with mixedorder/mixedsort when there is only + zero or one elements in the vector. + +2013-09-23 warnes + + * [r1716] Comment out empty sections in gtools-deprecated.Rd + + * [r1715] Update files for gtools 3.1.0 release + + * [r1714] Make 'addLast()' defunct. + + * [r1713] Mark 'addLast()' as defunct and move 'lastAdd()' function + to a separate file. + + * [r1712] Update for gtools 3.0.1 release + + * [r1711] Use 'suppressWarnings() instead of 'options(warn=-1)' in + 'mixedorder()'. + +2013-07-07 warnes + + * [r1705] Fix typo. + +2013-07-06 warnes + + * [r1704] Fix Rd warning. + + * [r1703] Include lastAdd in NAMESPACE + + * [r1702] Change assert from deprecated to defunct. + + * [r1701] Improve deprecation message + + * [r1700] Update for gtools 3.0.0 + + * [r1699] Create new function lastAdd to replace addLast and mark + addLast as deprecated. + +2013-07-05 warnes + + * [r1698] Point out that addLast() modifies the value of .Last in + the global environment. + + * [r1697] Point out that addLast() modifies the value of .Last in + the global environment. + + * [r1696] Update for gtools 2.7.2 mark 2 + + * [r1695] Remove cross-reference to (obsolete?) moc package + + * [r1694] Update for gtools 2.7.2 + + * [r1693] Update for R version 3.0.0 and later + +2013-03-17 warnes + + * [r1640] Fix error in smartbind: factor levels were not being + handled if the factor column was not present in the first data + frame. + +2012-06-19 warnes + + * [r1570] Update for gtools 2.7.0. + + * [r1569] Document new 'verbose' argument to smartbind(). + + * [r1568] Clean up R CMD check warnings. + +2012-05-04 warnes + + * [r1529] smartbind(): Improve handling of factors and ordered + factors. + +2011-10-05 warnes + + * [r1518] Update version number for release + + * [r1517] Add 'sep' argument to smartbind() to allow specification + of character used to separate components of constructed names + +2011-09-28 warnes + + * [r1513] smartbind(): Prevent coersion to data frame from mangling + column names. + + * [r1512] Add 'fill' argument to smartbind() to specify a value to + use for missing entries. + + * [r1511] Add 'fill' argument to smartbind() to specify a value to + use for missing entries. + +2010-08-14 warnes + + * [r1451] Modify mixedorder()/mixedsort() to better handle strings + containing multiple periods, like version numbers (e.g 1.1.2, + 1.2.1. 1.1.1.1). + +2010-05-01 warnes + + * [r1434] Update version number for new release + + * [r1433] Change Greg's email address to greg at warnes.net + + * [r1432] Fix error in checkRVersion() + +2010-04-28 ggrothendieck2 + + * [r1431] fixed problems with R CMD CHECK + +2009-05-09 warnes + + * [r1328] Escape $ in .Rd file to avoid latex issues + + * [r1327] Update NEWS and create softlinks for NEWS and ChangeLog + in top level directory + + * [r1326] Move actual NEWS file into inst. + + * [r1325] Update Greg's email address and fix Rd syntax errors + +2009-02-16 warnes + + * [r1313] Correct windows make flags as suggested by Brian Ripley. + +2008-08-15 warnes + + * [r1303] Add keywords() function to show /doc/KEYWORDS file + +2008-05-29 warnes + + * [r1285] Add newVersionAvailable() function to compare running and + latest available R versions + +2008-05-26 warnes + + * [r1284] Update license specification + + * [r1283] Remove 'assert' man page + +2008-05-22 warnes + + * [r1282] Finish rename of assert.R to assert-depricated.Rd + + * [r1281] Add checkRVersion.R file + + * [r1280] Rename again to get correct extension! + + * [r1279] Update NEWS for 2.5.0 + + * [r1278] Add man page for checkRVersion + + * [r1277] Rename assert-deprecated.R to assert.R to meet R file + name requirements. + + * [r1276] Add checkRVersion to NAMESPACE, and increment version in + DESCRIPTION. + + * [r1275] Remove broken SEE LSO reference + +2008-04-12 warnes + + * [r1259] Improve text explanation of how defmacro() and strmacro() + differ from function(). + + * [r1258] assert() is now deprecated in favor of base::stopifnot() + + * [r1257] Rename 'assert.R' to 'deprecated.R'. + + * [r1256] Assert is now deprecated in favor of base::stopifnot(), + so add call to .Deprecated() to inform the user. + +2007-11-30 warnes + + * [r1228] Update defnitions of odd() and even() to use modulus + operator instead of division. Prettier, I think, :-D + +2007-08-08 warnes + + * [r1121] Fix bug identified by R-2.6's check routings in + binsearch() + + * [r1120] Add the binsearch(), previously in the genetics package. + +2007-07-18 ggorjan + + * [r1100] typo fixed + +2007-04-12 warnes + + * [r1088] Add ask() function to prompt the user and collect a + single response. + +2007-04-07 warnes + + * [r1087] Fix improper escapes in regexp detected by R 2.5.0 + package check. + +2007-03-23 warnes + + * [r1083] Allow permutations for r>n provided repeats.allowed=TRUE + +2006-11-28 warnes + + * [r1023] Replace F with FALSE in smartbind example. + +2006-11-27 warnes + + * [r1022] Replace T with TRUE in smartbind example + + * [r1021] Temprary remove to reset binary flag + + * [r1020] Temprary remove to reset binary flag + + * [r1019] Add smartbind() to list of exported functions, and add + corresponding documentation file. + + * [r1018] Update my email address + +2006-11-14 ggorjan + + * [r1012] Removed executable property + +2006-08-02 warnes + + * [r977] Update my email address + +2006-05-05 nj7w + + * [r958] Fixed minor typo - in {value} - n was replaced by r + + * [r957] Fixed minor typos + +2006-03-01 warnes + + * [r903] Add smartbind function + +2006-01-18 warnes + + * [r845] Add concept tags to make mixedsort easier to locate. + +2005-12-21 warnes + + * [r837] Update version number and date + + * [r836] Note changes for 2.2.3 + + * [r835] Should now work on Windows + +2005-12-20 warnes + + * [r834] Temporary fix to allow setTCPNoDelay.c to compile on + Windows. If compiled on windows calling setTCPNoDelay will just + raise an error. + +2005-12-14 warnes + + * [r813] Change C++ comment to standard comment + +2005-12-13 nj7w + + * [r810] *** empty log message *** + + * [r809] Updated NEWS and removed ChangeLog + +2005-12-12 nj7w + + * [r800] Updated version for CRAN release + +2005-12-08 warnes + + * [r790] Add C source code for setTCPNoDelay. + +2005-12-01 nj7w + + * [r776] Updated Greg's email address + +2005-11-29 warnes + + * [r769] Add UseDynLib to NAMESPACE so the shared library gets + properly loaded. + + * [r768] - Remove debugging comments - Change return value on + success to "Success". + +2005-11-22 warnes + + * [r758] NAMESPACE + + * [r757] Update news for 2.2.1 release. + + * [r756] Fixes for R CMD check + + * [r755] Add setTCPNoDelay() function and documentation + + * [r745] New function 'addLast' that adds functions to R's .Last() + so that they will be executed when R is terminating. + +2005-09-22 warnes + + * [r678] More changes for strmacro(), also changes for 2.1.1 + release + + * [r677] Add strmaco() which defines functions that use strings for + macro definition + +2005-09-21 warnes + + * [r676] Add support for DOTS/... arguments to defmacro + +2005-09-12 nj7w + + * [r671] Updated Greg's email + +2005-09-02 nj7w + + * [r653] Exported assert + + * [r652] Updated the version number + + * [r651] Added NEWS + + * [r650] Added ChangeLog + + * [r649] Fixed syntax errors + +2005-09-02 warnes + + * [r648] Add assert() and documentation + + * [r647] Fix problem in defmacro.Rd file: don't use \code{} in the + example section. + +2005-08-31 warnes + + * [r645] Adding the defmacro() function, extracted from + + Lumley T. "Programmer's Niche: Macros in {R}", R News, 2001, Vol + 1, No. 3, pp 11--13, \url{http://CRAN.R-project.org/doc/Rnews/} + + * [r642] Add stand-alone DESCRIPTION file and remove old + DESCRIPTION.in file. + +2005-06-13 nj7w + + * [r626] Fixed a bug in mixedsort - check if "which.na" and + "which.blank" is numeric(0) before subsetting the datasets. + +2005-06-09 nj7w + + * [r625] Updating the version number, and various help files to + synchronize splitting of gregmisc bundle in 4 individual + components. + +2005-05-10 warnes + + * [r619] Fix handling of NA's in mixedorder. We were using a high + UTF character to try to put NA's at the end of the sort order, + but R 2.1.0 checks if characters are in the correct range. + Instead, we explicitly force NA's to the end. + +2005-04-07 warnes + + * [r606] - Add scat() function which writes its arguments to stderr + and flushes so that output is immediately displayed, but only if + 'getOption("DEBUG")' is true. + +2005-04-02 warnes + + * [r600] Move drop.levels() from gtools to gdata. + + * [r599] Minor reordering of functions in file + + * [r598] Move frameApply() to gdata package. + + * [r597] Fix error if only one value passed to mixedorder. + + * [r596] Add proper handling where more than one quantile obtains + the same value + +2005-04-01 warnes + + * [r595] Add CVS ID tag to file headers. + + * [r594] Fixes from Jim Rogers for R CMD check problems in + frameApply + +2005-03-31 warnes + + * [r591] Updates to drop.levels() and frameApply() from Jim Rogers + + * [r590] Add ELISA data set used by frameApply and drop.levels + examples + +2005-02-25 warnes + + * [r562] Replace 'T' with TRUE. + + * [r561] Remove dependency on ELISA data set for the example. + + * [r558] Add drop.levels, frameApply to namespace export. + +2005-02-15 warnes + + * [r542] Add frameApply and drop.levels contributed by Jim Rogers. + +2005-01-12 warnes + + * [r515] Add dependency on R 1.9.0+ to prevent poeple from + installing on old versions of R which don't support namespaces. + +2004-09-27 warneg + + * [r461] Updated to pass R CMD check. + +2004-09-03 warneg + + * [r446] initial bundle checkin + +2004-09-02 warneg + + * [r442] Initial revision + +2004-08-27 warnes + + * [r441] Fixed bug in mixedsort, and modified reorder.factor to use + mixedsort. + +2004-08-26 warnes + + * [r440] - Fix bug pointed out by Jim Rogers. - Use a more + distictive internal separator: $@$ instead of just $ - + Capitalization is now irrelevent for search order (unlike ASCII). + +2004-06-08 warnes + + * [r372] Nitin Jain added by= parameter to allow specifying + separation between groups. + +2004-05-26 warnes + + * [r345] Escape underscores in email addresses so Latex is happy. + + * [r343] Replace 'T' with 'TRUE' to pass R CMD check. + +2004-05-25 warnes + + * [r334] Remove extraneous comments. + + * [r333] Fix an error in the code when using repeats.allow=T and + r>2. Bug report and fix both due to Elizabeth Purdom + . + +2004-05-24 warnes + + * [r323] Check if argument is a vector before doing is.na to avoid + generating a warning. + + * [r322] Add invalid() function for testing if a parameter value is + non-missing, non-NA, non-NULL. + +2004-04-27 warnes + + * [r321] Replaced argument `as.list' with `simplify'. Updated + documentation, and updated examples appropriately. + +2004-04-26 warnes + + * [r320] Added as.list argument to return one list element per + evaluation. + +2004-03-26 warnes + + * [r303] Uncomment and fix large 'n' example. + + * [r301] - Update to match changes in running() - Add examples to + illustrate new arguments. - Modify running correlation plot + example to be more clear. + + * [r299] More of the same. + + * [r297] Fix bug discovered by Sean Davis . + The running function took an improper shortcut. When + allow.fewer=FALSE it was still passing shorter lists of elements + to the called function, and then overwriting the results for the + shorter lists with NAs. The code now skips evaluation of the + function on lists shorter