[adegenet-commits] r191 - in pkg: . R man misc misc/bug-report.1.2-2.02 misc/bug-report.1.2-2.03
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 13 12:23:23 CEST 2008
Author: jombart
Date: 2008-10-13 12:23:22 +0200 (Mon, 13 Oct 2008)
New Revision: 191
Added:
pkg/misc/bug-report.1.2-2.02/
pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx
pkg/misc/bug-report.1.2-2.02/readme.txt
pkg/misc/bug-report.1.2-2.03/
pkg/misc/bug-report.1.2-2.03/boot_coord.7.input
pkg/misc/bug-report.1.2-2.03/boot_dist.7.input
pkg/misc/bug-report.1.2-2.03/monboot_debug.r
pkg/misc/bug-report.1.2-2.03/monmonier-bug1.html
pkg/misc/bug-report.1.2-2.03/monmonier-bug2.html
pkg/misc/bug-report.1.2-2.03/orig_coord.input
pkg/misc/bug-report.1.2-2.03/orig_dist.input
Modified:
pkg/R/auxil.R
pkg/TODO
pkg/man/auxil.Rd
Log:
Added bug reports and adegenetTutorial function and doc.
Modified: pkg/R/auxil.R
===================================================================
--- pkg/R/auxil.R 2008-10-11 14:52:01 UTC (rev 190)
+++ pkg/R/auxil.R 2008-10-13 10:23:22 UTC (rev 191)
@@ -152,14 +152,39 @@
# Function adegenetWeb
#######################
adegenetWeb <- function(){
- cat("Opening url \"http://adegenet.r-forge.r-project.org/\" ...\n")
- browseURL("http://adegenet.r-forge.r-project.org/")
+ cat("Opening url \"http://adegenet.r-forge.r-project.org/\" ...\n")
+ browseURL("http://adegenet.r-forge.r-project.org/")
}
+############################
+# Function adegenetTutorial
+############################
+adegenetTutorial <- function(which=c("general","spca")){
+ which <- match.arg(which)
+ if(which=="general"){
+ url <- "http://adegenet.r-forge.r-project.org/files/adegenet.pdf"
+ cat("\n")
+ cat(" >> Seeking the general tutorial for adegenet.\n")
+ cat(" >> Opening url \"",url,"\".\n ", sep="")
+ cat("\n")
+ browseURL(url)
+ }
+ if(which=="spca"){
+ url <- "http://adegenet.r-forge.r-project.org/files/tutorial-spca.pdf"
+ cat("\n")
+ cat(" >> Seeking the sPCA tutorial for adegenet.\n")
+ cat(" >> Opening url \"",url,"\". \n", sep="")
+ cat("\n")
+ browseURL(url)
+ }
+}
+
+
+
###############
# '$' operator
###############
Modified: pkg/TODO
===================================================================
--- pkg/TODO 2008-10-11 14:52:01 UTC (rev 190)
+++ pkg/TODO 2008-10-13 10:23:22 UTC (rev 191)
@@ -27,6 +27,8 @@
# CODE ISSUES:
==============
* fix bug 1.2-2.01 (read.structure issue) -- fixed: was due to the default of "onerowperind" argument.
+* fix bug 1.2-2.02 (read.genetix issue)
+* fix bug 1.2-2.03 (monmonier issue)
# DOCUMENTATION ISSUES:
@@ -37,7 +39,7 @@
# NEW IMPLEMENTATIONS:
=====================
* color plot for the sPCA results, based on RGB representation of Cavalli-Sforza -- done(TJ)
-* loadingplot -- done(TJ)
+* loadingplot for plotting loadings of one axis -- done(TJ)
* adegenetTutorial function which opens the online tutorials
* allow for the use of na.replace and scaleGen in spca function -- done (TJ)
Modified: pkg/man/auxil.Rd
===================================================================
--- pkg/man/auxil.Rd 2008-10-11 14:52:01 UTC (rev 190)
+++ pkg/man/auxil.Rd 2008-10-13 10:23:22 UTC (rev 191)
@@ -2,14 +2,16 @@
\docType{methods}
\name{Auxiliary functions}
\alias{adegenetWeb}
+\alias{adegenetTutorial}
\alias{.rmspaces}
\alias{.genlab}
\alias{.readExt}
\title{ Utilities functions for adegenet}
\description{
These functions are mostly used internally in adegenet.
- The notable exception is \code{adegenetWeb}, which opens the adegenet
- website in the default navigator.\cr
+ The notable exceptions are \code{adegenetWeb} which opens the adegenet
+ website in the default navigator, and \code{adegenetTutorial} which
+ opens online tutorials for adegenet.\cr
The other functions are:\cr
- \code{.rmspaces}: remove peripheric spaces in a character string \cr
@@ -19,11 +21,14 @@
}
\usage{
adegenetWeb()
+adegenetTutorial(which=c("general","spca"))
.genlab(base, n)
}
\arguments{
- \item{base}{a character string forming the base of the labels}
- \item{n}{the number of labels to generate}
+ \item{which}{a character string being "general" or "spca", indicating
+ which tutorial should be opened.}
+ \item{base}{a character string forming the base of the labels}
+ \item{n}{the number of labels to generate}
}
\value{
For \code{.genlab}, a character vector of size "n".
