[Dplr-commits] r1034 - in pkg/dplR: R man

[noreply at r-forge.r-project.org]

Author: andybunn
Date: 2016-08-10 21:40:38 +0200 (Wed, 10 Aug 2016)
New Revision: 1034

Modified:
   pkg/dplR/R/rwl.report.R
   pkg/dplR/man/rwl.report.Rd
Log:
more tweaks to rwl.report

Modified: pkg/dplR/R/rwl.report.R
===================================================================
--- pkg/dplR/R/rwl.report.R	2016-08-09 20:15:13 UTC (rev 1033)
+++ pkg/dplR/R/rwl.report.R	2016-08-10 19:40:38 UTC (rev 1034)
@@ -1,8 +1,10 @@
-rwl.report <- function(rwl){
+rwl.report <- function(rwl, small.thresh = NA, big.thresh = NA){
   oldw <- getOption("warn")
   options(warn = -1)
   
   res <- list()
+  res$small.thresh <- small.thresh
+  res$big.thresh <- big.thresh
   # get a summary
   tmp.sum <- summary.rwl(rwl)
   res$nseries <- ncol(rwl)
@@ -33,14 +35,28 @@
   if(length(internalNAs)<1) res$internalNAs <- numeric(0)
   else res$internalNAs <- internalNAs
 
-  # wee rings
-  wee <- rwl > 0 & rwl < 0.005
-  wee <- apply(wee,2,which)
-  wee <- sapply(wee, function(x) {as.numeric(names(x))} )
-  wee <- wee[lapply(wee,length)>0]
-  if(length(wee)<1) res$small <- numeric(0)
-  else res$small <- wee
+  # small rings
+  if(is.na(small.thresh)) res$small <- numeric(0)
+  else {
+    small <- rwl > 0 & rwl < small.thresh
+    small <- apply(small,2,which)
+    small <- sapply(small, function(x) {as.numeric(names(x))} )
+    small <- small[lapply(small,length)>0]
+    if(length(small)<1) res$small <- numeric(0)
+    else res$small <- small
+  }
 
+  # big rings
+  if(is.na(big.thresh)) res$big <- numeric(0)
+  else {
+    big <- rwl > big.thresh
+    big <- apply(big,2,which)
+    big <- sapply(big, function(x) {as.numeric(names(x))} )
+    big <- big[lapply(big,length)>0]
+    if(length(big)<1) res$big <- numeric(0)
+    else res$big <- big
+  }
+  
   options(warn = oldw)
   class(res) <- "rwl.report"
   res
@@ -80,16 +96,31 @@
           sep = " ")
     }
   }
-  cat("-------------\n")
-  cat("Years with very small rings (< 0.005) listed by series \n")
-  if(length(x$small)==0) cat("    None \n")
-  else{
-    for(i in 1:length(x$small)){
-      tmp = x$small[[i]]
-      if(length(tmp)==0) next()
-      cat("   Series", names(x$small)[i],"--",tmp,"\n",  
-          sep = " ")
+  if(!is.na(x$small.thresh)){
+    cat("-------------\n")
+    cat("Years with values <", x$small.thresh, "listed by series \n")
+    if(length(x$small)==0) cat("    None \n")
+    else{
+      for(i in 1:length(x$small)){
+        tmp = x$small[[i]]
+        if(length(tmp)==0) next()
+        cat("   Series", names(x$small)[i],"--",tmp,"\n",  
+            sep = " ")
+      }
     }
   }
+  if(!is.na(x$big.thresh)){
+    cat("-------------\n")
+    cat("Years with values >", x$big.thresh, " listed by series \n")
+    if(length(x$big)==0) cat("    None \n")
+    else{
+      for(i in 1:length(x$big)){
+        tmp = x$big[[i]]
+        if(length(tmp)==0) next()
+        cat("   Series", names(x$big)[i],"--",tmp,"\n",  
+            sep = " ")
+      }
+    }
+  }
   invisible(x)
 }

Modified: pkg/dplR/man/rwl.report.Rd
===================================================================
--- pkg/dplR/man/rwl.report.Rd	2016-08-09 20:15:13 UTC (rev 1033)
+++ pkg/dplR/man/rwl.report.Rd	2016-08-10 19:40:38 UTC (rev 1034)
@@ -6,23 +6,28 @@
   This function generates a small report on a \code{rwl} (or \code{rwi}) object
   that gives the user some basic information on the data including the number of
   series, the span of the data, the mean interseries correlation, the number of
-  zeros, small rings, or internal \code{NA}, etc.
+  missing rings (zeros), internal \code{NA} values, and rings that are very small,
+  or very large.
 }
 \usage{
-rwl.report(rwl)
+rwl.report(rwl,small.thresh=NA,big.thresh=NA)
 }
 \arguments{
   \item{rwl}{a \code{data.frame} of ring widths with
     \code{rownames(\var{x})} containing years and \code{colnames(x)}
     containing each series \acronym{ID} such as produced by
     \code{\link{read.rwl}}}
+  \item{small.thresh}{a \code{numeric} value for the threshold value that will cause
+    small rings to be listed. If values is \code{NA} this will be omitted.}
+  \item{big.thresh}{a \code{numeric} value for the threshold value that will cause
+    large rings to be listed. If values is \code{NA} this will be omitted.}
 }
 \details{
   This report is a \code{list} containing the number of series, the mean length
   of all the series, the first year, last year, the mean first-order 
   autocorrelation (via \code{\link{summary.rwl}}), the mean interseries 
   correlation (via \code{\link{interseries.cor}}), the years where a series has 
-  a missing ring (zero), internal NA, or a very small ring (<0.005). 
+  a missing ring (zero), internal NA, very small ring, and very large rings. 
   
   This output of this function is not typically meant for the user to access 
   but has a \code{print} method that formats that data for the user.
@@ -37,11 +42,9 @@
 }
 \examples{
 data("gp.rwl")
-rwl.report(gp.rwl)
-foo <- gp.rwl
-foo[177,1] <- NA 
-foo[177:180,3] <- NA 
-foo[185,4] <- 0.001 
-rwl.report(foo)
+rwl.report(rwl = gp.rwl)
+# list very small (smallest 1pct) of rings as well
+one.pct <- quantile(gp.rwl[gp.rwl != 0], na.rm=TRUE, probs=0.01)
+rwl.report(rwl = gp.rwl, small.thresh = one.pct)
 }
 \keyword{ manip }