[Distr-commits] r793 - in branches/distr-2.4/pkg/distrMod: R man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 21 00:58:13 CET 2012
Author: stamats
Date: 2012-02-21 00:58:12 +0100 (Tue, 21 Feb 2012)
New Revision: 793
Modified:
branches/distr-2.4/pkg/distrMod/R/0distrModUtils.R
branches/distr-2.4/pkg/distrMod/R/SimpleL2ParamFamilies.R
branches/distr-2.4/pkg/distrMod/R/modifyModel.R
branches/distr-2.4/pkg/distrMod/man/modifyModel-methods.Rd
branches/distr-2.4/pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save
Log:
analogous updates as in trunk ... (checked separately)
Modified: branches/distr-2.4/pkg/distrMod/R/0distrModUtils.R
===================================================================
--- branches/distr-2.4/pkg/distrMod/R/0distrModUtils.R 2012-02-20 23:37:31 UTC (rev 792)
+++ branches/distr-2.4/pkg/distrMod/R/0distrModUtils.R 2012-02-20 23:58:12 UTC (rev 793)
@@ -277,12 +277,12 @@
else Delta <- function(x) Delta1(x)
Map.Delta[[i]] <- Delta
env.i <- environment(Map.Delta[[i]]) <- new.env()
- assign("i", i, env=env.i)
- assign("fct", fct, env=env.i)
- assign("fct0", fct0, env=env.i)
- assign("Delta", Delta, env=env.i)
- assign("Delta0", Delta0, env=env.i)
- assign("Delta1", Delta1, env=env.i)
+ assign("i", i, envir=env.i)
+ assign("fct", fct, envir=env.i)
+ assign("fct0", fct0, envir=env.i)
+ assign("Delta", Delta, envir=env.i)
+ assign("Delta0", Delta0, envir=env.i)
+ assign("Delta1", Delta1, envir=env.i)
if(withplot){
windows()
plot(x.seq, sapply(x.seq,Map.Delta[[i]]),
@@ -307,7 +307,7 @@
for(i in 1:Dim)
{ Map.phi1[[i]] <- function(x) evalRandVar(phi,x)[i] * p(distr)(x)
env.i <- environment(Map.phi1[[i]]) <- new.env()
- assign("i", i, env=env.i)
+ assign("i", i, envir=env.i)
}
phi1 <- EuclRandVariable(Map = Map.phi1, Domain = Reals())
@@ -333,19 +333,19 @@
phi0a <- approxfun(x.mu.seq, phi0, yleft = 0, yright = rev(phi0)[1])
env.i <- environment(phi1) <- new.env()
- assign("i", i, env=env.i)
+ assign("i", i, envir=env.i)
if(is(distr,"DiscreteDistribution"))
psi0 <- function(x) phi0a(x) * (x %in% support(mu))
else psi0 <- function(x) phi0a(x)
Map.psi[[i]] <- psi0
env.i <- environment(Map.psi[[i]]) <- new.env()
- assign("i", i, env=env.i)
- assign("fct", fct, env=env.i)
- assign("fct0", fct0, env=env.i)
- assign("psi0", psi0, env=env.i)
- assign("phi0a", phi0a, env=env.i)
- assign("phi0", phi0, env=env.i)
+ assign("i", i, envir=env.i)
+ assign("fct", fct, envir=env.i)
+ assign("fct0", fct0, envir=env.i)
+ assign("psi0", psi0, envir=env.i)
+ assign("phi0a", phi0a, envir=env.i)
+ assign("phi0", phi0, envir=env.i)
}
psi <- EuclRandVariable(Map = Map.psi, Domain = Reals())
Modified: branches/distr-2.4/pkg/distrMod/R/SimpleL2ParamFamilies.R
===================================================================
--- branches/distr-2.4/pkg/distrMod/R/SimpleL2ParamFamilies.R 2012-02-20 23:37:31 UTC (rev 792)
+++ branches/distr-2.4/pkg/distrMod/R/SimpleL2ParamFamilies.R 2012-02-20 23:58:12 UTC (rev 793)
@@ -215,7 +215,7 @@
prob <- main(param)["prob"]
size <- main(param)["size"]
xn <- 0:min(max(support(distribution)),
- qnbinom(1e-6,size=size,prob=prob,lower=FALSE),
+ qnbinom(1e-6,size=size,prob=prob,lower.tail=FALSE),
1e5)
I11 <- -sum((trigamma(xn+size)-trigamma(size))*dnbinom(xn,size=size,prob=prob))
I12 <- -1/prob
@@ -299,7 +299,7 @@
size <- main(param)["size"]
prob.0 <- size/(size+mean)
xn <- 0:min(max(support(distribution)),
- qnbinom(1e-6,size=size,prob=prob.0,lower=FALSE),
+ qnbinom(1e-6,size=size,prob=prob.0,lower.tail=FALSE),
1e5)
I11 <- -sum((trigamma(xn+size)-trigamma(size))*dnbinom(xn,size=size,prob=prob.0))
I12 <- -1/prob.0
@@ -694,7 +694,7 @@
EvenSymmetric(SymmCenter = loc)),
L2derivDistrSymm = DistrSymmList(SphericalSymmetry(),
NoSymmetry()),
- L2derivDistr = UnivarDistrList(Arcsine(),abs(Arcsine())),
+ L2derivDistr.0 = UnivarDistrList(Arcsine(),abs(Arcsine())),
FisherInfo.0 = matrix(c(1,0,0,1)/2,2,2,
dimnames = list(c("loc","scale"),
c("loc","scale"))),
Modified: branches/distr-2.4/pkg/distrMod/R/modifyModel.R
===================================================================
--- branches/distr-2.4/pkg/distrMod/R/modifyModel.R 2012-02-20 23:37:31 UTC (rev 792)
+++ branches/distr-2.4/pkg/distrMod/R/modifyModel.R 2012-02-20 23:58:12 UTC (rev 793)