@@ -33,6 +38,12 @@
\dontrun{
## this opens the adegenet website
adegenetWeb()
+
+## this opens the general tutorial for adegenet
+adegenetTutorial()
+
+## this opens the sPCA tutorial for adegenet
+adegenetTutorial("spca")
}
.genlab("Locus-",11)
Added: pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx
===================================================================
--- pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx (rev 0)
+++ pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx 2008-10-13 10:23:22 UTC (rev 191)
@@ -0,0 +1,638 @@
+18 D:\Master Laurent Labo\Program Files\Genetix\PhylogenClariasAlloz.gtx
+72 nombre de pop
+IDHM
+5 070 080 090 095 100
+IDHF
+11 070 075 080 090 095 100 110 130 140 150 180
+IPOF
+16 040 080 100 110 140 150 155 157 160 180 190 200 205 210 220 250
+MPI
+3 090 100 105
+ADH
+6 020 080 090 092 095 100
+PROT1
+5 080 085 090 100 110
+PROT2
+5 100 102 110 145 150
+PGM
+12 050 055 098 100 102 115 120 125 130 135 140 150
+MDH1
+5 020 060 100 105 200
+MDH2
+8 070 075 100 102 105 107 110 120
+PGI1
+11 002 050 100 150 180 200 220 230 350 400 500
+PGI2
+10 075 100 110 120 130 140 150 160 200 220
+LDH1
+2 100 200
+LDH2
+3 096 100 105
+6PGD
+4 050 055 090 100
+
+
+
+Clarias garieminus
+1
+ xxxx 100100 100100 100140 100100 100100 100100 100100 100100 100100 100100 100100 100100 100100 100100 100100
+
+C. intermedius (kereng Bengkirai, Kalimantan)
+4
+ 4196 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4197 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4199 100100 110110 220250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4266 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 002100 120120 200200 096096 100100
+
+C. intermedius (Bereng Bengkel, Kalimantan)
+17
+ 4060 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4001 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4002 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4061 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4062 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4063 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4064 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4065 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4066 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4067 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4068 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4069 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4070 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4071 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4075 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4072 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4074 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+
+C. intermedius (Palangkaraya, Kalimantan)
+5
+ 121B 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 125B 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 128B 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 130B 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 132B 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+
+C. intermedius (Bukit Pinang, Kalimantan)
+5
+ 4112 100100 110140 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4113 100100 140140 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4114 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4110 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4111 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+
+C. intermedius (Bengaris, Kalimantan)
+5
+ 4125 100100 110110 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4126 100100 110110 220250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4127 100100 110110 220250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4128 100100 110130 250250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+ 4129 100100 110110 220250 090090 090090 100100 150150 100100 100100 075075 100100 120120 200200 096096 100100
+
+C. meladerma (Palembang, Sumatra)
+15
+ 1522 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 1524 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
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+ 1557 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 1558 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 1559 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 100s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 101s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 102s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 103s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 104s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 105s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 106s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+
+C. meladerma (Tegineneng, Sumatra)
+11
+ 4 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 5 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 6 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 7 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 8 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 9 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ T1 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100350 100100 200200 096096 050050
+ T2 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ T3 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ T4 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ T5 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+
+C. meladerma (Pauh, Sumatra)
+4
+ 4281 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 050050
+ 4282 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 050050
+ 4283 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 050050
+ 4284 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 050050
+
+C. meladerma (Muara Bungo, Sumatra)
+4
+ 4286 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 050050
+ 4287 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 050050
+ 4289 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 050050
+ 4290 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 050050
+
+C. meladerma (Rengat, Sumatra)
+6
+ 1367 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 200200 120120 200200 096096 050050
+ 1370 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 200200 120120 200200 096096 050050
+ 1371 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 200200 120120 200200 096096 050050
+ 1368 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 200200 120120 200200 096096 050050
+ 1369 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 200200 120120 200200 096096 050050
+ 4822 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 120120 200200 096096 050050
+
+C. meladerma (Pakanbaru, Sumatra)
+9
+ 1399 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1400 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1402 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1403 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1404 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1405 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1406 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1407 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1401 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+
+C. meladerma (Kuala Pesaguan, Kalimantan)
+6
+ 4563 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 090090
+ 4562 090100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 100100 200200 096096 050090
+ 4561 090090 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 090090
+ 4550 090090 110110 190190 105105 050050 100100 150150 050100 100100 075105 100100 100100 200200 096096 090090
+ 4560 090090 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 090090
+ 4557 090090 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 100100 200200 096096 050090
+
+C. meladerma (Bangko, Sumatra)
+5
+ 1426 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1427 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1428 100100 110110 190190 105105 050050 100100 150150 050050 100100 075075 100100 120120 200200 096096 050050
+ 1469 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 120120 200200 096096 050050
+ 1471 100100 110110 190190 105105 050050 100100 150150 100100 100100 075075 100100 120120 200200 096096 050050
+
+C. meladerma (Palangkaraya, Kalimantan)
+16
+ 120b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 122b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 123b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 124b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 126b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 127b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 131b 100100 150150 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 133b 100100 110150 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 134b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 135b 100100 110150 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 136b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 137b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 139b 100100 110150 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 142b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 143b 100100 095110 157190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+ 145b 100100 110110 190190 105105 050050 100100 150150 125125 100100 075075 100100 100100 200200 096096 050050
+
+C. meladerma (Plaju, Sumatra)
+10
+ 81s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 82s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 83s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 84s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 85s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 86s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 87s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 88s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 89s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+ 90s 100100 110110 190190 105105 050050 100100 150150 150150 100100 075075 100100 100100 200200 096096 050050
+
+C. meladerma2 (Danau teluk, Jambi, Sumatra)
+3
+ 126 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+ 128 100100 110110 205205 105105 100100 100100 150150 050100 100100 105105 050150 120120 200200 096096 050050
+ 129 100100 110110 205205 105105 100100 100100 150150 050100 100100 105105 050050 120120 200200 096096 050050
+
+C. meladerma2 (Muara Bungo, Sumatra)
+3
+ 211 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+ 212 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+ 213 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+
+C. meladerma2 (Teluk Kuantan, Sumatra)
+2
+ 1320 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+ 1321 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+
+C. meladerma2 (Rengat, Sumatra)
+1
+ 1372 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+
+C. meladerma2 (Bangko, Sumatra)
+1
+ 1470 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+
+C. meladerma2 (Berbak, Sumatra)
+3
+ 4347 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+ 4350 100100 110110 205205 105105 100100 100100 150150 050050 100100 105105 150150 120120 200200 096096 050050
+ 4349 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+
+C. meladerma2 (Muara Jambi, Sumatra)
+2
+ 4377 100100 110110 205205 105105 100100 100100 150150 050100 100100 105105 050050 120120 200200 096096 050050
+ 4378 100100 110110 205205 105105 100100 100100 150150 050050 100100 105105 050150 120120 200200 096096 050050
