On the home run ....

green-striped-gecko · Nov 16, 2019 · 1f531cb · 1f531cb
1 parent 2d30eb8
commit 1f531cb
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Showing 67 changed files with 516 additions and 380 deletions.
diff --git a/R/gl.assign.r b/R/gl.assign.r
@@ -74,7 +74,7 @@ gl.assign <- function (x, unknown, nmin=10, dim=NULL, alpha= 0.05, threshold=0,
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.collapse.pval.r b/R/gl.collapse.pval.r
@@ -57,7 +57,7 @@ gl.collapse.pval <- function(fd,
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.collapse.r b/R/gl.collapse.r
@@ -71,7 +71,7 @@ gl.collapse <- function(fd,
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.collapse.recursive.r b/R/gl.collapse.recursive.r
@@ -81,7 +81,7 @@ gl.collapse.recursive <- function(x,
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.compliance.check.r b/R/gl.compliance.check.r
@@ -47,7 +47,7 @@ gl.compliance.check <- function (x, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }
@@ -108,7 +108,7 @@ gl.compliance.check <- function (x, verbose=NULL) {
   if (verbose >= 2){cat("  Checking verbosity flag\n")}
   if(is.null(x@other$verbose)){
     if (verbose >= 1){cat("    Creating verbosity flag\n")}
-    x <- utils.reset.verbosity(x,set.verbosity=2,verbose=0)
+    x <- utils.reset.verbosity(x,value=2,verbose=0)
   } else {
     if (verbose >= 1){cat("    Verbosity flag confirmed\n")}
   }
@@ -118,7 +118,13 @@ gl.compliance.check <- function (x, verbose=NULL) {
   if (verbose >= 2){cat("  Recalculating locus metrics\n")}
   x <- gl.recalc.metrics(x,verbose=verbose)
 
-  # Check that the individual metricx exist, and if not, create the df
+  # Check that the number of values in the loc.metrics dataframe is the same as the number of loci
+
+  if (nLoc(gl)!=nrow(gl@other$loc.metrics)) { 
+    cat("  The number of rows in the loc.metrics table does not match the number of loci! This is potentially a major problem if there is a mismatch of the loci with the metadata. Trace back to identify the cause.\n")  
+  }
+
+  # Check that the individual metrics exist, and if not, create the df
 
   if (verbose >= 2){cat("  Checking for individual metrics\n")}
   if(is.null(x@other$loc.metrics)){

diff --git a/R/gl.define.pop.r b/R/gl.define.pop.r
@@ -40,7 +40,7 @@ gl.define.pop <- function(x, ind.list, new, verbose=NULL){
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.dist.ind.r b/R/gl.dist.ind.r
@@ -63,7 +63,7 @@ gl.dist.ind <- function(x, method=NULL, plot=TRUE, boxplot="standard", range=1.5
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.dist.pop.r b/R/gl.dist.pop.r
@@ -55,7 +55,7 @@ gl.dist.pop <- function(x, method="euclidean", plot=TRUE, boxplot="standard", ra
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.drop.ind.r b/R/gl.drop.ind.r
@@ -45,7 +45,7 @@ gl.drop.ind <- function(x, ind.list, recalc=FALSE, mono.rm=FALSE, verbose=NULL){
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.drop.loc.r b/R/gl.drop.loc.r
@@ -40,7 +40,7 @@ gl.drop.loc <- function(x, loc.list=NULL, first=NULL, last=NULL, verbose=NULL){
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.drop.pop.r b/R/gl.drop.pop.r
@@ -49,7 +49,7 @@ gl.drop.pop <- function(x, pop.list, as.pop=NULL, recalc=FALSE, mono.rm=FALSE, v
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.edit.recode.ind.r b/R/gl.edit.recode.ind.r
@@ -29,8 +29,8 @@
 #' @param outpath -- path where to save the output file [default tempdir(), mandated by CRAN].
 #' @param recalc -- Recalculate the locus metadata statistics [default TRUE]
 #' @param mono.rm -- Remove monomorphic loci [default TRUE]
+#' @param verbose -- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]
 #' @return An object of class ("genlight") with the revised individual labels
-#' @param verbose -- verbose=0, silent; verbose=1, low verbosity; verbose=2, high verbosity [default 2]
 #' @import utils
 #' @export
 #' @author Arthur Georges (Post to \url{https://groups.google.com/d/forum/dartr})
@@ -43,30 +43,40 @@
 
 gl.edit.recode.ind <- function(x, out.recode.file=NULL, outpath=tempdir(), recalc=FALSE, mono.rm=FALSE, verbose=NULL){
 
-  # TIDY UP FILE SPECS
+# TRAP COMMAND, SET VERSION
 
   funname <- match.call()[[1]]
   build <- "Jacob"
   if (!is.null(out.recode.file)){
     outfilespec <- file.path(outpath, out.recode.file)
   }
-
-  # FLAG SCRIPT START
-  # set verbosity
-  if (is.null(verbose) & !is.null(x@other$verbose)) verbose=x@other$verbose
-  if (is.null(verbose)) verbose=2
-
+
+# SET VERBOSITY
+
+  if (is.null(verbose)){ 
+    if(!is.null(x@other$verbose)){ 
+      verbose <- x@other$verbose
+    } else { 
+      verbose <- 2
+    }
+  } 
 
   if (verbose < 0 | verbose > 5){
-    cat("  Warning: Parameter 'verbose' must be an integer between 0 [silent] and 5 [full report], set to 2\n")
+    cat(paste("  Warning: Parameter 'verbose' must be an integer between 0 [silent] and 5 [full report], set to 2\n"))
     verbose <- 2
   }
 