than the specified length when + allow.fewer=FALSE. + +2004-01-21 warnes + + * [r277] - Mark sprint() as depreciated. - Replace references to + sprint with capture.output() - Use match.arg for halign and + valign arguments to textplot.default. - Fix textplot.character so + that a vector of characters is properly displayed. Previouslt, + character vectors were plotted on top of each other. + +2003-12-03 warnes + + * [r253] - match function argument defaults with 'usage' + +2003-11-21 warnes + + * [r237] Removed 'deqn' call that was confusing things. + + * [r234] Add email address to author field + + * [r233] - new files + + * [r232] - Change 'T' to 'TRUE' in mixedsort.R - Add missing brace + in mixedsort.Rd + +2003-11-20 warnes + + * [r230] - Move 'odd' and 'even' functions to a separate file & + provide documentation + +2003-11-18 warnes + + * [r227] - Renamed smartsort to mixedsort and added documentation. + +2003-11-10 warnes + + * [r220] - Add files contributed by Arni Magnusson + . As well as some of my own. + +2003-05-23 warnes + + * [r196] - library() backported from 1.7-devel. This version of the + function adds the "pos=" argument to specify where in the search + path the library should be placed. + + - updated .First.lib to use library(...pos=3) for MASS to avoid + the 'genotype' data set in MASS from masking the genotype + funciton in genetics when it loads gregmisc + + - Added logit() inv.logit() matchcols() function and + corresponding docs + +2003-04-22 warnes + + * [r189] - Fixed tpyo in example that allowed combinations(500,2) + to run when it should have been ignred for testing.. + +2003-04-10 warnes + + * [r186] - Added note about the need to increase + options("expressions") to use large values for 'n'. Prompted by + bug report from Huan Huang n provided repeat.allowed=TRUE - Bumped up version number + +2002-08-01 warnes + + * [r114] - Corrected documentation mismatch for ci, ci.default. + + - Replaced all occurences of '_' for assignment with '<-'. + + - Replaced all occurences of 'T' or 'F' for 'TRUE' and 'FALSE' + with the spelled out version. + + - Updaded version number and date. + +2002-04-09 warneg + + * [r109] Checkin for version 0.5.3 + +2002-03-26 warneg + + * [r97] Initial Checkin + + * [r96] Initial checkin. + +2002-03-20 warneg + + * [r91] - Added definition of is.R function. + + - Added boxplot.formula + +2002-03-07 warneg + + * [r90] - Added documentation and example for running2 + + * [r89] - Added "running2", which handles both univariate and + bivariate cases - Modified "running" to call "running2" + +2002-02-05 warneg + + * [r75] - Fix typo that caused code meant to run only under S-Plus + to run under R, causing problems. + +2001-12-19 warneg + + * [r67] - Added code for %in%. + +2001-09-18 warneg + + * [r18] Release 0.3.2 + +2001-09-01 warneg + + * [r17] Initial checkin. + + * [r16] Release 0.3.0 + +2001-08-25 warneg + + * [r13] Initial CVS checkin. + + * [r11] Fixed a typo and a syntax error. + + * [r7] Initial Checkin + +2001-06-29 warneg + + * [r6] Initial revision. + Copied: pkg/gtools/NEWS (from rev 2190, pkg/gtools/inst/NEWS) =================================================================== --- pkg/gtools/NEWS (rev 0) +++ pkg/gtools/NEWS 2018-06-21 17:09:49 UTC (rev 2191) @@ -0,0 +1,369 @@ +gtools 3.7.0 - 2017-06-14 +------------------------- + +New functions: + +- Add capwords() function to apply standard capitalization rules + to a character string. + +Enhancements: + +- Add 'con' argument to ask() to allow specification of the + connection to query for input. For use under RStudio, use + ask(..., con=file('stdin')). + +- R/na.replace.R, man/na.replace.Rd: na.replace() now + accepts a function to provide the replcement value. + +- smartbind() has a new argument 'list' to pass a list of data frames, + /instead of/in addition to/ data frames as arguments. + +- Internal changes to bring code up to current CRAN guidelines. + +Bug Fixes: + +- smartbind() now works properly with empty column names + +- Correct error in smartbind() when column types don't + match. + +- Fix bug in smartbind's handling of factor levels. + +- Improve assignment of default names in smartbind(). + +- loadedPackages() to return data silently so that the results + don't get printed twice. + + +gtools 3.5.0 - 2015-04-28 +------------------------- + +New Functions: + +- New roman2int() functon to convert roman numerals to integers + without the range restriction of utils::as.roman(). + +- New asc() and chr() functions to convert between ASCII codes and + characters. (Based on the 'Data Debrief' blog entry for 2011-03-09 + at http://datadebrief.blogspot.com/2011/03/ascii-code-table-in-r.html). + +- New unByteCode() and unByteCodeAssign() functions to convert a + byte-code functon to an interpeted code function. + +- New assignEdgewise() function for making assignments into locked + environments. (Used by unByteCodeAssign().) + +Enhancements: + +- mixedsort() and mixedorder() now have arguments 'decreasing', + 'na.last', and 'blank.last' arguments to control sort ordering. + +- mixedsort() and mixedirdeR() now support Roman numerals via the + arguments 'numeric.type', and 'roman.case'. (Request by David + Winsemius, suggested code changes by Henrik Bengtsson.) + +- speed up mixedorder() (and hence mixedsort()) by moving + suppressWarnings() outside of lapply loops. (Suggestion by Henrik + Bengtsson.) + +- The 'q' argument to quantcut() now accept an integer + indicating the number of equally spaced quantile groups to + create. (Suggestion and patch submitted by Ryan C. Thompson.) + +Bug fixes: + +- Removed stray browser() call in smartbind(). + +- ddirichlet(x, alpha) was incorrectly returning NA when for any i, + x[i]=0 and alpha[i]=1. (Bug report by John Nolan.) + +Other changes: + +- Correct typographical errors in package description. + + +gtools 3.4.2 - 2015-04-06 +------------------------- + +New features: + +- New function loadedPackages() to display name, version, and path of + loaded packages (package namespaces). + +- New function: na.replace() to replace missing values within a + vector with a specified value.` + +Bug fixes: + +- Modify keywords() to work properly in R 3.4.X and later. + + +gtools 3.4.1 - 2014-05-27 +------------------------- + +Bug fixes: + +- smartbind() now converts all non-atomic type columns (except factor) + to type character instead of generating an opaque error message. + +Other changes: + +- the argument to ASCIIfy() is now named 'x' instead of 'string'. + +- minor formatting changes to ASCIIfy() man page. + +gtools 3.4.0 - 2014-04-14 +------------------------- + +New features: + +- New ASCIIfy() function to converts character vectors to ASCII + representation by escaping them as \x00 or \u0000 codes. + Contributed by Arni Magnusson. + + +gtools 3.3.1 - 2014-03-01 +------------------------- + +Bug fixes: + +- 'mixedorder' (and hence 'mixedsort') not properly handling + single-character strings between numbers, so that '1a2' was being + handled as a single string rather than being properly handled as + c('1', 'a', '2'). + + + +gtools 3.3.0 - 2014-02-11 +------------------------- + +New features: + +- Add the getDependencies() function to return a list of dependencies + for the specified package(s). Includes arguments to control whether + these dependencies should be constructed using information from + locally installed packages ('installed', default is TRUE), avilable + CRAN packages ('available', default is TRUE) and whether to include + base ('base', default=FALSE) and recommended ('recommended', default + is FALSE) packages. + +Bug fixes: + +- binsearch() was returning the wrong endpoint & value when the found + value was at the upper endpoint. + +gtools 3.2.1 - 2014-01-13 +------------------------- + +Bug fixes: + +- Resolve circular dependency with gdata + + +gtools 3.2.0 - 2014-01-11 +------------------------- + +New features: + +- The keywords() function now accepts a function or function name as + an argument and will return the list of keywords associated with the + named function. + +- New function stars.pval() which will generate p-value significance + symbols ('***', '**', etc.) + +Bug fixes: + +- R/mixedsort.R: mixedorder() was failing to correctly handle numbers + including decimals due to a faulty regular expression. + +Other changes: + +- capture() and sprint() are now defunct. + + +gtools 3.1.1 - 2013-11-06 +------------------------- + +Bug fixes: + +- Fix problem with mixedorder/mixedsort when there is zero or one + elements in the argument vector. + + +gtools 3.1.0 - 2013-09-22 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/r-gregmisc -r 2191 From noreply at r-forge.r-project.org Thu Jun 21 19:18:40 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 21 Jun 2018 19:18:40 +0200 (CEST) Subject: [R-gregmisc-commits] r2192 - pkg/gtools Message-ID: <20180621171840.B90CE18434C@r-forge.r-project.org> Author: warnes Date: 2018-06-21 19:18:40 +0200 (Thu, 21 Jun 2018) New Revision: 2192 Modified: pkg/gtools/ChangeLog pkg/gtools/DESCRIPTION pkg/gtools/NEWS Log: Update for gtools 3.8.1. Modified: pkg/gtools/ChangeLog =================================================================== --- pkg/gtools/ChangeLog 2018-06-21 17:09:49 UTC (rev 2191) +++ pkg/gtools/ChangeLog 2018-06-21 17:18:40 UTC (rev 2192) @@ -1,1059 +1,1416 @@ -2017-06-14 warnes +2018-06-19 16:48 warnes - * [r2169] DESCRIPTION, NAMESPACE, R/checkRVersion.R, + * DESCRIPTION, NAMESPACE: Update DESCRIPTION and NAMESPACE for + gtools 3.8.0. + +2018-06-19 16:43 warnes + + * R/split_path.R, man/split_path.Rd: Add spit_path() function. + +2018-06-19 16:43 warnes + + * R/baseOf.R, man/baseOf.Rd: Improvements to baseOf() function. + +2017-08-23 23:03 warnes + + * R/baseOf.R, man/baseOf.Rd: Add `baseOf` function and + documentation to support updated `gplots::venn` function. + (Provided by Steffen M?ller.) + +2017-08-23 22:59 warnes + + * R/roman2int.R, R/setTCPNoDelay.R: Use correct 'PACKAGE=' + parameter to '.C' calls. + +2017-06-14 19:44 warnes + + * inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog + +2017-06-14 19:42 warnes + + * DESCRIPTION, NAMESPACE, R/checkRVersion.R, R/newVersionAvailable.R, R/roman2int.R, R/setTCPNoDelay.R, - man/combinations.Rd, man/defmacro.Rd, src/gtools.h[ADD], - src/gtools_load.c[ADD], src/setTCPNoDelay.c, + man/combinations.Rd, man/defmacro.Rd, src/gtools.h, + src/gtools_load.c, src/setTCPNoDelay.c, tests/test_setTCPNoDelay.R: Explicitly register C routines used by gtools -2017-06-13 warnes +2017-06-13 00:16 warnes - * [r2168] man/combinations.Rd, man/defmacro.Rd: Update R News URLS + * man/combinations.Rd, man/defmacro.Rd: Update R News URLS -2017-06-12 warnes +2017-06-12 23:30 warnes - * [r2165] man/capwords.Rd: Update link for taxise::taxize_capwords - in gtools::capwords man page + * man/capwords.Rd: Update link for taxise::taxize_capwords in + gtools::capwords man page - * [r2164] inst/ChangeLog: Fix typos +2017-06-12 23:28 warnes - * [r2163] man/capwords.Rd: Update link for taxise::taxize_capwords - in gtools::capwords man page + * inst/ChangeLog: Fix typos - * [r2162] DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/NEWS: Update - meta files for gtools 3.7.0 +2017-06-12 23:28 warnes - * [r2161] tests/smartbind_emptynames.R: Fix test for smartbind with - empty column names + * man/capwords.Rd: Update link for taxise::taxize_capwords in + gtools::capwords man page - * [r2160] man/setTCPNoDelay.Rd, tests/test_setTCPNoDelay.R: Add - improved example to man page for