+
+C. meladerma2 (Arang Arang, Sumatra)
+5
+ 4369 100100 110110 205205 105105 100100 100100 150150 050100 100100 105105 050050 120120 200200 096096 050050
+ 4370 100100 110110 205205 105105 100100 100100 150150 050050 100100 105105 150150 120120 200200 096096 050050
+ 4371 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+ 4372 100100 110110 205205 105105 100100 100100 150150 050100 100100 105105 050050 120120 200200 096096 050050
+ 4373 100100 110110 205205 105105 100100 100100 150150 050100 100100 105105 150150 120120 200200 096096 050050
+
+C. meladerma2 (Palembang, Sumatra)
+3
+ 91s 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+ 95s 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+ 99s 100100 110110 205205 105105 100100 100100 150150 100100 100100 105105 050050 120120 200200 096096 050050
+
+C. nieuhofii (Palembang, Sumatra)
+5
+ 48 090090 110110 150180 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 49 090090 110110 110150 105105 090090 100100 100100 100100 100100 075105 100100 120140 200200 096096 050050
+ 50 090090 110110 110150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 51 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 52 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+
+C. nieuhofii (Tegineneng, Sumatra)
+5
+ 10 090090 110110 110150 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 11 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 12 090090 110110 110150 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 13 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 14 090090 110110 110150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+
+C. nieuhofii (Jambi, Sumatra)
+5
+ 182 080090 110110 110110 105105 090090 100100 100100 100100 100100 075105 100180 120120 200200 096096 050050
+ 183 090090 110110 110110 105105 090090 100100 100100 100100 100100 075105 100100 120120 200200 096096 050050
+ 184 080080 110110 110110 105105 090090 100100 100100 100100 100100 105105 100100 120120 200200 096096 050050
+ 185 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 186 090090 110110 110110 105105 090090 100100 100100 050100 100100 075075 100180 120140 200200 096096 050050
+
+C. nieuhofii (Ketapang, Kalimantan)
+13
+ 4483 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4484 090090 100110 150150 105105 090090 100100 100100 100100 100100 075105 100100 120140 200200 096096 050050
+ 4485 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4486 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4482 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4475 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4477 090090 070110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 4478 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4479 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4480 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4481 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4487 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 4488 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 140140 200200 096096 050050
+
+C. nieuhofii (Muara Bungo, Sumatra)
+3
+ 222 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 223 080080 110110 110110 105105 090090 100100 100100 100100 100100 075075 100200 120120 200200 096096 050050
+ 225 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+
+C. nieuhofii (Teluk Kuantan, Sumatra)
+3
+ 1322 090090 100110 110110 105105 090090 100100 100100 050100 100100 075075 100100 120140 200200 096096 050050
+ 1323 090090 100110 110110 105105 090090 100100 100100 050100 100100 075075 100100 120120 200200 096096 050050
+ 1324 090090 110110 110110 105105 090090 100100 100100 100100 020100 075075 100180 120120 200200 096096 050050
+
+C. nieuhofii (Pekanbaru, Sumatra)
+3
+ 1411 070090 110110 110150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 1413 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 1415 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+
+C. nieuhofii (Bangko, Sumatra)
+3
+ 1447 080090 110110 110150 105105 090090 100100 100100 100100 100100 075075 100200 120120 200200 096096 050050
+ 1448 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 1444 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100200 120120 200200 096096 050050
+
+C. nieuhofii (Samarinda, Kalimantan)
+3
+ 1800 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 100180 120120 200200 096096 050050
+ 1801 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 100180 120120 200200 096096 050050
+ 1802 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 100180 120120 200200 096096 050050
+
+C. nieuhofii (Bereng Bengkel, Kalimantan)
+6
+ 4146 090090 110110 040040 105105 090090 090090 100100 050100 100100 075075 100100 140140 200200 096096 050050
+ 4122 090090 110110 040040 105105 090090 090090 100100 050050 100100 075075 100100 120140 200200 096096 050050
+ 4149 090090 110110 040040 105105 090090 090090 100100 050050 100100 075075 100100 120140 200200 096096 050050
+ 4150 090090 110110 040040 105105 090090 090090 100100 050100 100100 075075 100100 140140 200200 096096 050050
+ 4147 090090 110110 040040 105105 090090 090090 100100 050050 100100 075075 100100 140140 200200 096096 050050
+ 4148 090090 110110 040040 105105 090090 090090 100100 050050 100100 075105 100100 120160 200200 096096 050050
+
+C. nieuhofii (Tanjung Selor, Kalimantan)
+2
+ 2151 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 100180 120120 200200 096096 050050
+ 2150 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 100180 120120 200200 096096 050050
+
+C. nieuhofii (Tanjung Redep, Kalimantan)
+13
+ 2116 090090 110110 040040 105105 090090 090090 100100 100150 100100 075075 100180 120120 200200 096096 050050
+ 2117 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 100180 120120 200200 096096 050050
+ 2118 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 2119 090090 110110 040040 105105 090090 090090 100100 100150 100100 075075 100180 120120 200200 096096 050050
+ 2120 090090 110110 040040 105105 090090 090090 100100 150150 100100 075075 100100 120120 200200 096096 050050
+ 2121 090090 110110 040040 105105 090090 090090 100100 150150 100100 075075 100100 120120 200200 096096 050050
+ 2122 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 2123 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 2124 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 180180 120120 200200 096096 050050
+ 2125 090090 110110 040040 105105 090090 090090 100100 100150 100100 075075 100100 120120 200200 096096 050050
+ 2126 090090 110110 040040 105105 090090 090090 100100 100150 100100 075075 100100 120120 200200 096096 050050
+ 2114 090090 110110 040040 105105 090090 090090 100100 100100 100100 075075 180180 120120 200200 096096 050050
+ 2115 090090 110110 040040 105105 090090 090090 100100 100150 100100 075075 100100 120120 200200 096096 050050
+
+C. nieuhofii (Sambas, Kalimantan)
+6
+ 4468 090090 110110 110150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4469 090090 110110 110150 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 4471 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4472 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100500 120120 200200 096096 050050
+ 4473 090090 110110 110150 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 4474 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+
+C. nieuhofii (Bengkayeng and Semitau, Kalimantan)
+3
+ 4456 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120140 200200 096096 050050
+ 4457 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4458 090090 110110 150150 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+
+C. nieuhofii (Tembilahan, Sumatra)
+5
+ 4974 080090 100110 110110 105105 090090 100100 100100 050100 100100 075075 100100 120120 200200 096096 050050
+ 4973 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 120120 200200 096096 050050
+ 4975 080080 110110 110110 105105 090090 100100 100100 100100 100100 075075 100200 120120 200200 096096 050050
+ 4976 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 140140 200200 096096 050050
+ 4977 080080 110110 110150 105105 090090 100100 100100 050050 100100 075075 100100 140140 200200 096096 050050
+
+C. nieuhofii (Rengat, Sumatra)
+4
+ 4788 090090 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 140140 200200 096096 050050
+ 4795 080080 110110 110110 105105 090090 100100 100100 100100 100100 075075 100200 140140 200200 096096 050050
+ 4798 080080 110110 110110 105105 090090 100100 100100 050100 100100 075075 180180 140140 200200 096096 050050
+ 4799 080080 110110 110110 105105 090090 100100 100100 100100 100100 075075 100100 140140 200200 096096 050050
+
+C. pseudonieuhofii (Semitau)
+1
+ 4649 090090 110110 110110 105105 090090 090090 100100 098102 100100 075075 100100 120120 200200 096096 050050
+
+C. olivaceus (Padang, Sumatra)
+19
+ 4900 100100 100180 150150 105105 090090 110110 150150 150150 060060 120120 100100 110140 200200 105105 100100
+ 4901 100100 100180 150150 105105 090090 110110 150150 150150 060060 120120 100100 140140 200200 105105 100100
+ 4902 100100 100180 150150 105105 090090 110110 150150 150150 060060 120120 100100 140140 200200 105105 100100
+ 4903 100100 100100 150150 105105 090090 110110 150150 150150 060060 120120 100100 140140 200200 105105 100100
+ 4904 100100 100100 150150 105105 090090 110110 150150 150150 060060 120120 100100 140140 200200 105105 100100
+ 4905 100100 100100 150150 105105 090090 110110 100150 150150 060060 120120 100100 140140 200200 105105 100100
+ 4906 100100 100100 150150 105105 090090 110110 150150 100150 060060 120120 100100 140140 200200 105105 100100
+ 4907 100100 100100 150150 105105 090090 110110 100150 150150 060060 120120 100220 140140 200200 105105 100100
+ 4908 100100 100100 150150 105105 090090 110110 150150 100150 060060 120120 100100 140140 200200 105105 100100
+ 4909 100100 100100 150150 105105 090090 110110 150150 150150 060060 120120 100100 140140 200200 105105 100100
+ 4910 100100 100110 150150 105105 090090 110110 150150 150150 060060 120120 100100 140140 200200 105105 100100
+ 4911 100100 100100 150150 105105 090090 110110 150150 150150 060060 120120 100220 140140 200200 105105 100100
+ 4912 100100 100100 150150 105105 090090 110110 150150 150150 060060 120120 100230 140140 200200 105105 100100
+ 4913 100100 100100 150150 105105 090090 110110 150150 150150 060060 120120 100100 140140 200200 105105 100100
+ 4914 100100 100110 150150 105105 090090 110110 150150 150150 060060 120120 100230 140140 200200 105105 100100
+ 4915 100100 100110 150150 105105 090090 110110 150150 150150 060060 120120 220220 140140 200200 105105 100100
+ 4916 100100 110110 150150 105105 090090 110110 150150 150150 060060 120120 100220 140140 200200 105105 100100
+ 4917 100100 100110 150150 105105 090090 110110 150150 150150 060060 120120 100100 140140 200200 105105 100100
+ 4918 100100 100100 150150 105105 090090 110110 150150 150150 060060 120120 100220 140140 200200 105105 100100
+
+C. olivaceus (Kutacane, Sumatra)
+1
+ 4958 100100 100100 150150 105105 090090 080090 100100 100100 060105 075075 100100 140140 200200 105105 100100
+
+C. punctatus (Nias, Sumatra)
+1
+ 1481 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Bukit Tinggi, sumatra)
+4
+ 1493 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 1494 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 1496 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 1495 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Palembang, Sumatra)