@@ -1,4 +1,52 @@
### move model from one parameter to the next...
+setMethod("modifyModel", signature(model = "ParamFamily", param = "ParamFamParameter"),
+ function(model, param, .withCall = TRUE, ...){
+ M <- model
+ theta <- c(main(param),nuisance(param))
+ M at distribution <- model at modifyParam(theta)
+ M at param <- param
+ #we loose symmetry if available ...
+ M at distrSymm <- NoSymmetry()
+
+ if(paste(M at fam.call[1]) == "ParamFamily")
+ fam.call <- eval(substitute(
+ call("ParamFamily",
+ name = name0,
+ distribution = distribution0,
+ distrSymm = distrSymm0,
+ param = param0,
+ props = props0,
+ startPar = startPar0,
+ makeOKPar = makeOKPar0,
+ modifyParam = modifyParam0,
+ ),
+ list( name0 = M at name,
+ distribution0 = M at distribution,
+ distrSymm0 = M at distrSymm,
+ param0 = M at param,
+ props0 = M at props,
+ startPar0 = M at startPar,
+ makeOKPar0 = M at startPar,
+ modifyParam0 = M at modifyParam,
+ )
+ ))
+ else{
+ fam.call <- model at fam.call
+ par.names <- names(theta)
+ call.n <- names(fam.call)
+ w <- which(call.n %in% par.names)
+ if(length(w))
+ fam.call <- fam.call[-w]
+ fam.call <- as.call(c(as.list(fam.call),theta))
+ }
+
+ M at fam.call <- fam.call
+ class(M) <- class(model)
+ return(M)
+ })
+
+
+### move model from one parameter to the next...
setMethod("modifyModel", signature(model = "L2ParamFamily", param = "ParamFamParameter"),
function(model, param, .withCall = TRUE, .withL2derivDistr = TRUE,
...){
Modified: branches/distr-2.4/pkg/distrMod/man/modifyModel-methods.Rd
===================================================================
--- branches/distr-2.4/pkg/distrMod/man/modifyModel-methods.Rd 2012-02-20 23:37:31 UTC (rev 792)
+++ branches/distr-2.4/pkg/distrMod/man/modifyModel-methods.Rd 2012-02-20 23:58:12 UTC (rev 793)
@@ -2,6 +2,7 @@
\docType{methods}
\alias{modifyModel-methods}
\alias{modifyModel}
+\alias{modifyModel,ParamFamily,ParamFamParameter-method}
\alias{modifyModel,L2ParamFamily,ParamFamParameter-method}
\alias{modifyModel,L2LocationFamily,ParamFamParameter-method}
\alias{modifyModel,L2ScaleFamily,ParamFamParameter-method}
@@ -16,6 +17,8 @@
}
\usage{
modifyModel(model, param,...)
+\S4method{modifyModel}{ParamFamily,ParamFamParameter}(model,param,
+ .withCall = TRUE, ...)
\S4method{modifyModel}{L2ParamFamily,ParamFamParameter}(model,param,
.withCall = TRUE, .withL2derivDistr = TRUE, ...)
\S4method{modifyModel}{L2LocationFamily,ParamFamParameter}(model,param, ...)
@@ -26,7 +29,7 @@
\S4method{modifyModel}{ExpScaleFamily,ParamFamParameter}(model,param, ...)