setTCPnoDelat() and fix test - function. +2017-06-12 23:21 warnes - * [r2159] man/ask.Rd: Add 'con' argument to ask() to allow - specification of the connection to query for input. + * DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/NEWS: Update meta + files for gtools 3.7.0 - * [r2158] R/capwords.R, man/capwords.Rd: Add capwords() function to - apply standard capitalization rules to a scharacter string. +2017-06-12 22:53 warnes -2017-05-23 warnes + * tests/smartbind_emptynames.R: Fix test for smartbind with empty + column names - * [r2145] R/ask.R, R/quantcut.R, R/smartbind.R: - Integrate changes - made by Mango Solutions at - https://github.com/MangoTheCat/SASxport. - Remove functions - duplicated from the Hmisc package. - Minor code cleanup. +2017-06-12 22:52 warnes -2016-08-24 warnes + * man/setTCPNoDelay.Rd, tests/test_setTCPNoDelay.R: Add improved + example to man page for setTCPnoDelat() and fix test function. - * [r2144] tests/test_setTCPNoDelay.R: Add more testing code. +2017-06-12 22:51 warnes -2016-08-15 warnes + * man/ask.Rd: Add 'con' argument to ask() to allow specification of + the connection to query for input. - * [r2143] inst/ChangeLog: Update ChangeLog +2017-06-12 22:49 warnes - * [r2142] DESCRIPTION: Update version number and date + * R/capwords.R, man/capwords.Rd: Add capwords() function to apply + standard capitalization rules to a scharacter string. - * [r2141] tests/test_setTCPNoDelay.R[ADD]: Add test code for - setTCPNoDelay +2017-05-23 15:55 warnes - * [r2140] R/setTCPNoDelay.R: Modify setTCPNoDelay to work with - current socket objects + * R/ask.R, R/quantcut.R, R/smartbind.R: - Integrate changes made by + Mango Solutions at https://github.com/MangoTheCat/SASxport. + - Remove functions duplicated from the Hmisc package. + - Minor code cleanup. - * [r2139] src/setTCPNoDelay.c: checkStatus() was not correctly - getting the error message. +2016-08-24 19:48 warnes -2016-04-22 warnes + * tests/test_setTCPNoDelay.R: Add more testing code. - * [r2127] NAMESPACE, R/capwords.R[ADD], man/capwords.Rd[ADD]: Add - capwords() function to properly capatilize strings for use in - titles +2016-08-15 19:17 warnes - * [r2126] R/na.replace.R, man/na.replace.Rd: na.replace() now - accepts a function providing the replcement value. + * inst/ChangeLog: Update ChangeLog -2015-11-24 warnes +2016-08-15 19:16 warnes - * [r2071] R/smartbind.R: Correct error when column types don't - match (reported by + * DESCRIPTION: Update version number and date -2015-10-15 warnes +2016-08-15 19:14 warnes - * [r2069] R/smartbind.R: smartbind() was not properly handling - columsn that were numeric on one df and character in the other - and other similar ctype conflicts. Fixed. + * tests/test_setTCPNoDelay.R: Add test code for setTCPNoDelay -2015-08-08 warnes +2016-08-15 19:14 warnes - * [r2067] tests/smartbind_emptynames.R[ADD]: Add half-hearted test - file + * R/setTCPNoDelay.R: Modify setTCPNoDelay to work with current + socket objects - * [r2066] R/smartbind.R: - Improve assignment of default names in - smartbind. - Disambiguate 'list' into an object named 'list' and - the function base::list() in smartbind(). +2016-08-15 19:13 warnes - * [r2065] DESCRIPTION, man/smartbind.Rd: Add example of using - 'list' argument to smartbind() man page. + * src/setTCPNoDelay.c: checkStatus() was not correctly getting the + error message. - * [r2064] R/smartbind.R, man/smartbind.Rd: - smartbind() gets a new - argument 'list' to pass a list of data frames, instead of/in - addition to data frames as arguments. - Fix bug in smartbind's - handling of factor levels. +2016-04-22 16:10 warnes -2015-07-14 warnes + * NAMESPACE, R/capwords.R, man/capwords.Rd: Add capwords() function + to properly capatilize strings for use in titles - * [r2057] R/loadedPackages.R, man/loadedPackages.Rd: Modify +2016-04-22 16:08 warnes + + * R/na.replace.R, man/na.replace.Rd: na.replace() now accepts a + function providing the replcement value. + +2015-11-24 17:58 warnes + + * R/smartbind.R: Correct error when column types don't match + (reported by + +2015-10-15 21:15 warnes + + * R/smartbind.R: smartbind() was not properly handling columsn that + were numeric on one df and character in the other and other + similar ctype conflicts. Fixed. + +2015-08-08 05:01 warnes + + * tests/smartbind_emptynames.R: Add half-hearted test file + +2015-08-08 03:14 warnes + + * R/smartbind.R: - Improve assignment of default names in + smartbind. + - Disambiguate 'list' into an object named 'list' and the + function + base::list() in smartbind(). + +2015-08-08 01:47 warnes + + * DESCRIPTION, man/smartbind.Rd: Add example of using 'list' + argument to smartbind() man page. + +2015-08-08 01:44 warnes + + * R/smartbind.R, man/smartbind.Rd: - smartbind() gets a new + argument 'list' to pass a list of data + frames, instead of/in addition to data frames as arguments. + - Fix bug in smartbind's handling of factor levels. + + +2015-07-14 21:19 warnes + + * R/loadedPackages.R, man/loadedPackages.Rd: Modify loadedPackages() to return data silently so that the results don't get printed twice. -2015-05-27 warnes +2015-05-27 17:01 warnes - * [r2049] data/badDend.rda[ADD], man/badDend.Rd[ADD], - man/unByteCode.Rd: Create local dataset to use in the example - code for unByteCode instead of relying on web access. + * data/badDend.rda, man/badDend.Rd, man/unByteCode.Rd: Create local + dataset to use in the example code for unByteCode instead of + relying on web access. - * [r2048] R/trimws.R: Fix missing closing paren. +2015-05-27 16:38 warnes - * [r2047] R/keywords.R, R/roman2int.R, R/trim.R[DEL], - R/trimws.R[ADD]: Two functions in gtools need to use either - gdata::trim() or base::trimws() (added in R 3.2.0). The previous - solution was to include gdata/R/gdata/R/trim.R in gtools using a - symbolic link. + * R/trimws.R: Fix missing closing paren. + +2015-05-27 16:36 warnes + + * R/keywords.R, R/roman2int.R, R/trim.R, R/trimws.R: Two functions + in gtools need to use either gdata::trim() or + base::trimws() (added in R 3.2.0). The previous solution was to + include gdata/R/gdata/R/trim.R in gtools using a symbolic link. Unfortunately, Rforge doesn't seem to like the symbolic link when building packages, and generates an error. So, instead, create the file trimws.R, which creates trimws() if - it isn't already available (e.g. via base::trimws), and modify - keywords() and roman2int() to use trimws() instead of - gdata::trim(). + it + isn't already available (e.g. via base::trimws), and modify + keywords() + and roman2int() to use trimws() instead of gdata::trim(). - * [r2046] man/roman2int.Rd[ADD]: Add man page for roman2int(). +2015-05-27 02:48 warnes - * [r2045] man/mixedsort.Rd: Remove extraneous closing paren. + * man/roman2int.Rd: Add man page for roman2int(). - * [r2044] NAMESPACE: Add roman2int() to exported function list. +2015-05-27 02:29 warnes - * [r2043] R/asc.R: Looks like we also lost the change of argument - name to chr(). Fixed. + * man/mixedsort.Rd: Remove extraneous closing paren. - * [r2042] R/asc.R: Somehow lost 'simplify=TRUE' argument to asc. - Fixed. +2015-05-27 02:26 warnes - * [r2041] DESCRIPTION: Update gtools version number to 3.5.0 + * NAMESPACE: Add roman2int() to exported function list. - * [r2040] DESCRIPTION, inst/ChangeLog, inst/NEWS: Update - DESCRIPTION, ChangeLog, NEWS +2015-05-27 02:26 warnes - * [r2039] R/mixedsort.R, man/mixedsort.Rd: Add roman numeral - support to mixedorder() and mixedsort(). + * R/asc.R: Looks like we also lost the change of argument name to + chr(). Fixed. - * [r2037] man/asc.Rd[ADD]: Add asc() and chr() functions for - converting between characters and ASCII codes +2015-05-27 02:23 warnes - * [r2036] R/roman2int.R: roman2int() now returns NA for invalid - roman numeral strings instead of generating an error. + * R/asc.R: Somehow lost 'simplify=TRUE' argument to asc. Fixed. - * [r2035] NAMESPACE: Add asc(), chr(), assignEdgewise(), - unByteCode(), and unByteCodeAssign() to package NAMESPACE. +2015-05-27 02:19 warnes - * [r2034] R/asc.R[ADD]: Add asc() and chr() functions for - converting between characters and ASCII codes + * DESCRIPTION: Update gtools version number to 3.5.0 -2015-05-26 warnes +2015-05-27 02:17 warnes - * [r2030] inst/ChangeLog[ADD]: Add changelog to svn repository + * DESCRIPTION, inst/ChangeLog, inst/NEWS: Update DESCRIPTION, + ChangeLog, NEWS -2015-05-25 warnes +2015-05-27 01:37 warnes - * [r2029] tests/test_ddirichlet.R: Add library call. + * R/mixedsort.R, man/mixedsort.Rd: Add roman numeral support to + mixedorder() and mixedsort(). - * [r2028] man/unByteCode.Rd: Fix typo and add documentation for - argument 'name'. +2015-05-27 00:21 warnes - * [r2027] man/mixedsort.Rd: Fix typo. + * man/asc.Rd: Add asc() and chr() functions for converting between + characters and ASCII codes - * [r2026] man/mixedsort.Rd: Add description of blanklast argument, - fix typo. +2015-05-27 00:20 warnes - * [r2025] man/quantcut.Rd: Change usage to match actual definition. + * R/roman2int.R: roman2int() now returns NA for invalid roman + numeral strings instead of generating an error. - * [r2024] man/mixedsort.Rd: Note characters sorting ignores case. +2015-05-27 00:19 warnes - * [r2023] man/mixedsort.Rd: Remove '...' from arglist to match - source code. + * NAMESPACE: Add asc(), chr(), assignEdgewise(), unByteCode(), and + unByteCodeAssign() to package NAMESPACE. - * [r2022] man/mixedsort.Rd: Replace unicode quotes with \code{..}. +2015-05-27 00:17 warnes -2015-05-23 warnes + * R/asc.R: Add asc() and chr() functions for converting between + characters and ASCII codes - * [r2021] tests/test_ddirichlet.R[ADD]: Add regression test - ddirichlet() bug for x[i]=0, alpha[i]=1: ddirichlet(x, alpha) was - returning NA rather than 0. +2015-05-26 16:22 warnes - * [r2020] R/dirichlet.R: ddirichlet() was incorrectly returning NA - when x[i]=0 and alpha[i]=1. In this case, the one calculation - became (-Inf * 0), which R evaluates to NaN. The correction is to - detect this case and substitute -Inf instead of NaN. + * inst/ChangeLog: Add changelog to svn repository -2015-05-08 warnes +2015-05-25 14:30 warnes - * [r2019] R/mixedsort.R: Summary: Speed up mixedorder by moving - suppressWarnings outside of lapply loops. (Suggestion by Henrik - Bengtsson.) + * tests/test_ddirichlet.R: Add library call. -2015-05-02 warnes +2015-05-25 14:29 warnes - * [r2018] Rename 'trunk' to 'pkg' for compatibility with R-forge + * man/unByteCode.Rd: Fix typo and add documentation for argument + 'name'. - * [r2017] Minor layout change. +2015-05-25 14:29 warnes - * [r2016] Remove stray 'svn' that was inserted into the code. + * man/mixedsort.Rd: Fix typo. - * [r2015] Add man page for unByteCode(), assignEdgeWise(), and +2015-05-25 14:16 warnes + + * man/mixedsort.Rd: Add description of blanklast argument, fix + typo. + +2015-05-25 14:13 warnes + + * man/quantcut.Rd: Change usage to match actual definition. + +2015-05-25 14:10 warnes + + * man/mixedsort.Rd: Note characters sorting ignores case. + +2015-05-25 14:08 warnes + + * man/mixedsort.Rd: Remove '...' from arglist to match source code. + +2015-05-25 14:05 warnes + + * man/mixedsort.Rd: Replace unicode quotes with \code{..