+3
+ 1531 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120130 200200 105105 100100
+ 1532 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120130 200200 105105 100100
+ 1533 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120130 200200 105105 100100
+
+C. punctatus (So Phisat, mekong, Thailand)
+1
+ 1571 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. batrachus (Dhaka, Bangladesh)
+4
+ 1845 100100 100100 080080 105105 020020 110110 150150 100100 200200 075075 100100 120120 200200 105105 100100
+ 1846 100100 100100 080080 105105 020020 110110 150150 100100 200200 075075 100100 120120 200200 105105 100100
+ 1847 100100 080100 080080 105105 020020 110110 150150 100100 200200 075075 100100 075120 200200 105105 100100
+ 1848 100100 100100 080080 105105 020020 110110 150150 135135 200200 075075 100100 120120 200200 105105 100100
+
+C. punctatus (Can Tho, mekong, Vietnam)
+4
+ 3054 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 3055 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 3056 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 3057 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Chau Doc, Mekong, Vietnam)
+16
+ 542s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 543s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 544s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 545s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 546s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 547s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 548s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 549s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 550s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 551s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 552s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 553s 100100 080080 080080 105105 020020 110110 150150 055100 200200 105105 100100 120120 200200 105105 100100
+ 554s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 555s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 556s 100100 080080 080080 105105 020020 110110 150150 055100 200200 105105 100100 100120 200200 105105 100100
+ 557s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Kuala Lumpur, Malaysia)
+4
+ 1982 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 1983 100100 080100 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 1984 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 100120 200200 105105 100100
+ 1985 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Medan, Sumatra)
+1
+ 4923 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Bukit Pinang, Kalimantan)
+3
+ 4104 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 4105 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 4107 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Tegineneng, Sumatra)
+3
+ 1987 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 1988 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 1989 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Palangkaraya, Kalimantan)
+3
+ 151s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 152s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 153s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Kotaagung, Sumatra)
+13
+ 154s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 155s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 156s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 157s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 158s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 159s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 160s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 161s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 162s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 163s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 164s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 165s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 166s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Plaju, Sumatra)
+9
+ 107s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 108s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 109s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 110s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 111s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 113s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 115s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 117s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 118s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Parung, Java)
+1
+ 119s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+
+C. punctatus (Depok, Java)
+21
+ 1s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 2s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 3s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 9s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 10s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 21s 100100 080080 080080 105105 020020 110110 150150 130130 200200 105105 100100 120120 200200 105105 100100
+ 22s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 23s 100100 080080 080080 105105 020020 110110 150150 130130 200200 105105 100100 120120 200200 105105 100100
+ 24s 100100 080080 080080 105105 020020 110110 150150 130130 200200 105105 100100 120120 200200 105105 100100
+ 26s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 27s 100100 080080 080080 105105 020020 110110 150150 130130 200200 105105 100100 120120 200200 105105 100100
+ 28s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 29s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 30s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 31s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 32s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 33s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 35s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 36s 100100 080080 080080 105105 020020 110110 150150 100130 200200 105105 100100 120120 200200 105105 100100
+ 39s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+ 40s 100100 080080 080080 105105 020020 110110 150150 100100 200200 105105 100100 120120 200200 105105 100100
+
+C. macrocephalus (Thabo, Mekong, Thailand)
+1
+ 278 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+
+C. macrocephalus (So Phisat, Mekong, Thailand)
+1
+ 284 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+
+C. macrocephalus (Can Tho, Mekong, Vietnam)
+19
+ 513 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 512 100100 110110 100100 105105 020020 110110 150150 100100 200200 075100 100100 150150 200200 105105 100100
+ 514 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 515 100100 110110 100100 105105 020020 110110 150150 100100 105200 075075 100100 150150 200200 105105 100100
+ 516 100100 110110 100100 105105 020020 110110 150150 100100 105200 075075 100100 150150 200200 105105 100100
+ 524 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 525 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 526 100100 110110 100100 105105 020020 110110 150150 100100 105200 075075 100100 150150 200200 105105 100100
+ 527 100100 110110 100100 105105 020020 110110 150150 100100 105200 075075 100100 150150 200200 105105 100100
+ 528 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 529 100100 110110 100100 105105 020020 110110 150150 100100 105200 075075 100100 150150 200200 105105 100100
+ 530 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 511 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 517 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150200 200200 105105 100100
+ 518 100100 110110 100100 105105 020020 110110 150150 100100 200200 100100 100100 150150 200200 105105 100100
+ 519 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 520 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 522 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+ 523 100100 110110 100100 105105 020020 110110 150150 100100 200200 075075 100100 150150 200200 105105 100100
+
+C. fuscus (Cam Pha, Vietnam)
+3
+ 3088 100100 080080 080080 105105 020020 110110 110110 055055 200200 075075 100100 120120 200200 105105 100100
+ 3087 100100 080080 080080 105105 020020 110110 110110 055055 200200 075075 100100 120120 200200 105105 100100
+ 3089 100100 080080 080080 105105 020020 110110 110110 100100 200200 075075 100100 120120 200200 105105 100100
+
+C. leiacanthus (Jambi, Sumatra)
+1
+ 1803 090090 110110 200200 105105 090090 090090 150150 100100 100100 105105 100100 120120 200200 096096 050050
+
+C. leiacanthus (Rengat, Sumatra)
+1
+ 4824 090090 075110 200200 105105 090090 090090 150150 100100 100100 105105 100100 120120 200200 096096 050050
+
+C. planiceps (Tanjung Redep, Kalimantan)
+1
+ 2127 090090 075110 210210 105105 090090 090090 100100 100100 100100 105105 100100 120120 200200 096096 050050
+
+C. microstomus (Tanjung Selor, Kalimantan)
+1
+ 2149 090090 110110 200200 105105 090090 090090 100100 100100 100100 105105 400400 200200 200200 096096 050050
+
+C. leiacanthus (Bengkayang, Kalimantan)
+6
+ 4451 090090 110110 200200 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4443 090090 110110 160200 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4450 090090 110110 200200 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4448 090090 110110 200200 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4445 090090 110110 200200 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4442 090090 110110 160160 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+
+C. leiacanthus (Sambas et Satong, Kalimantan)
+2
+ 4464 090090 110110 200200 105105 090090 090090 150150 100100 100100 105105 100100 120120 200200 096096 050050
+ 4459 090090 110110 200200 105105 090090 090090 150150 100100 100100 105105 100100 120120 200200 096096 050050
+
+C. pseudoleiacanthus (Satong, Kalimantan)
+11
+ 4505 090090 075075 210210 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4546 090090 075110 210210 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4545 090090 075110 210210 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4541 090090 075110 210210 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4538 090090 075110 210210 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4535 090090 075075 210210 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4527 090090 090090 210210 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4514 090090 075090 210210 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4511 090090 075075 210210 105105 090090 090090 150150 100115 100100 105105 100100 220220 200200 096096 050050
+ 4507 090090 075090 210210 105105 090090 090090 150150 100100 100100 105105 100100 220220 200200 096096 050050
+ 4544 090090 075110 210210 105105 090090 090090 150150 100115 100100 105105 100100 220220 200200 096096 050050
+
+C. kapuasensis (Nanga Pinoh, Kalimantan)
+1
+ 4676 090090 110110 210210 105105 090090 080090 150150 100100 100100 105105 100100 120120 200200 096096 050050
Added: pkg/misc/bug-report.1.2-2.02/readme.txt
===================================================================
--- pkg/misc/bug-report.1.2-2.02/readme.txt (rev 0)
+++ pkg/misc/bug-report.1.2-2.02/readme.txt 2008-10-13 10:23:22 UTC (rev 191)
@@ -0,0 +1,2 @@
+Fichier de E Paradis. Ne s'ouvre pas avec read.genetix, mais
+marcherait avec version de EP.