}
\arguments{
- \item{model}{an object of class \code{L2ParamFamily} --- the model to move.}
+ \item{model}{an object of class \code{ParamFamily} --- the model to move.}
\item{param}{an object of class \code{ParamFamParameter} --- the parameter to move to.}
\item{.withCall}{logical: shall slot \code{fam.call} be updated?}
\item{.withL2derivDistr}{logical: shall slot \code{L2derivDistr} be updated?}
Modified: branches/distr-2.4/pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save
===================================================================
--- branches/distr-2.4/pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2012-02-20 23:37:31 UTC (rev 792)
+++ branches/distr-2.4/pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2012-02-20 23:58:12 UTC (rev 793)
@@ -1,7 +1,8 @@
-R version 2.10.0 beta (2009-10-15 r50107)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.14.2 beta (2012-02-20 r58436)
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -17,77 +18,12 @@
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
-> ### * <HEADER>
-> ###
-> attach(NULL, name = "CheckExEnv")
-> assign("nameEx",
-+ local({
-+ s <- "__{must remake R-ex/*.R}__"
-+ function(new) {
-+ if(!missing(new)) s <<- new else s
-+ }
-+ }),
-+ pos = "CheckExEnv")
-> ## Add some hooks to label plot pages for base and grid graphics
-> assign("base_plot_hook",
-+ function() {
-+ pp <- par(c("mfg","mfcol","oma","mar"))
-+ if(all(pp$mfg[1:2] == c(1, pp$mfcol[2]))) {
-+ outer <- (oma4 <- pp$oma[4]) > 0; mar4 <- pp$mar[4]
-+ mtext(sprintf("help(\"%s\")", nameEx()), side = 4,
-+ line = if(outer)max(1, oma4 - 1) else min(1, mar4 - 1),
-+ outer = outer, adj = 1, cex = .8, col = "orchid", las=3)
-+ }
-+ },
-+ pos = "CheckExEnv")
-> assign("grid_plot_hook",
-+ function() {
-+ grid::pushViewport(grid::viewport(width=grid::unit(1, "npc") -
-+ grid::unit(1, "lines"), x=0, just="left"))
-+ grid::grid.text(sprintf("help(\"%s\")", nameEx()),
-+ x=grid::unit(1, "npc") + grid::unit(0.5, "lines"),
-+ y=grid::unit(0.8, "npc"), rot=90,
-+ gp=grid::gpar(col="orchid"))
-+ },
-+ pos = "CheckExEnv")
-> setHook("plot.new", get("base_plot_hook", pos = "CheckExEnv"))
-> setHook("persp", get("base_plot_hook", pos = "CheckExEnv"))
-> setHook("grid.newpage", get("grid_plot_hook", pos = "CheckExEnv"))
-> assign("cleanEx",
-+ function(env = .GlobalEnv) {
-+ rm(list = ls(envir = env, all.names = TRUE), envir = env)
-+ RNGkind("default", "default")
-+ set.seed(1)
-+ options(warn = 1)
-+ .CheckExEnv <- as.environment("CheckExEnv")
-+ delayedAssign("T", stop("T used instead of TRUE"),
-+ assign.env = .CheckExEnv)
-+ delayedAssign("F", stop("F used instead of FALSE"),
-+ assign.env = .CheckExEnv)
-+ sch <- search()
-+ newitems <- sch[! sch %in% .oldSearch]
-+ for(item in rev(newitems))
-+ eval(substitute(detach(item), list(item=item)))
-+ missitems <- .oldSearch[! .oldSearch %in% sch]
-+ if(length(missitems))
-+ warning("items ", paste(missitems, collapse=", "),
-+ " have been removed from the search path")
-+ },
-+ pos = "CheckExEnv")
-> assign("ptime", proc.time(), pos = "CheckExEnv")
-> ## at least one package changes these via ps.options(), so do this
-> ## before loading the package.
-> ## Use postscript as incomplete files may be viewable, unlike PDF.
-> ## Choose a size that is close to on-screen devices, fix paper
-> grDevices::ps.options(width = 7, height = 7, paper = "a4", reset = TRUE)
-> grDevices::postscript("distrMod-Ex.ps")
->
-> assign("par.postscript", graphics::par(no.readonly = TRUE), pos = "CheckExEnv")
-> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
+> pkgname <- "distrMod"
+> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('distrMod')
Loading required package: startupmsg
-:startupmsg> Utilities for start-up messages (version 0.7)
+:startupmsg> Utilities for start-up messages (version 0.7.3)
:startupmsg>
:startupmsg> For more information see ?"startupmsg",
:startupmsg> NEWS("startupmsg")
@@ -96,7 +32,8 @@
Loading required package: sfsmisc
Loading required package: SweaveListingUtils
:SweaveListingUtils> Utilities for Sweave together with
-:SweaveListingUtils> TeX listings package (version 0.4)
+:SweaveListingUtils> TeX listings package (version
+:SweaveListingUtils> 0.5.5)
:SweaveListingUtils>
:SweaveListingUtils> Some functions from package 'base'
:SweaveListingUtils> are intentionally masked ---see
@@ -115,16 +52,14 @@
:SweaveListingUtils> vignette("ExampleSweaveListingUtils").
-Attaching package: 'SweaveListingUtils'
+Attaching package: ‘SweaveListingUtils’
+The following object(s) are masked from ‘package:base’:
- The following object(s) are masked from package:base :
+ library, require
- library,
- require
-
-:distr> Object orientated implementation of distributions (version
-:distr> 2.2)
+:distr> Object oriented implementation of distributions (version
+:distr> 2.3.4)
:distr>
:distr> Attention: Arithmetics on distribution objects are
:distr> understood as operations on corresponding random variables
@@ -143,27 +78,23 @@
:distr> vignette("distr").