}. + +2015-05-23 22:21 warnes + + * tests/test_ddirichlet.R: Add regression test ddirichlet() bug for + x[i]=0, alpha[i]=1: + ddirichlet(x, alpha) was returning NA rather than 0. + +2015-05-23 22:12 warnes + + * R/dirichlet.R: ddirichlet() was incorrectly returning NA when + x[i]=0 and + alpha[i]=1. In this case, the one calculation became (-Inf * 0), + which R evaluates to NaN. The correction is to detect this case + and + substitute -Inf instead of NaN. + +2015-05-08 22:49 warnes + + * R/mixedsort.R: Summary: Speed up mixedorder by moving + suppressWarnings outside of + lapply loops. (Suggestion by Henrik Bengtsson.) + +2015-05-02 17:38 warnes + + * Rename 'trunk' to 'pkg' for compatibility with R-forge + +2015-05-02 13:50 warnes + + * Minor layout change. + +2015-05-02 13:48 warnes + + * Remove stray 'svn' that was inserted into the code. + +2015-05-02 13:47 warnes + + * Add man page for unByteCode(), assignEdgeWise(), and unByteCodeAssign() -2015-04-28 warnes +2015-04-28 04:27 warnes - * [r1976] Changes to mixedsort(): - Hands off objects that are not - character vectors to the default sort. - Add 'decreasing', - 'na.last', and 'blank.last' arguments. + * Changes to mixedsort(): + - Hands off objects that are not character vectors to the default + sort. + - Add 'decreasing', 'na.last', and 'blank.last' arguments. - * [r1975] Add private function 'checkReverseDependencies'. +2015-04-28 04:16 warnes -2015-04-23 warnes + * Add private function 'checkReverseDependencies'. - * [r1950] Update NEWS and ChangeLog +2015-04-23 21:53 warnes - * [r1949] - The 'q' argument to quantcut()'s 'q' now accept an - integer indicating the number of equally spaced quantile groups - to create. (Suggestion and patch submitted by Ryan C. Thompson.) + * Update NEWS and ChangeLog - * [r1946] Revers accidental text deletion: +2015-04-23 21:47 warnes - * [r1945] Update for gtools 3.4.3 + * - The 'q' argument to quantcut()'s 'q' now accept an integer + indicating the number of equally spaced quantile groups to + create. (Suggestion and patch submitted by Ryan C. Thompson.) - * [r1944] Remove debugging code and stray browser() call +2015-04-23 21:10 warnes -2015-04-14 warnes + * Revers accidental text deletion: - * [r1923] Fix typo +2015-04-23 21:09 warnes -2015-04-09 warnes + * Update for gtools 3.4.3 - * [r1921] Update gtools ChangeLog +2015-04-23 21:06 warnes - * [r1920] Move first()/last()/left()/right() to gdata. Add new - functions na.replace() and loadedPackages(). Add more text to - package description. + * Remove debugging code and stray browser() call -2015-04-08 warnes +2015-04-14 19:39 warnes - * [r1919] Move first/last/left/right to from gtools to gdata + * Fix typo -2015-04-06 warnes +2015-04-09 19:46 warnes - * [r1918] Correct URL + * Update gtools ChangeLog - * [r1917] Update NEWS and ChangeLog for gtools 3.5.0 +2015-04-09 19:45 warnes - * [r1916] Add ChangeLog files to repository + * Move first()/last()/left()/right() to gdata. + Add new functions na.replace() and loadedPackages(). + Add more text to package description. - * [r1915] Implement fix to keywords() needed for R-3.4.1, as - suggested by Kurt Hornik. +2015-04-08 19:55 warnes - * [r1914] - Export S3 methods for first(), last(), left() and - right(). - Ensure code matches man page for first(), last(), - left(), and right(). + * Move first/last/left/right to from gtools to gdata -2014-10-09 warnes +2015-04-06 22:09 warnes - * [r1897] Update for 3.5.0 release of gtools + * Correct URL - * [r1896] Make right() and left() S3 methods for classes data.frame - and matrix +2015-04-06 22:04 warnes -2014-08-27 warnes + * Update NEWS and ChangeLog for gtools 3.5.0 - * [r1872] Fix man page +2015-04-06 21:52 warnes - * [r1871] Finish adding first(), last(), left(), and right(). + * Add ChangeLog files to repository - * [r1870] Add functions first(), last(), left(), and right(). +2015-04-06 21:44 warnes -2014-05-28 warnes + * Implement fix to keywords() needed for R-3.4.1, as suggested by + Kurt + Hornik. - * [r1816] Update for gtools 3.4.1 +2015-04-06 21:40 warnes - * [r1815] Add test to ensure smartbind() properly handles Date - columns. + * - Export S3 methods for first(), last(), left() and right(). + - Ensure code matches man page for first(), last(), left(), and + right(). - * [r1814] smartbind: Convert non-native type columns (except - factor) to character. +2014-10-09 18:56 warnes -2014-04-18 arnima + * Update for 3.5.0 release of gtools - * [r1813] Main arg is 'x' like showNonASCII(x), preformatted notes - instead of verb +2014-10-09 18:52 warnes -2014-04-17 warnes + * Make right() and left() S3 methods for classes data.frame and + matrix - * [r1810] Update ASCIIfy man page to match source code and add - keywords +2014-08-27 00:44 warnes - * [r1809] Update NEWS for gtools 3.4.0 + * Fix man page - * [r1808] Add ASCIIfy function posted to RDevel by Arni Magnusson +2014-08-27 00:36 warnes -2014-03-01 warnes + * Finish adding first(), last(), left(), and right(). - * [r1776] Fix cut-and-paste error. +2014-08-27 00:12 warnes - * [r1775] Update files for gtools 3.3.1 release + * Add functions first(), last(), left(), and right(). - * [r1774] Fix bug in gtools::mixedorder regular expression for - regognizing numbers. (Periods weren't escaped). +2014-05-28 00:24 warnes -2014-02-11 warnes + * Update for gtools 3.4.1 - * [r1773] Create and use locate copy of tools:::.split_op_version. +2014-05-28 00:18 warnes - * [r1772] Update for gtools 3.3.0. + * Add test to ensure smartbind() properly handles Date columns. - * [r1771] Fix arguments +2014-05-28 00:14 warnes - * [r1770] Update arguments to match code. + * smartbind: Convert non-native type columns (except factor) to + character. - * [r1769] Add getDependencies() function to return a list of - package dependencies. +2014-04-18 18:11 arnima -2014-01-14 warnes + * Main arg is 'x' like showNonASCII(x), preformatted notes instead + of verb - * [r1768] Update for bug-fix release +2014-04-17 17:33 warnes - * [r1767] Add test file for binsearch() function. + * Update ASCIIfy man page to match source code and add keywords - * [r1766] Fixed bug where binsearch() returned the wrong endpoint & - value when the found value was at the upper endpoint. +2014-04-17 17:25 warnes -2014-01-13 warnes + * Update NEWS for gtools 3.4.0 - * [r1765] Fix typo +2014-04-17 16:56 warnes -2014-01-11 warnes + * Add ASCIIfy function posted to RDevel by Arni Magnusson - * [r1764] Update for gtools release 3.2.0 +2014-03-01 20:15 warnes - * [r1763] fixes for R CMD check + * Fix cut-and-paste error. - * [r1762] Fixes for gtools release 3.2.0 +2014-03-01 20:12 warnes -2013-12-23 warnes + * Update files for gtools 3.3.1 release - * [r1761] Extend the keywords() function to return keywords - associated with a specified topic via 'keywords(topic)'. +2014-03-01 20:02 warnes - * [r1760] Add keyword. + * Fix bug in gtools::mixedorder regular expression for regognizing + numbers. (Periods weren't escaped). - * [r1759] Add stars.pval() function to convert p-values into - significance symbols. +2014-02-11 17:44 warnes -2013-11-26 warnes + * Create and use locate copy of tools:::.split_op_version. - * [r1748] mixedorder() was failing to correctly handle numbers - including decimals due to a faulty regular expression. Prior to - the fix: +2014-02-11 17:25 warnes + + * Update for gtools 3.3.0. + +2014-02-11 17:19 warnes + + * Fix arguments + +2014-02-11 17:17 warnes + + * Update arguments to match code. + +2014-02-11 17:14 warnes + + * Add getDependencies() function to return a list of package + dependencies. + +2014-01-14 19:43 warnes + + * Update for bug-fix release + +2014-01-14 19:37 warnes + + * Add test file for binsearch() function. + +2014-01-14 15:56 warnes + + * Fixed bug where binsearch() returned the wrong endpoint & value + when the found value was at the upper endpoint. + +2014-01-13 18:16 warnes + + * Fix typo + +2014-01-11 23:39 warnes + + * Update for gtools release 3.2.0 + +2014-01-11 23:38 warnes + + * fixes for R CMD check + +2014-01-11 23:24 warnes + + * Fixes for gtools release 3.2.0 + +2013-12-23 18:48 warnes + + * Extend the keywords() function to return keywords associated with + a specified topic via 'keywords(topic)'. + +2013-12-23 16:08 warnes + + * Add keyword. + +2013-12-23 16:04 warnes + + * Add stars.pval() function to convert p-values into significance + symbols. + +2013-11-26 14:38 warnes + + * mixedorder() was failing to correctly handle numbers including + decimals due to a faulty regular expression. Prior to the fix: - > drr [1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg" > - gtools::mixedsort(drr) [1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 - mg" After the fix: + > drr + [1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg" + > gtools::mixedsort(drr) + [1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg" - > drr [1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg" > - mixedsort(drr) [1] "Dose 0.04 mg" "Dose 0.3 mg" "Dose 0.5 mg" + After the fix: + > drr + [1] "Dose 0.3 mg" "Dose 0.04 mg" "Dose 0.5 mg" + > mixedsort(drr) + [1] "Dose 0.04 mg" "Dose 0.3 mg" "Dose 0.5 mg" + In addition, an optimization was added that checked if the input - vector was numeric. If so, simply use the existing base::order - function. + vector + was numeric. If so, simply use the existing base::order function. -2013-11-18 warnes +2013-11-18 16:06 warnes - * [r1747] Use ".Deprecated" instead of warning. + * Use ".Deprecated" instead of warning. -2013-11-06 warnes +2013-11-06 14:53 warnes - * [r1746] Update files for gtools 3.1.1 + * Update files for gtools 3.1.1 - * [r1745] Fix problem with mixedorder/mixedsort when there is only - zero or one elements in the vector. +2013-11-06 14:51 warnes -2013-09-23 warnes + * Fix problem with mixedorder/mixedsort when there is only zero or + one elements in the vector. - * [r1716] Comment out empty sections in gtools-deprecated.Rd +2013-09-23 15:46 warnes - * [r1715] Update files for gtools 3.1.0 release + * Comment out empty sections in gtools-deprecated.Rd - * [r1714] Make 'addLast()' defunct. +2013-09-23 15:41 warnes - * [r1713] Mark 'addLast()' as defunct and move 'lastAdd()' function - to a separate file. + * Update files for gtools 3.1.0 release - * [r1712] Update for gtools 3.0.1 release +2013-09-23 15:37 warnes - * [r1711] Use 'suppressWarnings() instead of 'options(warn=-1)' in + * Make 'addLast()' defunct. + +2013-09-23 15:29 warnes + + * Mark 'addLast()' as defunct and move 'lastAdd()' function to a + separate file. + +2013-09-23 15:23 warnes + + * Update for gtools 3.0.1 release + +2013-09-23 15:19 warnes + + * Use 'suppressWarnings() instead of 'options(warn=-1)' in 'mixedorder()'. -2013-07-07 warnes +2013-07-07 00:11 warnes - * [r1705] Fix typo. + * Fix typo. -2013-07-06 warnes +2013-07-06 23:55 warnes - * [r1704] Fix Rd warning. + * Fix Rd warning. - * [r1703] Include lastAdd in NAMESPACE +2013-07-06 23:49 warnes - * [r1702] Change assert from deprecated to defunct. + * Include lastAdd in NAMESPACE - * [r1701] Improve deprecation message +2013-07-06 23:46 warnes - * [r1700] Update for gtools 3.0.0 + * Change assert from deprecated to defunct. - * [r1699] Create new function lastAdd to replace addLast and mark - addLast as deprecated. +2013-07-06 23:45 warnes -2013-07-05 warnes + * Improve deprecation message - * [r1698] Point out that addLast() modifies the value of .Last in - the global environment. +2013-07-06 23:43 warnes - * [r1697] Point out that addLast() modifies the value of .Last in - the global environment. + * Update for gtools 3.0.0 - * [r1696] Update for gtools 2.7.2 mark 2 +2013-07-06 23:26 warnes - * [r1695] Remove cross-reference to (obsolete?) moc package + * Create new function lastAdd to replace addLast and mark addLast + as deprecated. - * [r1694] Update for gtools 2.7.2 +2013-07-05 23:48 warnes - * [r1693] Update for R