+# FLAG SCRIPT START
+
   if (verbose >= 1){
-    cat("Starting",funname,"\n")
+    if(verbose==5){
+      cat("Starting",funname,"[ Build =",build,"]\n")
+    } else {
+      cat("Starting",funname,"\n")
+    }
   }
 
-  # STANDARD ERROR CHECKING
+# STANDARD ERROR CHECKING
 
   if(class(x)!="genlight") {
     stop("Fatal Error: genlight object required!\n")

diff --git a/R/gl.edit.recode.pop.r b/R/gl.edit.recode.pop.r
@@ -31,7 +31,7 @@
 #' @param outpath -- path where to save the output file [default tempdir(), mandated by CRAN].
 #' @param recalc -- Recalculate the locus metadata statistics if any individuals are deleted [default TRUE]
 #' @param mono.rm -- Remove monomorphic loci [default TRUE]
-#' @param verbose -- specify the level of verbosity: 0, silent, fatal errors only; 1, flag function begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2]
+#' @param verbose -- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]
 #' @return An object of class ("genlight") with the revised population assignments
 #' @import utils
 #' @export
@@ -43,27 +43,37 @@
 
 gl.edit.recode.pop <- function(x, pop.recode=NULL, out.recode.file=NULL, outpath=tempdir(), recalc=FALSE, mono.rm=FALSE, verbose=NULL) {
 
-# TIDY UP FILE SPECS
+# TRAP COMMAND, SET VERSION
 
   funname <- match.call()[[1]]
   build <- "Jacob"
   if (!is.null(out.recode.file)){
     outfilespec <- file.path(outpath, out.recode.file)
-  }
+  }  
+
+# SET VERBOSITY
 
-# FLAG SCRIPT START
-  # set verbosity
-  if (is.null(verbose) & !is.null(x@other$verbose)) verbose=x@other$verbose
-  if (is.null(verbose)) verbose=2
-
+  if (is.null(verbose)){ 
+    if(!is.null(x@other$verbose)){ 
+      verbose <- x@other$verbose
+    } else { 
+      verbose <- 2
+    }
+  } 
 
   if (verbose < 0 | verbose > 5){
-    cat("  Warning: Parameter 'verbose' must be an integer between 0 [silent] and 5 [full report], set to 2\n")
+    cat(paste("  Warning: Parameter 'verbose' must be an integer between 0 [silent] and 5 [full report], set to 2\n"))
     verbose <- 2
   }
 
+# FLAG SCRIPT START
+
   if (verbose >= 1){
-    cat("Starting",funname,"\n")
+    if(verbose==5){
+      cat("Starting",funname,"[ Build =",build,"]\n")
+    } else {
+      cat("Starting",funname,"\n")
+    }
   }
 
 # STANDARD ERROR CHECKING

diff --git a/R/gl.filter.callrate.r b/R/gl.filter.callrate.r
@@ -63,7 +63,7 @@
 
    if (verbose >= 1){
      if(verbose==5){
-       cat("Starting",funname,"[Build =",build,"\n")
+       cat("Starting",funname,"[ Build =",build,"]\n")
      } else {
        cat("Starting",funname,"\n")
      }

diff --git a/R/gl.filter.hamming.r b/R/gl.filter.hamming.r
@@ -65,7 +65,7 @@ gl.filter.hamming <- function(x, threshold=0.2, rs=5, pb=FALSE, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.heterozygosity.r b/R/gl.filter.heterozygosity.r
@@ -42,7 +42,7 @@ gl.filter.heterozygosity <- function(x, t.upper=0.7, t.lower=0, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.hwe.r b/R/gl.filter.hwe.r
@@ -49,7 +49,7 @@ gl.filter.hwe <- function(x, alpha=0.05, basis="any", bon=TRUE, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.maf.r b/R/gl.filter.maf.r
@@ -44,7 +44,7 @@ gl.filter.maf <- function(x, threshold=0.01, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.monomorphs.r b/R/gl.filter.monomorphs.r
@@ -47,7 +47,7 @@ gl.filter.monomorphs <- function (x, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.overshoot.r b/R/gl.filter.overshoot.r
@@ -42,7 +42,7 @@ gl.filter.overshoot <- function(x, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.pa.r b/R/gl.filter.pa.r
@@ -42,7 +42,7 @@ gl.filter.pa<-function(x, pop1, pop2, invers=FALSE, verbose=NULL){
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.rdepth.r b/R/gl.filter.rdepth.r
@@ -47,7 +47,7 @@ gl.filter.rdepth <- function(x, lower=5, upper=50, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.repeatability.r b/R/gl.filter.repeatability.r
@@ -47,7 +47,7 @@ gl.filter.repeatability <- function(x, threshold=0.99, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.secondaries.r b/R/gl.filter.secondaries.r
@@ -46,7 +46,7 @@ gl.filter.secondaries <- function(x, method="random", verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.filter.taglength.r b/R/gl.filter.taglength.r
@@ -45,7 +45,7 @@ gl.filter.taglength <- function(x, lower=20, upper=69, verbose=NULL) {
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }

diff --git a/R/gl.fixed.diff.r b/R/gl.fixed.diff.r
@@ -69,7 +69,7 @@ gl.fixed.diff <- function(x, tloc=0, test=FALSE, delta=0.02, reps=1000, mono.rm=
 
   if (verbose >= 1){
     if(verbose==5){
-      cat("Starting",funname,"[Build =",build,"\n")
+      cat("Starting",funname,"[ Build =",build,"]\n")
     } else {
       cat("Starting",funname,"\n")
     }