-Attaching package: 'distr'
+Attaching package: ‘distr’
+The following object(s) are masked from ‘package:stats’:
- The following object(s) are masked from package:stats :
+ df, qqplot, sd
- df,
- qqplot,
- sd
-
Loading required package: distrEx
Loading required package: evd
Loading required package: actuar
-Attaching package: 'actuar'
+Attaching package: ‘actuar’
+The following object(s) are masked from ‘package:grDevices’:
- The following object(s) are masked from package:grDevices :
+ cm
- cm
-
-:distrEx> Extensions of package distr (version 2.2)
+:distrEx> Extensions of package distr (version 2.3.2)
:distrEx>
:distrEx> Note: Packages "e1071", "moments", "fBasics" should be
:distrEx> attached /before/ package "distrEx". See distrExMASK().
@@ -176,18 +107,14 @@
:distrEx> vignette("distr").
-Attaching package: 'distrEx'
+Attaching package: ‘distrEx’
+The following object(s) are masked from ‘package:stats’:
- The following object(s) are masked from package:stats :
+ IQR, mad, median, var
- IQR,
- mad,
- median,
- var
-
Loading required package: RandVar
-:RandVar> Implementation of random variables (version 0.7)
+:RandVar> Implementation of random variables (version 0.8.1)
:RandVar>
:RandVar> For more information see ?"RandVar", NEWS("RandVar"), as
:RandVar> well as
@@ -197,8 +124,8 @@
Loading required package: MASS
Loading required package: stats4
-:distrMod> Object orientated implementation of probability models
-:distrMod> (version 2.2)
+:distrMod> Object oriented implementation of probability models
+:distrMod> (version 2.4)
:distrMod>
:distrMod> Some functions from pkg's 'base' and 'stats' are
:distrMod> intentionally masked ---see distrModMASK().
@@ -209,27 +136,32 @@
:distrMod> For more information see ?"distrMod",
:distrMod> NEWS("distrMod"), as well as
:distrMod> http://distr.r-forge.r-project.org/
-:distrMod> Package "distrDoc" provides a vignette to this package
+:distrMod> There is a vignette to this package; try
+:distrMod> vignette("distrMod").
+:distrMod> Package "distrDoc" provides a vignette to the other
+:distrMod> distrXXX packages,
:distrMod> as well as to several related packages; try
:distrMod> vignette("distr").
-Attaching package: 'distrMod'
+Attaching package: ‘distrMod’
+The following object(s) are masked from ‘package:stats4’:
- The following object(s) are masked from package:stats4 :
+ confint
- confint
+The following object(s) are masked from ‘package:stats’:
+ confint
- The following object(s) are masked from package:stats :
+The following object(s) are masked from ‘package:base’:
- confint
+ norm
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
-> assign(".oldNS", loadedNamespaces(), pos = 'CheckExEnv')
-> cleanEx(); nameEx("BetaFamily")
+> cleanEx()
+> nameEx("BetaFamily")
> ### * BetaFamily
>
> flush(stderr()); flush(stdout())
@@ -263,7 +195,7 @@
[1] "The Beta family is invariant in the following sense"
[2] "if (x_i)~Beta(s1,s2) then (1-x_i)~Beta(s2,s1)"
> FisherInfo(B1)
-An object of class “PosSemDefSymmMatrix”
+An object of class "PosSemDefSymmMatrix"
shape1 shape2
shape1 1.0000000 -0.6449341
shape2 -0.6449341 1.0000000
@@ -279,7 +211,8 @@
>
>
>
-> cleanEx(); nameEx("BiasType-class")
+> cleanEx()
+> nameEx("BiasType-class")
> ### * BiasType-class
>
> flush(stderr()); flush(stdout())
@@ -297,7 +230,8 @@
>
>
>
-> cleanEx(); nameEx("BinomFamily")
+> cleanEx()
+> nameEx("BinomFamily")
> ### * BinomFamily
>
> flush(stderr()); flush(stdout())
@@ -331,7 +265,7 @@
[2] "i.e., d(Binom(size, prob))(k)=d(Binom(size,1-prob))(size-k)"
> plot(B1)
> FisherInfo(B1)
-An object of class “PosSemDefSymmMatrix”
+An object of class "PosSemDefSymmMatrix"
prob
prob 133.3333
> checkL2deriv(B1)
@@ -345,7 +279,8 @@
>
>
>