version 3.0.0 and later + * Point out that addLast() modifies the value of .Last in the + global environment. -2013-03-17 warnes +2013-07-05 23:47 warnes - * [r1640] Fix error in smartbind: factor levels were not being - handled if the factor column was not present in the first data - frame. + * Point out that addLast() modifies the value of .Last in the + global environment. -2012-06-19 warnes +2013-07-05 23:34 warnes - * [r1570] Update for gtools 2.7.0. + * Update for gtools 2.7.2 mark 2 - * [r1569] Document new 'verbose' argument to smartbind(). +2013-07-05 23:33 warnes - * [r1568] Clean up R CMD check warnings. + * Remove cross-reference to (obsolete?) moc package -2012-05-04 warnes +2013-07-05 17:31 warnes - * [r1529] smartbind(): Improve handling of factors and ordered - factors. + * Update for gtools 2.7.2 -2011-10-05 warnes +2013-07-05 17:29 warnes - * [r1518] Update version number for release + * Update for R version 3.0.0 and later - * [r1517] Add 'sep' argument to smartbind() to allow specification - of character used to separate components of constructed names +2013-03-17 02:21 warnes -2011-09-28 warnes + * Fix error in smartbind: factor levels were not being handled if + the factor column was not present in the first data frame. - * [r1513] smartbind(): Prevent coersion to data frame from mangling - column names. +2012-06-19 19:00 warnes - * [r1512] Add 'fill' argument to smartbind() to specify a value to - use for missing entries. + * Update for gtools 2.7.0. - * [r1511] Add 'fill' argument to smartbind() to specify a value to - use for missing entries. +2012-06-19 14:00 warnes -2010-08-14 warnes + * Document new 'verbose' argument to smartbind(). - * [r1451] Modify mixedorder()/mixedsort() to better handle strings +2012-06-19 13:56 warnes + + * Clean up R CMD check warnings. + +2012-05-04 16:06 warnes + + * smartbind(): Improve handling of factors and ordered factors. + +2011-10-05 17:05 warnes + + * Update version number for release + +2011-10-05 16:53 warnes + + * Add 'sep' argument to smartbind() to allow specification of + character used to separate components of constructed names + +2011-09-28 22:56 warnes + + * smartbind(): Prevent coersion to data frame from mangling column + names. + +2011-09-28 22:53 warnes + + * Add 'fill' argument to smartbind() to specify a value to use for + missing entries. + +2011-09-28 22:53 warnes + + * Add 'fill' argument to smartbind() to specify a value to use for + missing entries. + +2010-08-14 19:28 warnes + + * Modify mixedorder()/mixedsort() to better handle strings containing multiple periods, like version numbers (e.g 1.1.2, 1.2.1. 1.1.1.1). -2010-05-01 warnes +2010-05-01 22:14 warnes - * [r1434] Update version number for new release + * Update version number for new release - * [r1433] Change Greg's email address to greg at warnes.net +2010-05-01 22:03 warnes - * [r1432] Fix error in checkRVersion() + * Change Greg's email address to greg at warnes.net -2010-04-28 ggrothendieck2 +2010-05-01 21:59 warnes - * [r1431] fixed problems with R CMD CHECK + * Fix error in checkRVersion() -2009-05-09 warnes +2010-04-28 17:23 ggrothendieck2 - * [r1328] Escape $ in .Rd file to avoid latex issues + * fixed problems with R CMD CHECK - * [r1327] Update NEWS and create softlinks for NEWS and ChangeLog - in top level directory +2009-05-09 03:35 warnes - * [r1326] Move actual NEWS file into inst. + * Escape $ in .Rd file to avoid latex issues - * [r1325] Update Greg's email address and fix Rd syntax errors +2009-05-09 03:26 warnes -2009-02-16 warnes + * Update NEWS and create softlinks for NEWS and ChangeLog in top + level directory - * [r1313] Correct windows make flags as suggested by Brian Ripley. +2009-05-09 03:15 warnes -2008-08-15 warnes + * Move actual NEWS file into inst. - * [r1303] Add keywords() function to show /doc/KEYWORDS file +2009-05-09 03:13 warnes -2008-05-29 warnes + * Update Greg's email address and fix Rd syntax errors - * [r1285] Add newVersionAvailable() function to compare running and - latest available R versions +2009-02-16 15:34 warnes -2008-05-26 warnes + * Correct windows make flags as suggested by Brian Ripley. - * [r1284] Update license specification +2008-08-15 13:15 warnes - * [r1283] Remove 'assert' man page + * Add keywords() function to show /doc/KEYWORDS file -2008-05-22 warnes +2008-05-29 23:19 warnes - * [r1282] Finish rename of assert.R to assert-depricated.Rd + * Add newVersionAvailable() function to compare running and latest + available R versions - * [r1281] Add checkRVersion.R file +2008-05-26 19:15 warnes - * [r1280] Rename again to get correct extension! + * Update license specification - * [r1279] Update NEWS for 2.5.0 +2008-05-26 15:04 warnes - * [r1278] Add man page for checkRVersion + * Remove 'assert' man page - * [r1277] Rename assert-deprecated.R to assert.R to meet R file - name requirements. +2008-05-22 16:40 warnes - * [r1276] Add checkRVersion to NAMESPACE, and increment version in + * Finish rename of assert.R to assert-depricated.Rd + +2008-05-22 16:35 warnes + + * Add checkRVersion.R file + +2008-05-22 16:34 warnes + + * Rename again to get correct extension! + +2008-05-22 16:30 warnes + + * Update NEWS for 2.5.0 + +2008-05-22 16:17 warnes + + * Add man page for checkRVersion + +2008-05-22 16:16 warnes + + * Rename assert-deprecated.R to assert.R to meet R file name + requirements. + +2008-05-22 16:15 warnes + + * Add checkRVersion to NAMESPACE, and increment version in DESCRIPTION. - * [r1275] Remove broken SEE LSO reference +2008-05-22 16:14 warnes -2008-04-12 warnes + * Remove broken SEE LSO reference - * [r1259] Improve text explanation of how defmacro() and strmacro() - differ from function(). +2008-04-12 19:42 warnes - * [r1258] assert() is now deprecated in favor of base::stopifnot() + * Improve text explanation of how defmacro() and strmacro() differ + from + function(). - * [r1257] Rename 'assert.R' to 'deprecated.R'. +2008-04-12 19:19 warnes - * [r1256] Assert is now deprecated in favor of base::stopifnot(), - so add call to .Deprecated() to inform the user. + * assert() is now deprecated in favor of base::stopifnot() -2007-11-30 warnes +2008-04-12 19:19 warnes - * [r1228] Update defnitions of odd() and even() to use modulus - operator instead of division. Prettier, I think, :-D + * Rename 'assert.R' to 'deprecated.R'. -2007-08-08 warnes +2008-04-12 19:14 warnes - * [r1121] Fix bug identified by R-2.6's check routings in - binsearch() + * Assert is now deprecated in favor of base::stopifnot(), so add + call to + .Deprecated() to inform the user. - * [r1120] Add the binsearch(), previously in the genetics package. +2007-11-30 18:05 warnes -2007-07-18 ggorjan + * Update defnitions of odd() and even() to use modulus operator + instead of division. Prettier, I think, :-D - * [r1100] typo fixed +2007-08-08 13:52 warnes -2007-04-12 warnes + * Fix bug identified by R-2.6's check routings in binsearch() - * [r1088] Add ask() function to prompt the user and collect a - single response. +2007-08-08 13:48 warnes -2007-04-07 warnes + * Add the binsearch(), previously in the genetics package. - * [r1087] Fix improper escapes in regexp detected by R 2.5.0 - package check. +2007-07-18 11:48 ggorjan [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/r-gregmisc -r 2192 From noreply at r-forge.r-project.org Thu Jun 21 19:19:14 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 21 Jun 2018 19:19:14 +0200 (CEST) Subject: [R-gregmisc-commits] r2193 - pkg/gtools Message-ID: <20180621171914.306C71870C7@r-forge.r-project.org> Author: warnes Date: 2018-06-21 19:19:13 +0200 (Thu, 21 Jun 2018) New Revision: 2193 Modified: pkg/gtools/NEWS Log: Update news file for gtools 3.8.1. Modified: pkg/gtools/NEWS =================================================================== --- pkg/gtools/NEWS 2018-06-21 17:18:40 UTC (rev 2192) +++ pkg/gtools/NEWS 2018-06-21 17:19:13 UTC (rev 2193) @@ -3,7 +3,7 @@ Behind the scenes: -- Remove softlinks +- Remove softlinks per request from Uwe Ligges gtools 3.8.0 - 2018-06-20 ------------------------- From noreply at r-forge.r-project.org Mon Jun 25 16:52:46 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 25 Jun 2018 16:52:46 +0200 (CEST) Subject: [R-gregmisc-commits] r2194 - pkg/gmodels Message-ID: <20180625145246.61E13180B4D@r-forge.r-project.org> Author: warnes Date: 2018-06-25 16:52:45 +0200 (Mon, 25 Jun 2018) New Revision: 2194 Removed: pkg/gmodels/ChangeLog pkg/gmodels/NEWS Log: Remove NEWS and ChangeLog soft links Deleted: pkg/gmodels/ChangeLog =================================================================== --- pkg/gmodels/ChangeLog 2018-06-21 17:19:13 UTC (rev 2193) +++ pkg/gmodels/ChangeLog 2018-06-25 14:52:45 UTC (rev 2194) @@ -1 +0,0 @@ -link inst/ChangeLog \ No newline at end of file Deleted: pkg/gmodels/NEWS =================================================================== --- pkg/gmodels/NEWS 2018-06-21 17:19:13 UTC (rev 2193) +++ pkg/gmodels/NEWS 2018-06-25 14:52:45 UTC (rev 2194) @@ -1 +0,0 @@ -link inst/NEWS \ No newline at end of file From noreply at r-forge.r-project.org Mon Jun 25 16:53:15 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 25 Jun 2018 16:53:15 +0200 (CEST) Subject: [R-gregmisc-commits] r2195 - in pkg/gmodels: . inst Message-ID: <20180625145315.392A4180B4D@r-forge.r-project.org> Author: warnes Date: 2018-06-25 16:53:14 +0200 (Mon, 25 Jun 2018) New Revision: 2195 Added: pkg/gmodels/ChangeLog pkg/gmodels/NEWS Removed: pkg/gmodels/inst/ChangeLog pkg/gmodels/inst/NEWS Log: Move NEWS and ChangeLog to top level. Copied: pkg/gmodels/ChangeLog (from rev 2194, pkg/gmodels/inst/ChangeLog) =================================================================== --- pkg/gmodels/ChangeLog (rev 0) +++ pkg/gmodels/ChangeLog 2018-06-25 14:53:14 UTC (rev 2195) @@ -0,0 +1,834 @@ +2018-06-20 20:51 warnes + + * DESCRIPTION, inst/ChangeLog: Update DESCRIPTION and ChangeLog for + gmodels 2.16.1 + +2018-06-20 20:50 warnes + + * NAMESPACE: Remove obsolete functions. + +2018-06-20 20:46 warnes + + * R/fit.contrast.R, man/ci.Rd, man/estimable.Rd, + man/fit.contrast.Rd: Fix R CMD check issues. + +2018-06-20 20:42 warnes + + * R/ci.R: Remove trailing whitespace + +2018-06-20 20:40 warnes + + * R/est_p_ci.R: Use base::trimws() instead of gdata::trim() + +2018-06-20 20:35 warnes + + * test: Remove duplicated/incorrect 'test' directory. + +2017-06-12 23:53 warnes + + * DESCRIPTION: Update imports + +2017-06-12 23:53 warnes + + * NAMESPACE: Add imports for base R packages to NAMESPACE + +2017-06-05 21:27 warnes + + * inst/NEWS: Update NEWS and ChangeLog files for 2.18.0. + +2016-08-15 19:11 warnes + + * test, test/lme-test.R, test/test_estimable_mlm.R: Add tests for + mlm and (obsolete) lme + +2016-08-15 19:05 warnes + + * R/est_p_ci.R: Add est_p_ci generic and lm method + +2016-08-12 17:15 warnes + + * DESCRIPTION, NAMESPACE, R/ci.R, R/fit.contrast.R, inst/ChangeLog, + inst/NEWS, man/ci.Rd, man/estimable.Rd, man/fit.contrast.Rd: + Updates... + +2015-07-22 00:53 warnes + + * DESCRIPTION: Update gmodels DESCRIPTION + +2015-07-22 00:48 warnes + + * test, tests, tests/lme-test.R: Renamed 'test' directory to + 'tests', commented out tests for lme4 which has a changed API + +2015-07-20 23:38 warnes + + * DESCRIPTION, NAMESPACE: Changs to squash new R CMD check warnings + +2015-07-19 03:22 warnes + + * DESCRIPTION, NAMESPACE, R/ci.R, R/est.mer.R, R/estimable.R, + R/fit.contrast.R, R/to.est.R, inst/NEWS, man/ci.Rd, + man/estimable.Rd, man/fit.contrast.Rd: - Removed references to + 'mer' objects, sincel the nlme4 update is