Added: pkg/misc/bug-report.1.2-2.03/boot_coord.7.input
===================================================================
--- pkg/misc/bug-report.1.2-2.03/boot_coord.7.input (rev 0)
+++ pkg/misc/bug-report.1.2-2.03/boot_coord.7.input 2008-10-13 10:23:22 UTC (rev 191)
@@ -0,0 +1,88 @@
+ X Y
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+p83 -86.3884 36.9428
+p84 -81.7417 36.2492
+p85 -86.3738 42.0353
+p86 -79.8633 35.8202
Added: pkg/misc/bug-report.1.2-2.03/boot_dist.7.input
===================================================================
--- pkg/misc/bug-report.1.2-2.03/boot_dist.7.input (rev 0)
+++ pkg/misc/bug-report.1.2-2.03/boot_dist.7.input 2008-10-13 10:23:22 UTC (rev 191)
@@ -0,0 +1,87 @@
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+0.382228 0.145976 1.92374 0.518508 1.47902 0.0960731 0.393118 0.265998 0.8572 -2.83855 2.06947 0.208439 2.54548 -2.83855 2.23421 -2.83855 0.394854 3.20182 2.14466 2.26224 1.01352 0.454466 2.03799 -2.83855 -2.83855 1.00221 -2.83855 2.35488 1.28186 0.0685972 2.10977 2.27139 0.286571 2.14774 0.268201 2.1819 -2.83855 1.61227 3.90735 1.54031 -2.83855 0.479513 0.243746 -2.83855 -2.83855 2.22801 2.38243 0.226945 0.360527 1.96702 0.369859 -2.83855 -2.83855 0.189188 0.204282 0.317704 2.55931 2.22814 1.50726 0.530525 0.191522 0.420753 0.286112 0.195838 0.14062 2.1221 2.35083 2.06313 -2.83855 2.95653 0.246943 0.23601 0.474804 0.475387 0.09338 2.06533 2.28719 2.29228 0.31405 0.396729 2.11143 2.20937 0.493526 0 0.131657 1.70158 0.531535
+0.283436 0.15457 1.82097 0.396388 1.43823 0.131394 0.304955 0.22692 0.701813 -2.34282 1.83551 0.223113 2.24881 -2.34282 2.02217 -2.34282 0.295573 3.59142 1.93402 2.01206 0.946551 0.306826 1.87204 -2.34282 -2.34282 1.00877 -2.34282 2.08108 1.31384 0.304555 1.89289 2.02636 0.254334 1.93458 0.212904 1.96602 -2.34282 1.3727 4.35545 1.29 -2.34282 0.526516 0.209124 -2.34282 -2.34282 1.98787 2.15137 0.228222 0.428975 1.85408 0.539866 -2.34282 -2.34282 0.167941 0.166095 0.251855 2.2516 1.99709 1.77409 0.425461 0.182088 0.339049 0.253259 0.0333127 0.145697 1.92213 2.16016 1.8458 -2.34282 2.90718 0.223304 0.206295 0.595201 0.369627 0.0328034 1.88505 2.03116 2.03895 0.260539 0.298674 1.89218 1.97569 0.553906 0.131657 0 1.79209 0.431852
+2.98616 2.45795 6.29106 3.49383 0.0755979 1.18323 3.278 3.01061 4.55761 -1.3453 0.392231 2.63514 0.605879 -1.3453 0.387885 -1.3453 3.22019 2.81586 0.355747 0.404071 0.247082 0.81427 0.327377 -1.3453 -1.3453 0.151824 -1.3453 0.455328 0.054415 1.59057 0.360772 0.422243 3.11788 0.354425 2.49972 0.338677 -1.3453 4.24561 3.29106 0.423927 -1.3453 2.08162 2.52484 -1.3453 -1.3453 0.387428 0.47984 2.4628 1.65548 0.349246 0.56753 -1.3453 -1.3453 1.14356 2.38444 3.08979 0.600368 0.372307 2.23593 0.62138 2.47334 3.31936 2.95979 1.47369 2.39232 0.35188 0.5969 0.328366 -1.3453 1.26834 2.57518 2.73045 1.47515 3.26195 1.9191 0.329598 0.418763 0.428585 2.99144 3.12781 0.361265 0.380097 1.25437 1.70158 1.79209 0 0.642182
+1.24819 0.890368 3.59747 1.52514 0.483614 0.285433 1.38123 1.17559 2.20438 -2.43957 0.888499 0.992567 1.1544 -2.43957 1.02729 -2.43957 1.33404 2.28684 0.940776 0.97232 0.319818 0.181392 0.931379 -2.43957 -2.43957 0.244682 -2.43957 1.01355 0.398703 0.533558 0.916866 0.992678 1.23861 0.938387 0.957901 0.920982 -2.43957 2.43698 2.86907 0.539442 -2.43957 0.777329 0.981763 -2.43957 -2.43957 0.959939 1.13413 0.909377 0.630363 0.975742 0.207463 -2.43957 -2.43957 0.178673 0.870997 1.25423 1.1442 0.979843 1.19346 0.158329 0.94668 1.39706 1.1975 0.288974 0.875292 0.941439 1.19041 0.845222 -2.43957 2.10364 0.987834 1.0265 0.405361 1.39442 0.572345 0.927514 0.984526 0.995494 1.18928 1.30608 0.914806 0.955347 0.261166 0.531535 0.431852 0.642182 0
Added: pkg/misc/bug-report.1.2-2.03/monboot_debug.r
===================================================================
--- pkg/misc/bug-report.1.2-2.03/monboot_debug.r (rev 0)
+++ pkg/misc/bug-report.1.2-2.03/monboot_debug.r 2008-10-13 10:23:22 UTC (rev 191)
@@ -0,0 +1,89 @@
+## monboot.r
+## An R program designed to take geographic coordinates and a genetic distance matrices produced by a companion C++ program (monboot.cxx)
+## and compute a Monmonier's barrier.
+## In addition, the program is designed to take many bootstrapped matrices for analysis.
+## The goal of the bootstrap is to find the highly likely region where there is a major genetic break on the landscape.
+
+## Algorithm
+# Compute Monmonier barrier on original data. Output that info.
+# Read in original coordinates. Store.
+# Read in genetic distance matrix. Store.
+# Compute network.
+# compute barrier.