-> cleanEx(); nameEx("CauchyLocationScaleFamily")
+> cleanEx()
+> nameEx("CauchyLocationScaleFamily")
> ### * CauchyLocationScaleFamily
>
> flush(stderr()); flush(stdout())
@@ -380,7 +315,7 @@
[3] "with location parameter 'loc' and scale parameter 'scale'"
> plot(C1)
> FisherInfo(C1)
-An object of class “PosDefSymmMatrix”
+An object of class "PosDefSymmMatrix"
loc scale
loc 0.5 0.0
scale 0.0 0.5
@@ -399,7 +334,8 @@
>
>
>
-> cleanEx(); nameEx("Confint-class")
+> cleanEx()
+> nameEx("Confint-class")
> ### * Confint-class
>
> flush(stderr()); flush(stdout())
@@ -457,9 +393,9 @@
list(fval = fval0, mat = mat0)
}
Trafo / derivative matrix at which estimate was produced:
- scale shape
-shape 0.00 1
-rate -8.55 0
+ scale shape
+shape 0.000 1
+rate -8.549 0
> print(ci, digits = 4, show.details="medium")
A[n] asymptotic (CLT-based) confidence interval:
2.5 % 97.5 %
@@ -477,7 +413,8 @@
>
>
>
-> cleanEx(); nameEx("Estimate-class")
+> cleanEx()
+> nameEx("Estimate-class")
> ### * Estimate-class
>
> flush(stderr()); flush(stdout())
@@ -519,7 +456,8 @@
>
>
>
-> cleanEx(); nameEx("Estimator")
+> cleanEx()
+> nameEx("Estimator")
> ### * Estimator
>
> flush(stderr()); flush(stdout())
@@ -555,7 +493,8 @@
>
>
>
-> cleanEx(); nameEx("EvenSymmetric-class")
+> cleanEx()
+> nameEx("EvenSymmetric-class")
> ### * EvenSymmetric-class
>
> flush(stderr()); flush(stdout())
@@ -574,7 +513,8 @@
>
>
>
-> cleanEx(); nameEx("EvenSymmetric")
+> cleanEx()
+> nameEx("EvenSymmetric")
> ### * EvenSymmetric
>
> flush(stderr()); flush(stdout())
@@ -602,7 +542,8 @@
>
>
>
-> cleanEx(); nameEx("ExpScaleFamily")
+> cleanEx()
+> nameEx("ExpScaleFamily")
> ### * ExpScaleFamily
>
> flush(stderr()); flush(stdout())
@@ -642,10 +583,10 @@
{
((x - 0)/1 * LogDeriv((x - 0)/1) - 1)/1
}
-<environment: 0x7f7e928>
+<environment: 0x6fe53e8>
> checkL2deriv(E1)
-precision of centering: -1.511810e-06
+precision of centering: -1.51181e-06
precision of Fisher information:
scale
scale -2.61793e-05
@@ -655,7 +596,8 @@
>
>
>
-> cleanEx(); nameEx("FunSymmList-class")
+> cleanEx()
+> nameEx("FunSymmList-class")
> ### * FunSymmList-class
>
> flush(stderr()); flush(stdout())
@@ -669,7 +611,7 @@
>
> new("FunSymmList", list(NonSymmetric(), EvenSymmetric(SymmCenter = 1),
+ OddSymmetric(SymmCenter = 2)))
-An object of class “FunSymmList”
+An object of class "FunSymmList"
[[1]]
type of symmetry: non-symmetric function
NULL
@@ -687,7 +629,8 @@
>
>
>
-> cleanEx(); nameEx("FunSymmList")
+> cleanEx()
+> nameEx("FunSymmList")
> ### * FunSymmList
>
> flush(stderr()); flush(stdout())
@@ -701,7 +644,7 @@
>
> FunSymmList(NonSymmetric(), EvenSymmetric(SymmCenter = 1),
+ OddSymmetric(SymmCenter = 2))
-An object of class “FunSymmList”
+An object of class "FunSymmList"
[[1]]
type of symmetry: non-symmetric function
NULL
@@ -728,7 +671,8 @@
>
>
>
-> cleanEx(); nameEx("GammaFamily")
+> cleanEx()
+> nameEx("GammaFamily")
> ### * GammaFamily
>
> flush(stderr()); flush(stdout())
@@ -761,12 +705,12 @@
[1] "The Gamma family is scale invariant via the parametrization"
[2] "'(nu,shape)=(log(scale),shape)'"
> FisherInfo(G1)
-An object of class “PosSemDefSymmMatrix”
+An object of class "PosSemDefSymmMatrix"
scale shape
scale 1 1.000000
shape 1 1.644934
> checkL2deriv(G1)
-precision of centering: -1.511810e-06 1.312514e-06
+precision of centering: -1.51181e-06 1.312514e-06
precision of Fisher information:
scale shape
scale -2.617930e-05 -7.165188e-06
@@ -777,7 +721,8 @@
>
>
>
-> cleanEx(); nameEx("GumbelLocationFamily")
+> cleanEx()
+> nameEx("GumbelLocationFamily")
> ### * GumbelLocationFamily
>
> flush(stderr()); flush(stdout())
@@ -815,10 +760,10 @@
{
LogDeriv(x - 0)
}
-<environment: 0x85ba170>
+<environment: 0x237d900>
> checkL2deriv(G1)
-precision of centering: 1.511810e-06