not backwards + compatible with my code. + - Removed 'require' calls. + +2015-07-19 02:34 warnes + + * DESCRIPTION, inst/ChangeLog, inst/NEWS: Update DESCRIPTION, + ChangeLog, and NEWS for gmodels 2.16.1 + +2015-07-19 02:30 warnes + + * R/ci.R, man/ci.Rd: ci.binom() was using an incorrect method for + calculating binomial confidence interval. The revised code + calculates the Clopper-Pearson 'exect' interval, which is + *conservative* due to the discrete nature of the binomial + distribution. + +2015-05-02 17:38 warnes + + * Rename 'trunk' to 'pkg' for compatibility with R-forge + +2015-04-06 21:52 warnes + + * Add ChangeLog files to repository + +2014-07-24 15:18 warnes + + * Update NEWS for gmodels 2.16.0 + +2014-07-24 15:14 warnes + + * - Estimable now adds the class 'estimable' to returned objects. + - New ci() method for estimable objects. + - Minor improvemets to man page formatting. + +2013-07-18 14:09 warnes + + * Looks like Brian Ripley repackaged for R 3.0.0 and bumped version + number, so change it to 2.15.5 + +2013-07-18 13:57 warnes + + * Update for gmodels 2.15.4 + +2013-07-18 13:54 warnes + + * Update to current Rd syntax + +2013-07-18 13:46 warnes + + * Correct bug in estimable.mlm + +2013-07-15 18:13 warnes + + * Remove unused argument to ci.mer + +2012-06-28 00:49 warnes + + * Update for gmodels version 2.15.3. + +2012-06-28 00:47 warnes + + * Move percentile() function to a separate file. + +2012-06-28 00:41 warnes + + * Update est.mer() to support new S4 "mer" class. + +2012-06-28 00:40 warnes + + * Make lme4 example executable. + +2012-06-27 22:42 warnes + + * Add test code submitted by Ariel.Muldoon at oregonstate.edu. + +2012-04-19 22:09 warnes + + * Update for release 2.15.2 + +2012-04-19 22:07 warnes + + * Update version and date. + +2012-04-19 22:06 warnes + + * The 'Design' package has been replaced my 'rms', so update man + page references. + +2012-04-19 22:05 warnes + + * More fixes for support of S4 'mer' class from lme4 package. + +2012-04-19 21:13 warnes + + * Split long line. + +2012-04-19 17:50 warnes + + * Changes to pass R CMD check + +2011-12-14 18:17 warnes + + * Improve formatting of ci.mer(). + +2011-12-14 18:14 warnes + + * Modify est.mer to work with recent lme4 'mer' S4 objects. + +2011-01-16 22:17 warnes + + * Fix warnings reported by R CMD check. Update version number to + 2.15.1. + +2009-05-09 05:29 warnes + + * Add tests for lme4 'mer' objects + +2009-05-09 05:04 warnes + + * Update for 2.15.0 + +2009-05-09 05:02 warnes + + * Update description for 2.15.0 + +2009-05-09 05:01 warnes + + * Add support for lme4's 'mer' objects + +2009-05-09 05:00 warnes + + * Add support for lme4's 'mer' objects + +2009-05-09 04:53 warnes + + * Fix .Rd syntax error + +2009-05-09 04:37 warnes + + * Add softlinks for ChangeLog and NEWS to top level dir for + convenience + +2009-05-09 04:36 warnes + + * Move ChangeLog and NEWS files into inst directory + +2009-05-09 04:00 warnes + + * Update Greg's email address + +2008-04-10 14:05 warnes + + * Improve languages a bit + +2008-01-02 16:56 warnes + + * Update Marc's email address + +2007-12-12 21:16 warnes + + * Move copyright notice for Randall's contributions from License + section to Author section of the DESCRIPTION file. + +2007-12-07 22:21 warnes + + * Update DESCRIPTION and NEWS for release 2.14.1 + +2007-12-07 22:10 warnes + + * Correct minor typos in man page for estimable() + +2007-12-07 22:09 warnes + + * Add support for lme models to estimable() + +2007-12-07 22:07 warnes + + * Replace non-ascii characters in Soren's name with (equivalent?) + ascii character to avoid character encoding issues. + +2007-10-22 02:24 warnes + + * Clarify GPL version + +2007-07-26 00:20 warnes + + * Add support for mlm to estimable(). + +2007-07-26 00:10 warnes + + * Add estimable method for mlm objects + +2007-03-09 22:35 warnes + + * Remove stray character + +2007-03-09 20:10 warnes + + * Update NEWS file. + +2007-03-09 20:07 warnes + + * Update version number + +2007-03-09 20:06 warnes + + * Minor code formatting changes + +2007-03-09 20:06 warnes + + * Flip lower and upper interval in ci.lmer(). Add example to man + page. + +2007-03-09 19:43 warnes + + * Fix some old email addressses that got missed + +2006-11-29 00:11 warnes + + * Update for 2.13.1 + +2006-11-29 00:05 warnes + + * Correct declartion of S3 methods for estimable() + +2006-11-29 00:05 warnes + + * Add additional suggested packages + +2006-11-29 00:04 warnes + + * - Add generic + - Fix code vs. doc inconsistiencies + +2006-11-28 22:38 warnes + + * Remove extraneous comma that causes errors in R 2.5.0 + +2006-11-27 20:45 warnes + + * Update for 2.13.1 + +2006-11-27 20:36 warnes + + * Add missing export of methods for estimable() + +2006-11-14 22:25 ggorjan + + * Removed executable property + +2006-08-02 22:21 warnes + + * Update my email address + +2006-06-06 19:17 nj7w + + * Updated ci, estimable and fit.contrast as per Randall Johnson + +2006-06-05 21:00 nj7w + + * Additions as per Randall C Johnson + +2006-06-05 20:59 nj7w + + * Additions as per Randall C Johnson + +2006-06-05 20:57 nj7w + + * - New function to estimate CI's and p-values using mcmcsamp() + from the + Matrix package + +2006-05-05 18:29 nj7w + + * Fixed an error: According to Marc Schwartz - there was an error + when a matrix without dimnames(or names(dimnames)) was passed as + x argument + +2005-12-13 16:03 nj7w + + * Removed ChangeLog + +2005-12-13 16:02 nj7w + + * Updated NEWS + +2005-12-12 21:57 nj7w + + * Updated version number for CRAN + +2005-12-04 06:27 warnes + + * Update for 2.11.0 + +2005-12-04 06:12 warnes + + * Integration of code changes suggested by Randall C Johnson to add + support for lmer (lme version 4) objects to ci(), estimable(), + and + fit.contrast(). + + Addition of simplified coefficient specificaiton for estimable() + based on a function provided by Randall C Johnson. It is now + possible to do things like: + estimable(reg, c("xB"=1,"xD"=-1) ) + instead of: + estimable(reg, c( 0, 1, 0, -1) ) + which should make estimable much easier to use for large models. + +2005-12-01 16:54 nj7w + + * Updated Greg's email address + +2005-10-27 11:21 warnes + + * Update version number. Bump minor version since we added + functionality. + +2005-10-27 10:33 warnes + + * Add ci.binom() to NAMESPACE, bump version + +2005-10-26 13:39 warnes + + * Add ci.binom + +2005-10-25 21:18 warnes + + * Add gdata::nobs to import list. Needed by ci() + +2005-09-12 15:44 nj7w + + * Updated Greg's email + +2005-09-07 15:31 nj7w + + * Fixed man page + +2005-09-06 21:34 nj7w + + * Updated DESCRIPTION + +2005-09-06 21:34 nj7w + + * Added NEWS + +2005-09-06 16:21 nj7w + + * Fixed the Package name + +2005-09-02 23:10 nj7w + + * Added ChangeLog + +2005-08-31 16:28 nj7w + + * Added DESCRIPTION file + +2005-08-31 16:27 nj7w + + * removed DESCRIPTION.in + +2005-07-11 21:35 nj7w + + * Revision based on Marc Schwartz's suggestions: + 1) Added 'dnn' argument to enable specification of dimnames as + per table() + 2) Corrected bug in SPSS output for 1d table, where proportions + were being printed and not percentages ('%' output) + +2005-06-09 14:20 nj7w + + * Updating the version number, and various help files to + synchronize splitting of gregmisc bundle in 4 individual + components. + +2005-06-09 14:13 nj7w + + * Updates by Marc Schwartz: + CrossTable: + + # Revision 2.0 2005/04/27 + # Added 'format = "d"' to all table count output + # so that large integers do not print in + # scientific notation + +2005-05-13 18:59 nj7w + + * 1) Using dQuote.ascii function in read.xls as the new version of + dQuote doesn't work proprly with UTF-8 locale. + 2) Modified CrossTable.Rd usage in gmodels + 3) Modified heatmap.2 usage in gplots. + +2005-05-11 13:51 warnes + + * Add dependency on gdata::frameApply. + +2005-03-31 20:32 warnes + + * Add ceofFrame function to NAMESPACE + +2005-03-31 19:05 warnes + + * coefFrame example needs to properly load ELISA data from gtools + package + +2005-03-31 18:31 warnes + + * Ensure that each file has $Id$ header, and no $Log$ + +2005-03-31 18:30 warnes + + * Add coefFrame() function contributed by Jim Rogers + +2005-01-18 19:53 warnes + + * Removed Windows Line Endings + +2005-01-14 21:40 nj7w + + * Updated the manual to reflect prop.chisq change in its R file. + +2005-01-14 19:14 warnes + + * Nitin added display of the Chisquare contribution of each cell, + as suggested + by Greg Snow. + +2005-01-12 20:50 warnes + + * Add dependency on R 1.9.0+ to prevent poeple from installing on + old + versions of R which don't support namespaces. + +2004-12-23 19:32 nj7w + + * Split the function print.CrossTable.vector in two parts - for SAS + behaiour and SPSS behaviour. Also put the code of printing + statistics in a function 'print.statistics' + +2004-12-21 22:38 warnes + + * Added & extended changes made by Nitin to implement 'SPSS' + format, as suggested by + Dirk Enzmann . + +2004-09-30 21:03 warneg + + * Fix typos. + +2004-09-27 21:01 warneg + + * Updated to pass R CMD check. + +2004-09-03 22:44 warneg + + * Add explicit package to call to quantcut in example. + +2004-09-03 17:27 warneg + + * initial bundle checkin + +2004-09-02 17:14 warneg + + * Initial revision + +2004-05-25 02:57 warnes + + * Updates from Mark Schwartz. + +2004-04-13 11:41 warnes + + * Fix latex warning: it doesn't like double subscripts. + +2004-03-26 22:28 warnes + + * Reflect movement of code from 'mva' package to 'stats' in R + 1.9.0. + +2004-03-25 20:09 warnes + + * - Estimable was reporting sqrt(X^2) rather than X^2 in the + output. + - Provide latex math markup for linear algebra expressions in + help text. + - Other clarifications in help text + +2004-03-25 18:17 warnes + + * Add enhancements to estimable() provided by S?ren H?jsgaard + \email{sorenh at agrsci.dk}: + + I have made a modified version of the function [..] which + 1) also works on geese and gee objects and + 2) can test hypotheses af the forb L * beta = beta0 both as a + single Wald test and row-wise for each row in L. + +2003-11-17 21:40 warnes + + * - Fix incorrect handling of glm objects by fit.contrast, as + reported + by Ulrich Halekoh, Phd . + + - Add regression test code to for this bug. + +2003-08-07 03:49 warnes + + * - Fixed incorrect denominator in standard error for mean in + ci.default. + +2003-04-22 17:24 warnes + + * - the variable 'df' was used within the lme code section + overwriting + the argument 'df'. + +2003-03-12 17:58 warnes + + * - Fixed a typo in the example + - Added to lme example + +2003-03-07 15:48 warnes + + * - Minor changes to code to allow the package to be provided as an + S-Plus chapter. + +2003-01-30 21:53 warnes + + * - Renamed 'contrast.lm' to 'fit.contrast'. This new name is more + descriptive and makes it easier to create and use methods for + other + classes, eg lme. + + - Enabled fit.contrast for lme object now that Doug Bates has + provided + the necessary support for contrasts in the nlme package. + + - New contrast.lm function which generates a 'depreciated' + warning and + calls fit.contrast + + - Updated help text to match changes. + +2003-01-30 21:41 warnes + + * - Removed argument 'correct' and now print separate corrected + values + for 2 x 2 tables. + - Added arguments 'prop.r', 'prop.c' and 'prop.t' to toggle + printing + of row, col and table percentages. Default is TRUE. + - Added argument 'fisher' to toggle fisher exact test. Default is + FALSE. + - Added McNemar test to statistics and argument 'mcnemar' to + toggle + test. Default is FALSE. + - Added