+# Output barrier.
+# Perform bootstrap analysis. (loop)
+# Input filenames are predetermined based on companion C++ output.
+# Read in coordinates. Store.
+# Read in genetic distance matrix. Store.
+# Compute network.
+# compute barrier.
+# Output barrier.
+
+#############################
+
+#### User defined variables (to be changed to appropriate when used)
+
+pathname <- "monmonierwork/EV/EVmonboot/" #base path for directory that all input and output data will be in
+#numboot <- 1000 #number of bootstrap replicates to run
+b <- 7
+
+## Input files
+orig_coord_filename <- paste(pathname, "orig_coord.input", sep = "")
+boot_coord_base_filename <- paste(pathname, "boot_coord.", sep = "")
+orig_dist_filename <- paste(pathname, "orig_dist.input", sep ="")
+boot_dist_base_filename <- paste(pathname, "boot_dist.", sep = "")
+
+## Output files
+orig_mon_filename <- paste(pathname, "orig_mon.out", sep = "")
+boot_mon_filename <- paste(pathname, "boot_mon.out", sep = "")
+
+#### Necessary libraries
+
+library(spdep)
+library(ade4)
+library(adegenet)
+
+#### Main program
+
+## 1. Computing Monmonier barrier on original data.
+
+# Read in coordinates and genetic matrix
+orig_coords <- read.table(orig_coord_filename)
+numpops <- length(orig_coords[,1])
+orig_Da <- read.table(orig_dist_filename)
+orig_Da <- as.dist(orig_Da)
+
+# Compute the barrier
+orig_cn <- chooseCN(orig_coords, ask=FALSE, type=1)
+orig_mon <- optimize.monmonier(coords, Da, cn, threshold=0)
+orig_mon <- monmonier(orig_coords, orig_Da, orig_cn, threshold=0, nrun=1, skip.local.diff = rep(1, 1)) #threshold is arbitrarily set at 0
+plot(orig_mon)
+
+# Output barrier info -- for now only outputting data from run1
+write.table(orig_mon$run1$dir1$path, file=orig_mon_filename, sep="\t")
+write.table(orig_mon$run1$dir2$path, file=orig_mon_filename, sep="\t", append = TRUE, col.names = FALSE)
+
+## 2. Performing the bootstrap analyses
+
+#clear the output files
+write("",file=boot_mon_filename)
+
+#for (b in 1:numboot)
+#{
+ # Read in coordinates and genetic matrix
+ coords <- read.table(paste(boot_coord_base_filename, b, ".input", sep=""))
+ numpops <- length(coords[,1])
+ Da <- read.table(paste(boot_dist_base_filename, b, ".input", sep=""))
+ Da <- as.dist(Da)
+
+ # Calc monmonier barrier
+ cn <- chooseCN(coords, ask=FALSE, type=1)
+ mon <- monmonier(coords, Da, cn, threshold=0, nrun=1, skip.local.diff = rep(1, 1)) #threshold is arbitrarily set at 0
+ mon <- optimize.monmonier(coords, Da, cn, threshold=0)
+# plot(mon)
+
+ # Output info
+ write.table(cbind(rep(b), mon$run1$dir1$path), file=boot_mon_filename, sep="\t", append = TRUE, col.names = FALSE)
+ write.table(cbind(rep(b), mon$run1$dir2$path), file=boot_mon_filename, sep="\t", append = TRUE, col.names = FALSE)
+# write("\n",file=boot_mon_filename, sep="\t", append = TRUE)
+#}
Added: pkg/misc/bug-report.1.2-2.03/monmonier-bug1.html
===================================================================
--- pkg/misc/bug-report.1.2-2.03/monmonier-bug1.html (rev 0)
+++ pkg/misc/bug-report.1.2-2.03/monmonier-bug1.html 2008-10-13 10:23:22 UTC (rev 191)
@@ -0,0 +1,46 @@
+<html>
+<head>
+<title>adegenet: monmonier bug</title>
+<link rel="important stylesheet" href="chrome://messenger/skin/messageBody.css">
+</head>
+<body>
+<table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part1"><tr><td><b>Subject: </b>adegenet: monmonier bug</td></tr><tr><td><b>From: </b>Yi-Hsin Erica Tsai <erica.tsai at duke.edu></td></tr><tr><td><b>Date: </b>Thu, 09 Oct 2008 16:24:21 -0400</td></tr></table><table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part2"><tr><td><b>To: </b>jombart at biomserv.univ-lyon1.fr</td></tr></table><br>
+<div class="moz-text-flowed">Hi,
+<br>
+<br>I have been using your adegenet R package to compute some Monmonier
+boundaries. For the most part, the package behaves excellently and does
+what I need it to do. However, in many of my runs I encounter these
+same errors:
+<br>
+<br>> orig_mon <- optimize.monmonier(coords, Da, cn, threshold=0)
+<br>Boundaries computed (required: 10)
+<br>1 Error in
+checkNext(result[[run]]$dir1[[length(result[[run]]$dir1)]]$M, :
+<br> CheckAllSeg failure (returned value=10, i.e. unchanged, not
+computed). Please report the bug.
+<br>
+<br>or
+<br>
+<br>> mon <- monmonier(coords, Da, cn, threshold=0, nrun=1, skip.local.diff
+= rep(1, 1))
+<br>Error in checkNext(result[[run]]$dir1[[length(result[[run]]$dir1)]]$M, :
+<br> CheckAllSeg failure (returned value=10, i.e. unchanged, not
+computed). Please report the bug.
+<br>
+<br>Do you have any idea what is causing this? Or how can I fix this
+problem? I can send you my input data and code if that is helpful.
+<br>
+<br>Best,
+<br>--Erica Tsai
+<br>
+<br><div class="moz-txt-sig"><span class="moz-txt-tag">-- <br></span>Yi-Hsin Erica Tsai
+<br>Ph.D. Candidate
+<br>Department of Biology (Manos Lab)
+<br>Duke University
+<br>
+<br><a class="moz-txt-link-freetext" href="http://www.duke.edu/~yet2/">http://www.duke.edu/~yet2/</a>
+<br><a class="moz-txt-link-abbreviated" href="mailto:erica.tsai at duke.edu">erica.tsai at duke.edu</a>
+<br>
+<br>
+<br></div></div></body>
+</html>
Added: pkg/misc/bug-report.1.2-2.03/monmonier-bug2.html
===================================================================
--- pkg/misc/bug-report.1.2-2.03/monmonier-bug2.html (rev 0)
+++ pkg/misc/bug-report.1.2-2.03/monmonier-bug2.html 2008-10-13 10:23:22 UTC (rev 191)
@@ -0,0 +1,528 @@
+<html>
+<head>
+<title>Re: adegenet: monmonier bug</title>
+<link rel="important stylesheet" href="chrome://messenger/skin/messageBody.css">
+</head>
+<body>
+<table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part1"><tr><td><b>Subject: </b>Re: adegenet: monmonier bug</td></tr><tr><td><b>From: </b>Yi-Hsin Erica Tsai <erica.tsai at duke.edu></td></tr><tr><td><b>Date: </b>Fri, 10 Oct 2008 11:31:00 -0400</td></tr></table><table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part2"><tr><td><b>To: </b>Thibaut Jombart <jombart at biomserv.univ-lyon1.fr></td></tr></table><br>
+<div class="moz-text-flowed">Hi Thibaut,
+<br>
+<br>Thanks for taking the time to look into this for me. Good luck on
+finishing your dissertation. I too am trying to finish, so I completely
+understand your stress and need to prioritize.