+precision of centering: 1.51181e-06
precision of Fisher information:
loc
loc -2.61793e-05
@@ -828,7 +773,8 @@
>
>
>
-> cleanEx(); nameEx("InfoNorm")
+> cleanEx()
+> nameEx("InfoNorm")
> ### * InfoNorm
>
> flush(stderr()); flush(stdout())
@@ -841,9 +787,9 @@
> ### ** Examples
>
> InfoNorm()
-An object of class “InfoNorm”
+An object of class "InfoNorm"
Slot "QuadForm":
-An object of class “PosSemDefSymmMatrix”
+An object of class "PosSemDefSymmMatrix"
[,1]
[1,] 1
@@ -853,7 +799,8 @@
Slot "fct":
function (x)
QuadFormNorm(x, A = A)
-<environment: 0x7e98768>
+<bytecode: 0x7971630>
+<environment: 0x7970930>
>
> ## The function is currently defined as
@@ -865,7 +812,8 @@
>
>
>
-> cleanEx(); nameEx("L2GroupFamily-class")
+> cleanEx()
+> nameEx("L2GroupFamily-class")
> ### * L2GroupFamily-class
>
> flush(stderr()); flush(stdout())
@@ -884,7 +832,8 @@
>
>
>
-> cleanEx(); nameEx("L2LocationFamily-class")
+> cleanEx()
+> nameEx("L2LocationFamily-class")
> ### * L2LocationFamily-class
>
> flush(stderr()); flush(stdout())
@@ -901,7 +850,8 @@
>
>
>
-> cleanEx(); nameEx("L2LocationFamily")
+> cleanEx()
+> nameEx("L2LocationFamily")
> ### * L2LocationFamily
>
> flush(stderr()); flush(stdout())
@@ -918,7 +868,8 @@
>
>
>
-> cleanEx(); nameEx("L2LocationScaleFamily-class")
+> cleanEx()
+> nameEx("L2LocationScaleFamily-class")
> ### * L2LocationScaleFamily-class
>
> flush(stderr()); flush(stdout())
@@ -935,7 +886,8 @@
>
>
>
-> cleanEx(); nameEx("L2LocationScaleFamily")
+> cleanEx()
+> nameEx("L2LocationScaleFamily")
> ### * L2LocationScaleFamily
>
> flush(stderr()); flush(stdout())
@@ -952,7 +904,8 @@
>
>
>
-> cleanEx(); nameEx("L2LocationUnknownScaleFamily")
+> cleanEx()
+> nameEx("L2LocationUnknownScaleFamily")
> ### * L2LocationUnknownScaleFamily
>
> flush(stderr()); flush(stdout())
@@ -970,7 +923,8 @@
>
>
>
-> cleanEx(); nameEx("L2ParamFamily-class")
+> cleanEx()
+> nameEx("L2ParamFamily-class")
> ### * L2ParamFamily-class
>
> flush(stderr()); flush(stdout())
@@ -1007,7 +961,8 @@
>
>
>
-> cleanEx(); nameEx("L2ParamFamily")
+> cleanEx()
+> nameEx("L2ParamFamily")
> ### * L2ParamFamily
>
> flush(stderr()); flush(stdout())
@@ -1024,7 +979,8 @@
>
>
>
-> cleanEx(); nameEx("L2ScaleFamily-class")
+> cleanEx()
+> nameEx("L2ScaleFamily-class")
> ### * L2ScaleFamily-class
>
> flush(stderr()); flush(stdout())
@@ -1041,7 +997,8 @@
>
>
>
-> cleanEx(); nameEx("L2ScaleFamily")
+> cleanEx()
+> nameEx("L2ScaleFamily")
> ### * L2ScaleFamily
>
> flush(stderr()); flush(stdout())
@@ -1058,7 +1015,8 @@
>
>
>
-> cleanEx(); nameEx("L2ScaleUnknownLocationFamily")
+> cleanEx()
+> nameEx("L2ScaleUnknownLocationFamily")
> ### * L2ScaleUnknownLocationFamily
>
> flush(stderr()); flush(stdout())
@@ -1076,7 +1034,8 @@
>
>
>
-> cleanEx(); nameEx("LnormScaleFamily")
+> cleanEx()
+> nameEx("LnormScaleFamily")
> ### * LnormScaleFamily
>
> flush(stderr()); flush(stdout())
@@ -1119,7 +1078,7 @@
{
((x - 0)/1 * LogDeriv((x - 0)/1) - 1)/1
}
-<environment: 0x8275218>
+<environment: 0x9d15510>
> checkL2deriv(L1)
precision of centering: -0.003003394
@@ -1132,7 +1091,8 @@
>
>
>
-> cleanEx(); nameEx("MCEstimate-class")
+> cleanEx()
+> nameEx("MCEstimate-class")
> ### * MCEstimate-class
>
> flush(stderr()); flush(stdout())
@@ -1193,7 +1153,8 @@
>
>
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
-> cleanEx(); nameEx("MCEstimator")
+> cleanEx()
+> nameEx("MCEstimator")
> ### * MCEstimator
>
> flush(stderr()); flush(stdout())
@@ -1320,7 +1281,8 @@
>
>
>
-> cleanEx(); nameEx("MDEstimator")
+> cleanEx()
+> nameEx("MDEstimator")
> ### * MDEstimator
>
> flush(stderr()); flush(stdout())
@@ -1363,10 +1325,10 @@
samplesize: 50
estimate:
scale shape
-0.3296938 4.2907460
+0.3419487 4.1663559
Criterion:
CvM distance
- 0.02872404