code to generate an invisible return list containing + table + counts, proportions and the results of the appropriate + statistical tests. + +2003-01-30 14:58 warnes + + * - Added explicit check to ensure that the number of specified + contrasts is less than or equal to the ncol - 1. Previously, this + failed with an obtuse error message when the contrast matrix had + row + names, and silently dropped contrasts over ncol-1. + +2002-11-04 14:13 warnes + + * - Moved fisher.test() to after table is printed, so that table is + still printed in the event that fisher.test() results in errors. + +2002-10-29 23:06 warnes + + * - Fixes to fast.svd to make it actually work. + - Updates to man page to fix mistmatches between code and docs + and to + fix warnings. + +2002-10-29 23:00 warnes + + * - Moved make.contrasts to a separate file. + - Enhanced make contrasts to better label contrast matrix, to + give + how.many a default value, and to coerce vectors into row + matrixes. + - Added help page for make.contrasts. + - Added link from contrasts.lm seealso to make.contrasts. + +2002-10-29 19:29 warnes + + * Initial checkin for fast.prcomp() and fast.svd(). + +2002-09-26 12:11 warnes + + * - Added note and example code to illustrate how to properly + compute + contrasts for the first factor in the model. + +2002-09-24 19:12 warnes + + * - Fixed a typo. + +2002-09-23 14:27 warnes + + * - Fixed syntax errors in barplot2.Rd and CrossTable.Rd + - Fixed incorrect translation of 'F' (distribution) to 'FALSE' in + glh.test.Rd + +2002-09-23 13:59 warnes + + * - Modified all files to include CVS Id and Log tags. + +2002-09-23 13:38 warnes + + * - Added CrossTable() and barplot2() code and docs contributed by + Marc Schwartz. + - Permit combinations() to be used when r>n provided + repeat.allowed=TRUE + - Bumped up version number + +2002-08-01 19:37 warnes + + * - Corrected documentation mismatch for ci, ci.default. + + - Replaced all occurences of '_' for assignment with '<-'. + + - Replaced all occurences of 'T' or 'F' for 'TRUE' and 'FALSE' + with + the spelled out version. + + - Updaded version number and date. + +2002-04-09 00:51 warneg + + * Checkin for version 0.5.3 + +2002-03-26 21:22 warneg + + * - Changed methods to include '...' to match the generic. + - Updated for version 0.5.1 + +2002-03-26 15:30 warneg + + * Removed incorrect link to 'contrast' from seealso. + +2002-02-20 20:09 warneg + + * Minor changes, typo and formatting fixes. + +2002-01-17 23:51 warneg + + * - Fixed errror in last example by adding 'conf.int' parameter to + 'estimable' call. + +2002-01-17 23:42 warneg + + * - Fixed typo in code that resulted in an syntax error. + +2002-01-10 17:35 warneg + + * - print.glh.test() was using cat() to printing the call. This + didn't work and + generated an error. + +2001-12-19 20:06 warneg + + * - Fixed display of formulae. + - Added description of return value + +2001-12-19 20:05 warneg + + * - Removed extra element of return object. + +2001-12-18 22:14 warneg + + * - Updated documentation to reflect change of parameters from + 'alpha' + to 'conf.int', including the new optional status of the + confidence + intervals. + +2001-12-18 22:12 warneg + + * - Modified to make confidence intervals optional. Changed 'alpha' + parameter giving significance level to 'conf.int' giving + confidence + level. + +2001-12-18 21:36 warneg + + * - Added summary.glh.test to alias, usage, and example sections. + +2001-12-18 21:34 warneg + + * - Modified to work correctly when obj is of class 'aov' by + specifying + summary.lm instead of summary. This ensures that the summary + object + has the fields we need. + + - Moved detailed reporting of results from 'print' to 'summary' + function and added a simpler report to 'print' + +2001-12-18 21:27 warneg + + * - Modified to work correctly when obj is of class 'aov' by + specifying + summary.lm instead of summary. This ensures that the summary + object + has the fields we need. + +2001-12-18 00:45 warneg + + * Initial checkin. + +2001-12-17 18:59 warneg + + * - Fixed spelling errors. + +2001-12-17 18:52 warneg + + * - Fixed the link to contrasts.lm. + - Rephrased title/description to be more clear. + +2001-12-10 19:35 warneg + + * Renamed 'contrsts.coeff.Rd' to 'estimable.Rd' corresponding to + function rename. + +2001-12-10 19:26 warneg + + * renamed from contrast.coeff.R to estimable.R (incorrectly via + contrast.lm.R) + +2001-12-07 19:50 warneg + + * - Added text noting that lme is now supported. + +2001-12-07 19:19 warneg + + * - Fixed typo: DF column was being filled in with p-value. + +2001-12-07 18:49 warneg + + * - Added ci.lme method to handle lme objects. + +2001-10-16 23:15 warneg + + * Fixed unbalanced brace. + +2001-08-25 05:52 warneg + + * - Added CVS header. + - Added my email address. + +2001-05-30 13:23 warneg + + * Initial revision + Copied: pkg/gmodels/NEWS (from rev 2194, pkg/gmodels/inst/NEWS) =================================================================== --- pkg/gmodels/NEWS (rev 0) +++ pkg/gmodels/NEWS 2018-06-25 14:53:14 UTC (rev 2195) @@ -0,0 +1,168 @@ +Version 2.18.0 - 2018-06-19 +--------------------------- + +Bug fixes: + +- ci.binom() was using an incorrect method for calcuating binomial + conficence intervals. It now calculates the Clopper-Pearson 'exect' + interval, which is *conservative* due to the discrete nature of the + binomial distribution. + +Other Changes: + +- Support for lme4 objects has been removed due to incompatible + changes to the lme4 package. + +Version 2.16.0 - 2014-07-24 +--------------------------- + +New features: + +- The estimable() function now returns objects that are of class + 'estimable'. + +- The confidence interval function ci() now has a method for + 'estimable' objects, with the same layout as for 'lm' objects, + making it easier to combine confidence information about model + parameters and estimable functions into a single table. + + +Version 2.15.5 - 2013-07-18 +--------------------------- + +Bug fixes: + +- Correct error in estimable.mlm() that caused it to always fail. Added + test code to prevent future issues. + +Other Changes: + +- Update man page file for ci() to current Rd syntax. +- Remove unused argument to ci.mer() + + +Version 2.15.3 - 2012-06-27 +--------------------------- + +Bug fixes: + +- Update est.mer() to work with "mer" object changes introduced in + lme4 version 0.999999-0. + + +Version 2.15.2 - 2012-04-19 +--------------------------- + +Bug fixes: + +- Update est.mer() to work with recent versions of lme4 which changed + 'mer' objects from S3 to S4 class + +- Changes to pass new R CMD check tests + +- The 'Design' package has been replaced my 'rms', so update man page + references. + + +Version 2.15.1 - 2011-01-16 +--------------------------- + +Bug fixes: + +- Fix warnings reported by new versions of R CMD check. + + +Version 2.15.0 +-------------- + +New features: + +- Add support for 'mer' model from lme4. + +Bug fixes: + +- Correct several minor .Rd syntax errors + +- Move extra copyright text to Author field instead of License field. + + +Version 2.14.1 +-------------- + +New features: + +- Add support for 'lme' objects to estimable(). + +Other: + +- Fix minor typos in manual page for estimable(). + +Version 2.14.0 +-------------- + +New Features: + +- Add support for 'mlm' objects to estimable + + +Version 2.13.2 +-------------- + +Bug Fixes: + +- Lower and upper end of confidence interval for lmer objects were + reversed in est.lmer(). + +- Correct Greg's email address in two help files. + + +Version 2.13.1 +-------------- + +Bug Fixes: + +- Problem: R CMD check errors under development version of R 2.5.0 + Solution: + - Add additional packages to 'Suggests' list in DESCRIPTION + - Remove extra trailing comma in function calls + - fix various code/doc inconsistencies + +- Problem: estimable() was failing for lmer objects. + Solution: + - Create a generic estimable() + - Move old function to estimable.default() + - Add estimable.lmer() to the exported methods list in NAMESPACE + + +Version 2.13.0 +-------------- + + +Version 2.12.0 +-------------- + +- Updated Greg's email address. + +- Add support for lmer (lme version 4) objects to ci(), estimable(), + and fit.contrast() via code contributed by Randall C Johnson. + +- Add simplfied coefficient specification to estimable() based on a + function provided by Randall C Johnson. It is now possible to do + things like: + estimable(reg, c("xB"=1,"xD"=-1)) + instead of: + estimable(reg, c( 0, 1, 0, -1)) + which should make estimable() much easier to use for large models. + +Version 2.1.0 +------------- + +Version 2.0.8 +------------- + + - Added DESCRIPTION and removed DESCRIPTION.in + + - Updated CrossTable.R + + - Updated NAMESPACE file + Deleted: pkg/gmodels/inst/ChangeLog =================================================================== --- pkg/gmodels/inst/ChangeLog 2018-06-25 14:52:45 UTC (rev 2194) +++ pkg/gmodels/inst/ChangeLog 2018-06-25 14:53:14 UTC (rev 2195) @@ -1,834 +0,0 @@ -2018-06-20 20:51 warnes - - * DESCRIPTION, inst/ChangeLog: Update DESCRIPTION and ChangeLog for - gmodels 2.16.1 - -2018-06-20 20:50 warnes - - * NAMESPACE: Remove obsolete functions. - -2018-06-20 20:46 warnes - - * R/fit.contrast.R, man/ci.Rd, man/estimable.Rd, - man/fit.contrast.Rd: Fix R CMD check issues. - -2018-06-20 20:42 warnes - - * R/ci.R: Remove trailing whitespace - -2018-06-20 20:40 warnes - - * R/est_p_ci.R: Use base::trimws() instead of gdata::trim() - -2018-06-20 20:35 warnes - - * test: Remove duplicated/incorrect 'test' directory. - -2017-06-12 23:53 warnes - - * DESCRIPTION: Update imports - -2017-06-12 23:53 warnes - - * NAMESPACE: Add imports for base R packages to NAMESPACE - -2017-06-05 21:27 warnes - - * inst/NEWS: Update NEWS and ChangeLog files for 2.18.0. - -2016-08-15 19:11 warnes - - * test, test/lme-test.R, test/test_estimable_mlm.R: Add tests for - mlm and (obsolete) lme - -2016-08-15 19:05 warnes - - * R/est_p_ci.R: Add est_p_ci generic and lm method - -2016-08-12 17:15 warnes - - * DESCRIPTION, NAMESPACE, R/ci.R, R/fit.contrast.R, inst/ChangeLog, - inst/NEWS, man/ci.Rd, man/estimable.Rd, man/fit.contrast.Rd: - Updates... - -2015-07-22 00:53 warnes - - * DESCRIPTION: Update gmodels DESCRIPTION - -2015-07-22 00:48 warnes - - * test, tests, tests/lme-test.R: Renamed 'test' directory to - 'tests', commented out tests for lme4 which has a changed API - -2015-07-20 23:38 warnes - - * DESCRIPTION, NAMESPACE: Changs to squash new R CMD check warnings - -2015-07-19 03:22 warnes - - * DESCRIPTION, NAMESPACE, R/ci.R, R/est.mer.R, R/estimable.R, - R/fit.contrast.R, R/to.est.R, inst/NEWS, man/ci.Rd, - man/estimable.Rd, man/fit.contrast.Rd: - Removed references to - 'mer' objects, sincel the nlme4 update is not backwards - compatible with my code. - - Removed 'require' calls. - -2015-07-19 02:34 warnes - - * DESCRIPTION, inst/ChangeLog, inst/NEWS: Update DESCRIPTION, - ChangeLog, and NEWS for gmodels 2.16.1 - -2015-07-19 02:30 warnes - - * R/ci.R, man/ci.Rd: ci.binom() was using an incorrect method for - calculating binomial confidence interval. The revised code - calculates the Clopper-Pearson 'exect' interval, which is - *conservative* due to the discrete nature of the binomial - distribution. - -2015-05-02 17:38 warnes - - * Rename 'trunk' to 'pkg' for compatibility with R-forge - -2015-04-06 21:52 warnes - - * Add ChangeLog files to repository - -2014-07-24 15:18 warnes - - * Update NEWS for gmodels 2.16.0 - -2014-07-24 15:14 warnes - - * - Estimable now adds the class 