+<br>
+<br>I've attached 4 example input files (for two sets of analyses) and my R
+program. I should explain that my program is designed to take
+geographic coordinates and genetic distance matrices from a companion
+C++ program that has generated many bootstrapped replicates of the
+original data (within orig_coord.input and orig_dist.input). I've
+commented out the loop and just provided you with one of the
+bootstrapped datasets to give you an example. For most of the datasets,
+there is no problem, but for a few I get the checkNext error. And this
+occurs with both the optimize.monmonier() and monmonier() function.
+Occasionally I get different error generation with the two functions, so
+I included both in the code for you. I hope that this is not too
+painful to debug.
+<br>
+<br>Let me know if you need any other information.
+<br>
+<br>Best wishes,
+<br>--Erica
+<br>
+<br>Thibaut Jombart wrote:
+<br><blockquote type=cite>Yi-Hsin Erica Tsai wrote:
+<br><blockquote type=cite>Hi,
+<br>
+<br>I have been using your adegenet R package to compute some Monmonier
+boundaries. For the most part, the package behaves excellently and
+does what I need it to do. However, in many of my runs I encounter
+these same errors:
+<br>
+<br>> orig_mon <- optimize.monmonier(coords, Da, cn, threshold=0)
+<br>Boundaries computed (required: 10)
+<br>1 Error in
+checkNext(result[[run]]$dir1[[length(result[[run]]$dir1)]]$M, :
+<br> CheckAllSeg failure (returned value=10, i.e. unchanged, not
+computed). Please report the bug.
+<br>
+<br>or
+<br>
+<br>> mon <- monmonier(coords, Da, cn, threshold=0, nrun=1,
+skip.local.diff = rep(1, 1))
+<br>Error in checkNext(result[[run]]$dir1[[length(result[[run]]$dir1)]]$M, :
+<br> CheckAllSeg failure (returned value=10, i.e. unchanged, not
+computed). Please report the bug.
+<br>
+<br>Do you have any idea what is causing this? Or how can I fix this
+problem? I can send you my input data and code if that is helpful.
+<br>
+<br>Best,
+<br>--Erica Tsai
+<br>
+<br></blockquote>Dear Erica,
+<br>
+<br>thanks very much for reporting the bug.This apparently comes from the C
+code used to check whether two segments intersect or not, meaning, it's
+going to be a pain de debug. ;-) I would indeed need a sample input data
+along with the code generating the bug. Can you also check that you are
+using the latest version of adegenet ? You can find it from:
+<br><a class="moz-txt-link-freetext" href="https://r-forge.r-project.org/R/?group_id=120">https://r-forge.r-project.org/R/?group_id=120</a>
+<br>this is the devel version, but it is as stable as the previous version.
+<br>
+<br>If the bug persists in the most recent version, I'll do my best to fix
+it ASAP. But I defend my PhD soon, meaning I might not have time for
+debuging. Anyhow, I will try to help, there might be other
+methodological approaches that you could use instead of monmonier (in
+the worst case).
+<br>
+<br>Best,
+<br>
+<br>Thibaut.
+<br></blockquote><div class="moz-txt-sig"><span class="moz-txt-tag">-- <br></span>Yi-Hsin Erica Tsai
+<br>Ph.D. Candidate
+<br>Department of Biology (Manos Lab)
+<br>Duke University
+<br>
+<br><a class="moz-txt-link-freetext" href="http://www.duke.edu/~yet2/">http://www.duke.edu/~yet2/</a>
+<br><a class="moz-txt-link-abbreviated" href="mailto:erica.tsai at duke.edu">erica.tsai at duke.edu</a>
+<br></div></div><div class="moz-text-plain"><pre wrap><BR><HR WIDTH="90%" SIZE=4><BR> X Y
+p0 -89.0311 34.3384
+p1 -87.6552 34.5483
+p2 -93.0393 39.6296
+p3 -93.2925 34.496
+p4 -84.8857 42.1998
+p5 -85.3305 38.4027
+p6 -89.9049 32.2554
+p7 -92.3323 38.4949
+p8 -92.8899 39.0059
+p9 -67.1444 38.5308
+p10 -75.6451 46.1659
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+p12 -66.5537 42.9626
+p13 -67.5288 34.003
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+p15 -70.0515 37.0327
+p16 -91.3187 32.1164
+p17 -76.2884 32.7725
+p18 -75.9968 41.1327
+p19 -83.911 46.0539
+p20 -83.3281 41.3248
+p21 -81.3413 39.0665
+p22 -72.7547 38.8173
+p23 -93.5288 43.3597
+p24 -93.0662 46.1723
+p25 -85.877 41.6247
+p26 -67.41 38.3368
+p27 -72.036 45.5491
+p28 -86.9218 42.3802
+p29 -90.0102 38.2261
+p30 -77.1043 46.5183
+p31 -69.7878 41.7878
+p32 -91.6317 38.6964
+p33 -71.0223 42.2373
+p34 -89.5206 33.6854
+p35 -74.5634 39.284
+p36 -70.2271 33.1359
+p37 -92.134 40.4471
+p38 -75.6307 32.0343
+p39 -82.4898 41.6329
+p40 -92.3884 41.8196
+p41 -83.4605 30.933
+p42 -88.942 33.3668
+p43 -67.6255 37.5781
+p44 -68.9248 32.1566
+p45 -68.8237 38.7231
+p46 -91.5607 42.9196
+p47 -88.3155 33.4319
+p48 -86.3621 31.1936
+p49 -69.0623 37.5674
+p50 -88.1345 40.0828
+p51 -66.9727 31.7458
+p52 -73.3938 31.3243
+p53 -75.2069 37.0284
+p54 -90.8219 32.122
+p55 -91.5848 33.4218
+p56 -72.1159 38.0412
+p57 -89.0611 45.9546
+p58 -76.5942 32.6935
+p59 -82.9741 39.0116
+p60 -88.1857 35.4594
+p61 -93.2226 35.3815
+p62 -92.0837 34.3679
+p63 -81.1802 36.1173
+p64 -86.9282 36.3393
+p65 -72.5699 38.0313
+p66 -67.7316 42.3928
+p67 -79.4768 41.4973
+p68 -72.5127 33.8267
+p69 -91.8244 44.6666
+p70 -86.2438 33.3093
+p71 -92.5973 31.7469
+p72 -76.6958 34.2998
+p73 -93.281 34.6151
+p74 -84.3974 37.3567
+p75 -72.6725 39.4342
+p76 -74.1053 43.218
+p77 -70.5708 43.0517
+p78 -93.4855 35.4858
+p79 -90.6871 35.004
+p80 -75.8569 44.7105
+p81 -73.7178 40.1038
+p82 -76.663 34.6691
+p83 -86.3884 36.9428
+p84 -81.7417 36.2492
+p85 -86.3738 42.0353
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+</pre></div><div class="moz-text-plain"><pre wrap><BR><HR WIDTH="90%" SIZE=4><BR> X Y
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+p2 -84.57 39.15
+p3 -79.35 37.5667
+p4 -76.6 40.4333
+p5 -74.9083 41.1633
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+p84 -79.6644 43.5523
+p85 -77.8 41.65
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+</pre></div><div class="moz-text-plain"><pre wrap><BR><HR WIDTH="90%" SIZE=4><BR>0 4 2.25 5 4.25 4 5.11111 4 5 4.44444 4 5 5 1 4.53061 1 5 5 4 5 5.64 4.30556 4 4.55556 5.11111 4.33333 8.18367 0.836735 0.5625 1.32653 1 0.916667 1 5 7 4.04 1 4 1 1.08 4.16 1 5 4.32653 4.69444 4.125 5 4.5 5 4.08163 4.5102 5 4.18367 4.0625 4.04 4.25 5 4.5102 5 5 5 1 1 1 2 2 1.40816 2 7 0.183673 1 2 1 11 1 1 7.04082 1 1.625 3.41667 1 0.703125 1.16667 10.4444 4.39062 4.36735 5.18367
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+</pre></div><div class="moz-text-plain"><pre wrap><BR><HR WIDTH="90%" SIZE=4><BR>## monboot.r
+## An R program designed to take geographic coordinates and a genetic distance matrices produced by a companion C++ program (monboot.cxx)
+## and compute a Monmonier's barrier.