+ 0.02879881
>
> ## von Mises minimum distance estimator with default mu
> MDEstimator(x = x, ParamFamily = G, distance = CvMDist,
@@ -1379,15 +1341,15 @@
samplesize: 50
estimate:
scale shape
- 0.32969378 4.29074603
- (0.08369777) (1.03063291)
+ 0.34194869 4.16635591
+ (0.08687677) (0.99985006)
asymptotic (co)variance (multiplied with samplesize):
scale shape
-scale 0.3502659 -4.007671
-shape -4.0076714 53.110210
+scale 0.3773787 -4.026502
+shape -4.0265023 49.985008
Criterion:
CvM distance
- 0.02872404
+ 0.02879881
> #*** variance routine is still in testing phase so not yet
> #*** exported to namespace
> ## von Mises minimum distance estimator with mu = N(0,1)
@@ -1400,10 +1362,10 @@
samplesize: 50
estimate:
scale shape
-0.3543892 4.0587606
+0.3407495 4.2127808
Criterion:
CvM distance
- 0.01586171
+ 0.01574483
>
> ## Total variation minimum distance estimator
> ## gamma distributions are discretized
@@ -1446,7 +1408,8 @@
>
>
>
-> cleanEx(); nameEx("MLEstimator")
+> cleanEx()
+> nameEx("MLEstimator")
> ### * MLEstimator
>
> flush(stderr()); flush(stdout())
@@ -1592,8 +1555,8 @@
> require(MASS)
> (res1 <- fitdistr(x, "gamma"))
shape rate
- 3.0117832 1.8655645
- (0.5721423) (0.3856279)
+ 3.0117885 1.8655681
+ (0.5721425) (0.3856279)
>
> ## comparison
> ## shape
@@ -1636,8 +1599,8 @@
> distrModoptions("show.details" = "minimal")
> res1
shape rate
- 3.0117832 1.8655645
- (0.5721423) (0.3856279)
+ 3.0117885 1.8655681
+ (0.5721425) (0.3856279)
> res2
Evaluations of Maximum likelihood estimate:
-------------------------------------------
@@ -1694,7 +1657,114 @@
>
>
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
-> cleanEx(); nameEx("NonSymmetric-class")
+> cleanEx()
+> nameEx("NBinomFamily")
+> ### * NBinomFamily
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: NbinomFamily
+> ### Title: Generating function for Nbinomial families
+> ### Aliases: NbinomFamily NbinomwithSizeFamily NbinomMeanSizeFamily
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> (N1 <- NbinomFamily(size = 25, prob = 0.25))
+An object of class "NbinomFamily"
+### name: Negative Binomial family
+
+### distribution: Distribution Object of Class: Nbinom
+ size: 25
+ prob: 0.25
+
+### param: An object of class "ParamFamParameter"
+name: probability of success
+prob: 0.25
+fixed part of param.:
+ size: 25
+
+### props:
+[1] ""
+> plot(N1)
+> FisherInfo(N1)
+An object of class "PosSemDefSymmMatrix"
+ prob
+prob 533.3333
+> checkL2deriv(N1)
+precision of centering: 0.001177892
+precision of Fisher information:
+ prob
+prob -0.1601189
+$maximum.deviation
+[1] 0.1601189
+
+> (N1.w <- NbinomwithSizeFamily(size = 25, prob = 0.25))
+An object of class "NbinomwithSizeFamily"
+### name: Negative Binomial family
+
+### distribution: Distribution Object of Class: Nbinom
+ size: 25
+ prob: 0.25
+
+### param: An object of class "ParamFamParameter"
+name: NegBinomParameter
+size: 25
+prob: 0.25
+
+### props:
+[1] ""
+> plot(N1.w)
+> FisherInfo(N1.w)
+An object of class "PosSemDefSymmMatrix"
+ size prob
+size 0.03044946 -4.0000
+prob -4.00000000 533.3333
+> checkL2deriv(N1.w)
+precision of centering: -6.245978e-06 0.001177892
+precision of Fisher information:
+ size prob
+size -4.182531e-06 0.0008481424
+prob 8.481424e-04 -0.1601189384
+$maximum.deviation
+[1] 0.1601189
+
+> (N2.w <- NbinomMeanSizeFamily(size = 25, mean = 75))
+An object of class "NbinomMeanSizeFamily"
+### name: Negative Binomial family
+
+### distribution: Distribution Object of Class: Nbinom
+ size: 25
+ prob: 0.25
+
+### param: An object of class "ParamFamParameter"
+name: probability of success
+size: 25
+mean: 75
+
+### props:
+[1] ""
+> plot(N2.w)
+> FisherInfo(N2.w)
+An object of class "PosSemDefSymmMatrix"
+ size mean