'estimable' to returned objects. - - New ci() method for estimable objects. - - Minor improvemets to man page formatting. - -2013-07-18 14:09 warnes - - * Looks like Brian Ripley repackaged for R 3.0.0 and bumped version - number, so change it to 2.15.5 - -2013-07-18 13:57 warnes - - * Update for gmodels 2.15.4 - -2013-07-18 13:54 warnes - - * Update to current Rd syntax - -2013-07-18 13:46 warnes - - * Correct bug in estimable.mlm - -2013-07-15 18:13 warnes - - * Remove unused argument to ci.mer - -2012-06-28 00:49 warnes - - * Update for gmodels version 2.15.3. - -2012-06-28 00:47 warnes - - * Move percentile() function to a separate file. - -2012-06-28 00:41 warnes - - * Update est.mer() to support new S4 "mer" class. - -2012-06-28 00:40 warnes - - * Make lme4 example executable. - -2012-06-27 22:42 warnes - - * Add test code submitted by Ariel.Muldoon at oregonstate.edu. - -2012-04-19 22:09 warnes - - * Update for release 2.15.2 - -2012-04-19 22:07 warnes - - * Update version and date. - -2012-04-19 22:06 warnes - - * The 'Design' package has been replaced my 'rms', so update man - page references. - -2012-04-19 22:05 warnes - - * More fixes for support of S4 'mer' class from lme4 package. - -2012-04-19 21:13 warnes - - * Split long line. - -2012-04-19 17:50 warnes - - * Changes to pass R CMD check - -2011-12-14 18:17 warnes - - * Improve formatting of ci.mer(). - -2011-12-14 18:14 warnes - - * Modify est.mer to work with recent lme4 'mer' S4 objects. - -2011-01-16 22:17 warnes - - * Fix warnings reported by R CMD check. Update version number to - 2.15.1. - -2009-05-09 05:29 warnes - - * Add tests for lme4 'mer' objects - -2009-05-09 05:04 warnes - - * Update for 2.15.0 - -2009-05-09 05:02 warnes - - * Update description for 2.15.0 - -2009-05-09 05:01 warnes - - * Add support for lme4's 'mer' objects - -2009-05-09 05:00 warnes - - * Add support for lme4's 'mer' objects - -2009-05-09 04:53 warnes - - * Fix .Rd syntax error - -2009-05-09 04:37 warnes - - * Add softlinks for ChangeLog and NEWS to top level dir for - convenience - -2009-05-09 04:36 warnes - - * Move ChangeLog and NEWS files into inst directory - -2009-05-09 04:00 warnes - - * Update Greg's email address - -2008-04-10 14:05 warnes - - * Improve languages a bit - -2008-01-02 16:56 warnes - - * Update Marc's email address - -2007-12-12 21:16 warnes - - * Move copyright notice for Randall's contributions from License - section to Author section of the DESCRIPTION file. - -2007-12-07 22:21 warnes - - * Update DESCRIPTION and NEWS for release 2.14.1 - -2007-12-07 22:10 warnes - - * Correct minor typos in man page for estimable() - -2007-12-07 22:09 warnes - - * Add support for lme models to estimable() - -2007-12-07 22:07 warnes - - * Replace non-ascii characters in Soren's name with (equivalent?) - ascii character to avoid character encoding issues. - -2007-10-22 02:24 warnes - - * Clarify GPL version - -2007-07-26 00:20 warnes - - * Add support for mlm to estimable(). - -2007-07-26 00:10 warnes - - * Add estimable method for mlm objects - -2007-03-09 22:35 warnes - - * Remove stray character - -2007-03-09 20:10 warnes - - * Update NEWS file. - -2007-03-09 20:07 warnes - - * Update version number - -2007-03-09 20:06 warnes - - * Minor code formatting changes - -2007-03-09 20:06 warnes - - * Flip lower and upper interval in ci.lmer(). Add example to man - page. - -2007-03-09 19:43 warnes - - * Fix some old email addressses that got missed - -2006-11-29 00:11 warnes - - * Update for 2.13.1 - -2006-11-29 00:05 warnes - - * Correct declartion of S3 methods for estimable() - -2006-11-29 00:05 warnes - - * Add additional suggested packages - -2006-11-29 00:04 warnes - - * - Add generic - - Fix code vs. doc inconsistiencies - -2006-11-28 22:38 warnes - - * Remove extraneous comma that causes errors in R 2.5.0 - -2006-11-27 20:45 warnes - - * Update for 2.13.1 - -2006-11-27 20:36 warnes - - * Add missing export of methods for estimable() - -2006-11-14 22:25 ggorjan - - * Removed executable property - -2006-08-02 22:21 warnes - - * Update my email address - -2006-06-06 19:17 nj7w - - * Updated ci, estimable and fit.contrast as per Randall Johnson - -2006-06-05 21:00 nj7w - - * Additions as per Randall C Johnson - -2006-06-05 20:59 nj7w - - * Additions as per Randall C Johnson - -2006-06-05 20:57 nj7w - - * - New function to estimate CI's and p-values using mcmcsamp() - from the - Matrix package - -2006-05-05 18:29 nj7w - - * Fixed an error: According to Marc Schwartz - there was an error - when a matrix without dimnames(or names(dimnames)) was passed as - x argument - -2005-12-13 16:03 nj7w - - * Removed ChangeLog - -2005-12-13 16:02 nj7w - - * Updated NEWS - -2005-12-12 21:57 nj7w - - * Updated version number for CRAN - -2005-12-04 06:27 warnes - - * Update for 2.11.0 - -2005-12-04 06:12 warnes - - * Integration of code changes suggested by Randall C Johnson to add - support for lmer (lme version 4) objects to ci(), estimable(), - and - fit.contrast(). - - Addition of simplified coefficient specificaiton for estimable() - based on a function provided by Randall C Johnson. It is now - possible to do things like: - estimable(reg, c("xB"=1,"xD"=-1) ) - instead of: - estimable(reg, c( 0, 1, 0, -1) ) - which should make estimable much easier to use for large models. - -2005-12-01 16:54 nj7w - - * Updated Greg's email address - -2005-10-27 11:21 warnes - - * Update version number. Bump minor version since we added - functionality. - -2005-10-27 10:33 warnes - - * Add ci.binom() to NAMESPACE, bump version - -2005-10-26 13:39 warnes - - * Add ci.binom - -2005-10-25 21:18 warnes - - * Add gdata::nobs to import list. Needed by ci() - -2005-09-12 15:44 nj7w - - * Updated Greg's email - -2005-09-07 15:31 nj7w - - * Fixed man page - -2005-09-06 21:34 nj7w - - * Updated DESCRIPTION - -2005-09-06 21:34 nj7w - - * Added NEWS - -2005-09-06 16:21 nj7w - - * Fixed the Package name - -2005-09-02 23:10 nj7w - - * Added ChangeLog - -2005-08-31 16:28 nj7w - - * Added DESCRIPTION file - -2005-08-31 16:27 nj7w - - * removed DESCRIPTION.in - -2005-07-11 21:35 nj7w - - * Revision based on Marc Schwartz's suggestions: - 1) Added 'dnn' argument to enable specification of dimnames as - per table() - 2) Corrected bug in SPSS output for 1d table, where proportions - were being printed and not percentages ('%' output) - -2005-06-09 14:20 nj7w - - * Updating the version number, and various help files to - synchronize splitting of gregmisc bundle in 4 individual - components. - -2005-06-09 14:13 nj7w - - * Updates by Marc Schwartz: - CrossTable: - - # Revision 2.0 2005/04/27 - # Added 'format = "d"' to all table count output - # so that large integers do not print in - # scientific notation - -2005-05-13 18:59 nj7w - - * 1) Using dQuote.ascii function in read.xls as the new version of - dQuote doesn't work proprly with UTF-8 locale. - 2) Modified CrossTable.Rd usage in gmodels - 3) Modified heatmap.2 usage in gplots. - -2005-05-11 13:51 warnes - - * Add dependency on gdata::frameApply. - -2005-03-31 20:32 warnes - - * Add ceofFrame function to NAMESPACE - -2005-03-31 19:05 warnes - - * coefFrame example needs to properly load ELISA data from gtools - package - -2005-03-31 18:31 warnes - - * Ensure that each file has $Id$ header, and no $Log$ - -2005-03-31 18:30 warnes - - * Add coefFrame() function contributed by Jim Rogers - -2005-01-18 19:53 warnes - - * Removed Windows Line Endings - -2005-01-14 21:40 nj7w - - * Updated the manual to reflect prop.chisq change in its R file. - -2005-01-14 19:14 warnes - - * Nitin added display of the Chisquare contribution of each cell, - as suggested - by Greg Snow. - -2005-01-12 20:50 warnes - - * Add dependency on R 1.9.0+ to prevent poeple from installing on - old - versions of R which don't support namespaces. - -2004-12-23 19:32 nj7w - - * Split the function print.CrossTable.vector in two parts - for SAS - behaiour and SPSS behaviour. Also put the code of printing - statistics in a function 'print.statistics' - -2004-12-21 22:38 warnes - - * Added & extended changes made by Nitin to implement 'SPSS' - format, as suggested by - Dirk Enzmann . - -2004-09-30 21:03 warneg - - * Fix typos. - [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/r-gregmisc -r 2195 From noreply at r-forge.r-project.org Mon Jun 25 17:21:33 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 25 Jun 2018 17:21:33 +0200 (CEST) Subject: [R-gregmisc-commits] r2196 - pkg/gmodels Message-ID: <20180625152133.D7C3E184C3D@r-forge.r-project.org> Author: warnes Date: 2018-06-25 17:21:33 +0200 (Mon, 25 Jun 2018) New Revision: 2196 Modified: pkg/gmodels/ChangeLog pkg/gmodels/DESCRIPTION pkg/gmodels/NEWS Log: gmodels release 2.18.1 Modified: pkg/gmodels/ChangeLog =================================================================== --- pkg/gmodels/ChangeLog 2018-06-25 14:53:14 UTC (rev 2195) +++ pkg/gmodels/ChangeLog 2018-06-25 15:21:33 UTC (rev 2196) @@ -1,3 +1,25 @@ +2018-06-25 14:53 warnes + + * ChangeLog, NEWS, inst/ChangeLog, inst/NEWS: Move NEWS and + ChangeLog to top level. + +2018-06-25 14:52 warnes + + * ChangeLog, NEWS: Remove NEWS and ChangeLog soft links + +2018-06-20 21:06 warnes + + * inst/ChangeLog: Update ChangeLog for gmodels 2.18.0. + +2018-06-20 21:04 warnes + + * DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS for gmodels + 2.18.0. + +2018-06-20 21:02 warnes + + * NAMESPACE: Add imports from stats package. + 2018-06-20 20:51 warnes * DESCRIPTION, inst/ChangeLog: Update DESCRIPTION and ChangeLog for Modified: pkg/gmodels/DESCRIPTION =================================================================== --- pkg/gmodels/DESCRIPTION 2018-06-25 14:53:14 UTC (rev 2195) +++ pkg/gmodels/DESCRIPTION 2018-06-25 15:21:33 UTC (rev 2196) @@ -1,6 +1,6 @@ Package: gmodels -Version: 2.18.0 -Date: 2018-06-19 +Version: 2.18.1 +Date: 2018-06-25 Title: Various R Programming Tools for Model Fitting Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley, and Randall C Johnson. Contributions from Randall C. Johnson are Copyright Modified: pkg/gmodels/NEWS =================================================================== --- pkg/gmodels/NEWS 2018-06-25 14:53:14 UTC (rev 2195) +++ pkg/gmodels/NEWS 2018-06-25 15:21:33 UTC (rev 2196) @@ -1,3 +1,11 @@ +Version 2.18.1 - 2018-06-25 +--------------------------- + +Other Changes: + +- Remove soft-links for NEWS and ChangeLog files for platform portability. + + Version 2.18.0 - 2018-06-19 --------------------------- From noreply at r-forge.r-project.org Mon Jun 25 21:12:18 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 25 Jun 2018 21:12:18 +0200 (CEST) Subject: [R-gregmisc-commits] r2197 - pkg/gtools/man Message-ID: <20180625191218.B7F6518127C@r-forge.r-project.org> Author: warnes Date: 2018-06-25 21:12:18 +0200 (Mon, 25 Jun 2018) New Revision: 2197 Modified: pkg/gtools/man/unByteCode.Rd Log: Fix typographical error. Modified: pkg/gtools/man/unByteCode.Rd =================================================================== --- pkg/gtools/man/unByteCode.Rd 2018-06-25 15:21:33 UTC (rev 2196) +++ pkg/gtools/man/unByteCode.Rd 2018-06-25 19:12:18 UTC (rev 2197) @@ -45,7 +45,7 @@ \note{ These functions are not intended as a permanent solution to issues with byte-code compilation or interpretation. Any such issues should - be promtply reported to the R maintainers via the R Bug Tracking + be promptly reported to the R maintainers via the R Bug Tracking System at \url{https://bugs.r-project.org} and via the R-devel mailing list \url{https://stat.ethz.ch/mailman/listinfo/r-devel}. }