+## In addition, the program is designed to take many bootstrapped matrices for analysis.
+## The goal of the bootstrap is to find the highly likely region where there is a major genetic break on the landscape.
+
+## Algorithm
+# Compute Monmonier barrier on original data. Output that info.
+# Read in original coordinates. Store.
+# Read in genetic distance matrix. Store.
+# Compute network.
+# compute barrier.
+# Output barrier.
+# Perform bootstrap analysis. (loop)
+# Input filenames are predetermined based on companion C++ output.
+# Read in coordinates. Store.
+# Read in genetic distance matrix. Store.
+# Compute network.
+# compute barrier.
+# Output barrier.
+
+#############################
+
+#### User defined variables (to be changed to appropriate when used)
+
+pathname <- "monmonierwork/EV/EVmonboot/" #base path for directory that all input and output data will be in
+#numboot <- 1000 #number of bootstrap replicates to run
+b <- 7
+
+## Input files
+orig_coord_filename <- paste(pathname, "orig_coord.input", sep = "")
+boot_coord_base_filename <- paste(pathname, "boot_coord.", sep = "")
+orig_dist_filename <- paste(pathname, "orig_dist.input", sep ="")
+boot_dist_base_filename <- paste(pathname, "boot_dist.", sep = "")
+
+## Output files
+orig_mon_filename <- paste(pathname, "orig_mon.out", sep = "")
+boot_mon_filename <- paste(pathname, "boot_mon.out", sep = "")
+
+#### Necessary libraries
+
+library(spdep)
+library(ade4)
+library(adegenet)
+
+#### Main program
+
+## 1. Computing Monmonier barrier on original data.
+
+# Read in coordinates and genetic matrix
+orig_coords <- read.table(orig_coord_filename)
+numpops <- length(orig_coords[,1])
+orig_Da <- read.table(orig_dist_filename)
+orig_Da <- as.dist(orig_Da)
+
+# Compute the barrier
+orig_cn <- chooseCN(orig_coords, ask=FALSE, type=1)
+orig_mon <- optimize.monmonier(coords, Da, cn, threshold=0)
+orig_mon <- monmonier(orig_coords, orig_Da, orig_cn, threshold=0, nrun=1, skip.local.diff = rep(1, 1)) #threshold is arbitrarily set at 0
+plot(orig_mon)
+
+# Output barrier info -- for now only outputting data from run1
+write.table(orig_mon$run1$dir1$path, file=orig_mon_filename, sep="\t")
+write.table(orig_mon$run1$dir2$path, file=orig_mon_filename, sep="\t", append = TRUE, col.names = FALSE)
+
+## 2. Performing the bootstrap analyses
+
+#clear the output files
+write("",file=boot_mon_filename)
+
+#for (b in 1:numboot)
+#{
+ # Read in coordinates and genetic matrix
+ coords <- read.table(paste(boot_coord_base_filename, b, ".input", sep=""))
+ numpops <- length(coords[,1])
+ Da <- read.table(paste(boot_dist_base_filename, b, ".input", sep=""))
+ Da <- as.dist(Da)
+
+ # Calc monmonier barrier
+ cn <- chooseCN(coords, ask=FALSE, type=1)
+ mon <- monmonier(coords, Da, cn, threshold=0, nrun=1, skip.local.diff = rep(1, 1)) #threshold is arbitrarily set at 0
+ mon <- optimize.monmonier(coords, Da, cn, threshold=0)
+# plot(mon)
+
+ # Output info
+ write.table(cbind(rep(b), mon$run1$dir1$path), file=boot_mon_filename, sep="\t", append = TRUE, col.names = FALSE)
+ write.table(cbind(rep(b), mon$run1$dir2$path), file=boot_mon_filename, sep="\t", append = TRUE, col.names = FALSE)
+# write("\n",file=boot_mon_filename, sep="\t", append = TRUE)
+#}
+</pre></div></body>
+</html>
Added: pkg/misc/bug-report.1.2-2.03/orig_coord.input
===================================================================
--- pkg/misc/bug-report.1.2-2.03/orig_coord.input (rev 0)
+++ pkg/misc/bug-report.1.2-2.03/orig_coord.input 2008-10-13 10:23:22 UTC (rev 191)
@@ -0,0 +1,88 @@
+ X Y
+p0 -79.0189 36.0983
+p1 -84.0333 42.1333
+p2 -84.57 39.15
+p3 -79.35 37.5667
+p4 -76.6 40.4333
+p5 -74.9083 41.1633
+p6 -73.1033 41.3233
+p7 -73.2583 41.4717
+p8 -72.7933 41.8383
+p9 -72.345 43.7133
+p10 -72.0733 43.345
+p11 -71.945 43.3583
+p12 -72.95 43.9725
+p13 -82.5833 36.1667
+p14 -76.503 42.4076
+p15 -87.6 33.26
+p16 -82.5003 35.62
+p17 -82.5 35.62
+p18 -75.21 40.04
+p19 -80.9506 38.0262
+p20 -80.1 39.5096
+p21 -81.0389 41.3287
+p22 -84.3635 41.6407
+p23 -85.6346 40.7719
+p24 -87.0752 39.9362
+p25 -86.7253 39.2905
+p26 -86.1456 38.208
+p27 -85.6532 37.9257
+p28 -86.0978 37.1835
+p29 -85.5952 36.0438
+p30 -84.2186 36.3093
+p31 -83.0286 38.2015
+p32 -89.3447 37.6483
+p33 -77.46 38.37
+p34 -77.08 35.04
+p35 -79.2098 41.3461
+p36 -83.8313 34.2357
+p37 -83.003 39.962
+p38 -89.0967 33.2067
+p39 -88.8509 33.2925
+p40 -70.6527 41.3919
+p41 -79.022 35.9798
+p42 -82.9991 39.6401
+p43 -77.4546 41.6968
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Added: pkg/misc/bug-report.1.2-2.03/orig_dist.input
===================================================================
--- pkg/misc/bug-report.1.2-2.03/orig_dist.input (rev 0)
+++ pkg/misc/bug-report.1.2-2.03/orig_dist.input 2008-10-13 10:23:22 UTC (rev 191)
@@ -0,0 +1,87 @@
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