+size 3.044946e-02 1600.091
+mean 1.600091e+03 85342933.607
+> checkL2deriv(N2.w)
+precision of centering: -6.245978e-06 -0.4711755
+precision of Fisher information:
+ size mean
+size -4.182531e-06 -3.392695e-01
+mean -3.392695e-01 -2.562107e+04
+$maximum.deviation
+[1] 25621.07
+
+>
+>
+>
+>
+> cleanEx()
+> nameEx("NonSymmetric-class")
> ### * NonSymmetric-class
>
> flush(stderr()); flush(stdout())
@@ -1712,7 +1782,8 @@
>
>
>
-> cleanEx(); nameEx("NonSymmetric")
+> cleanEx()
+> nameEx("NonSymmetric")
> ### * NonSymmetric
>
> flush(stderr()); flush(stdout())
@@ -1737,7 +1808,8 @@
>
>
>
-> cleanEx(); nameEx("NormLocationFamily")
+> cleanEx()
+> nameEx("NormLocationFamily")
> ### * NormLocationFamily
>
> flush(stderr()); flush(stdout())
@@ -1777,7 +1849,8 @@
>
>
>
-> cleanEx(); nameEx("NormLocationScaleFamily")
+> cleanEx()
+> nameEx("NormLocationScaleFamily")
> ### * NormLocationScaleFamily
>
> flush(stderr()); flush(stdout())
@@ -1811,7 +1884,7 @@
[3] "with location parameter 'loc' and scale parameter 'scale'"
> plot(N1)
> FisherInfo(N1)
-An object of class “PosDefSymmMatrix”
+An object of class "PosDefSymmMatrix"
mean sd
mean 1 0
sd 0 2
@@ -1827,7 +1900,8 @@
>
>
>
-> cleanEx(); nameEx("NormLocationUnknownScaleFamily")
+> cleanEx()
+> nameEx("NormLocationUnknownScaleFamily")
> ### * NormLocationUnknownScaleFamily
>
> flush(stderr()); flush(stdout())
@@ -1863,7 +1937,7 @@
[3] "with location parameter 'loc' and scale parameter 'scale'"
> plot(N1)
> FisherInfo(N1)
-An object of class “PosDefSymmMatrix”
+An object of class "PosDefSymmMatrix"
mean sd
mean 1 0
sd 0 2
@@ -1879,7 +1953,8 @@
>
>
>
-> cleanEx(); nameEx("NormScaleFamily")
+> cleanEx()
+> nameEx("NormScaleFamily")
> ### * NormScaleFamily
>
> flush(stderr()); flush(stdout())
@@ -1914,7 +1989,7 @@
[3] "with scale parameter 'scale'"
> plot(N1)
> FisherInfo(N1)
-An object of class “PosDefSymmMatrix”
+An object of class "PosDefSymmMatrix"
sd
sd 2
> checkL2deriv(N1)
@@ -1928,7 +2003,8 @@
>
>
>
-> cleanEx(); nameEx("NormScaleUnknownLocationFamily")
+> cleanEx()
+> nameEx("NormScaleUnknownLocationFamily")
> ### * NormScaleUnknownLocationFamily
>
> flush(stderr()); flush(stdout())
@@ -1964,7 +2040,7 @@
[3] "with location parameter 'loc' and scale parameter 'scale'"
> plot(N1)
> FisherInfo(N1)
-An object of class “PosDefSymmMatrix”
+An object of class "PosDefSymmMatrix"
sd mean
sd 1 0
mean 0 2
@@ -1980,7 +2056,8 @@
>
>
>
-> cleanEx(); nameEx("NormType-class")
+> cleanEx()
+> nameEx("NormType-class")
> ### * NormType-class
>
> flush(stderr()); flush(stdout())
@@ -2001,13 +2078,15 @@
return(abs(x))
else return(sqrt(colSums(x^2)))
}
+<bytecode: 0x72c71b8>
<environment: namespace:distrMod>
> name(EuclNorm)
[1] "EuclideanNorm"
>
>
>
-> cleanEx(); nameEx("NormType")
+> cleanEx()
+> nameEx("NormType")
> ### * NormType
>
> flush(stderr()); flush(stdout())
@@ -2020,7 +2099,7 @@
> ### ** Examples
>
> NormType()
-An object of class “NormType”
+An object of class "NormType"
Slot "name":
[1] "EuclideanNorm"
@@ -2031,12 +2110,14 @@
return(abs(x))
else return(sqrt(colSums(x^2)))
}
+<bytecode: 0x72c71b8>
<environment: namespace:distrMod>
>
>
>
-> cleanEx(); nameEx("OddSymmetric-class")
+> cleanEx()
+> nameEx("OddSymmetric-class")
> ### * OddSymmetric-class
>
> flush(stderr()); flush(stdout())
@@ -2055,7 +2136,8 @@
>
>
>
-> cleanEx(); nameEx("OddSymmetric")
+> cleanEx()
+> nameEx("OddSymmetric")
> ### * OddSymmetric
>
> flush(stderr()); flush(stdout())
@@ -2083,7 +2165,8 @@
>
>
>
-> cleanEx(); nameEx("ParamFamParameter-class")
+> cleanEx()
+> nameEx("ParamFamParameter-class")
> ### * ParamFamParameter-class
>
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/distr -r 793
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