[adegenet-commits] r1038 - pkg/R www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Oct 23 12:12:17 CEST 2012
Author: jombart
Date: 2012-10-23 12:12:16 +0200 (Tue, 23 Oct 2012)
New Revision: 1038
Modified:
pkg/R/import.R
www/literature.html
Log:
- added function fasta2DNAbin
- +1ref
Modified: pkg/R/import.R
===================================================================
--- pkg/R/import.R 2012-10-19 14:24:29 UTC (rev 1037)
+++ pkg/R/import.R 2012-10-23 10:12:16 UTC (rev 1038)
@@ -1243,11 +1243,16 @@
## read and process chunks
while(length(txt)>0){
+ ## clean memory ##
+ invisible(gc())
+
+ ## progression... ##
COUNT <- COUNT + 1
if(!quiet) {
for(i in 1:(COUNT*chunkSize)) cat(".")
}
+ ## process txt ##
nb.ind <- length(grep("^>", txt))
IND.LAB <- c(IND.LAB, sub(">","",txt[grep("^>", txt)])) # find individuals' labels
txt <- split(txt, rep(1:nb.ind, each=LINES.PER.IND)) # split per individuals
@@ -1260,6 +1265,7 @@
## temp <- as.list(apply(matrix(unlist(txt), byrow=TRUE, nrow=length(txt)),2,unique)) # alleles current genomes
## POOL <- mapply(function(x,y) unique(c(x,y)), POOL, temp, SIMPLIFY=FALSE) # update global pool
+ ## scan file further ##
lines.to.skip <- lines.to.skip + nb.ind*LINES.PER.IND
txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, n=LINES.PER.IND*chunkSize)
}
Modified: www/literature.html
===================================================================
--- www/literature.html 2012-10-19 14:24:29 UTC (rev 1037)
+++ www/literature.html 2012-10-23 10:12:16 UTC (rev 1038)
@@ -51,13 +51,8 @@
style="color: rgb(0, 153, 0);">. doi: 10.1093/bioinformatics/btr521 [</span><a
style="color: rgb(0, 153, 0);"
href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
-
to
-
-
-
the
-
bublisher's
website</a><span style="color: rgb(0, 153, 0);">]</span> <br
style="color: rgb(0, 153, 0);">
@@ -80,18 +75,19 @@
<br>
- the paper presenting the <span style="font-style: italic;">spatial
principal component analysis</span> (<span style="font-style: italic;">sPCA</span>,
-
function
<span style="font-family: monospace; color: rgb(255, 0, 0);">spca</span>),
global
-and local tests (<span
+and
+local tests (<span
style="font-family: monospace; color: rgb(255, 0, 0);">global.rtest</span>
and <span style="font-family: monospace; color: rgb(255, 0, 0);">local.rtest</span>):<br>
<b>Jombart T, </b>Devillard S, Dufour AB, Pontier D<b> </b>(2008)<b> </b>Revealing
cryptic
-spatial patterns in genetic variability by a new multivariate
+spatial
+patterns in genetic variability by a new multivariate
method. <span style="font-style: italic;">Heredity</span> <span
style="font-weight: bold;">101</span>: 92-103. doi:
10.1038/hdy.2008.34 [<a
@@ -118,13 +114,8 @@
style="font-style: italic;">Heredity</span>. Doi: 10.1038/hdy.2010.78<br>
<br>
- the paper introducing the <span style="font-style: italic;">Discriminant
-
Analysis
-
-
-
of
-
Principal
Components</span> (<span style="font-style: italic;">DAPC</span>,
functions <span style="font-family: monospace;"><span
@@ -216,7 +207,6 @@
Molecular data provide strong evidence of natural hybridization between
native and introduced lineages of <i>Phragmites australis</i> in North
America. <span style="font-style: italic;">Biological Invasions</span>.
-
doi:
10.1007/s10530-010-9699-6.<br>
<br>
@@ -306,7 +296,6 @@
style="font-style: italic;">Animal Genetics </span><span
style="font-weight: bold;">41</span>: 47-63.<br>
</span><span class="authors"><span style="white-space: nowrap;">[20]
-
Denis
Laloë</span>, <span style="white-space: nowrap;">Katayoun
Moazami-Goudarzi</span>, <span style="white-space: nowrap;">Johannes
@@ -338,7 +327,8 @@
class="citation_date">2010</span> <span class="citation_article_title">Insights
into
-the Genetic History of French Cattle from Dense SNP Data on 47
+the
+Genetic History of French Cattle from Dense SNP Data on 47
Worldwide Breeds. </span> <span style="font-style: italic;"
class="citation_journal_title">PLoS ONE</span><span
class="citation_issue"> <span style="font-weight: bold;">5(9)</span>:</span>
@@ -365,7 +355,8 @@
speciation in the pine processionary moth (<em>Thaumetopoea pityocampa</em>,
Lepidoptera,
-Notodontidae). <span style="font-style: italic;">Journal
+Notodontidae).
+<span style="font-style: italic;">Journal
of Evolutionary Biology</span>, no.
doi: 10.1111/j.1420-9101.2010.02147.x<br>
</p>
@@ -380,7 +371,8 @@
class="citation_date">2010</span> <span class="citation_article_title">Population
Genetic
-Differences along a Latitudinal Cline between Original and
+Differences
+along a Latitudinal Cline between Original and
Recently Colonized Habitat in a Butterfly. </span> <span
style="font-style: italic;" class="citation_journal_title">PLoS ONE</span><span
class="citation_issue"> 5(11):</span> <span
@@ -391,7 +383,8 @@
strains of the red flour beetle. <span style="font-style: italic;">Journal
of
-Applied Entomology</span>, no.
+Applied
+Entomology</span>, no.
doi: 10.1111/j.1439-0418.2010.01593.x<br>
</p>
<p class="authors">[28] Jessica A. Satkoski Trask, Ripan S. Malhi, Sree
@@ -435,7 +428,8 @@
class="citation_date">2011</span> <span class="citation_article_title">Phylogeography
and
-Taxonomy of <i>Trypanosoma brucei</i>. </span> <span
+Taxonomy
+of <i>Trypanosoma brucei</i>. </span> <span
class="citation_journal_title">PLoS Negl Trop Dis</span><span
class="citation_issue"> 5(2):</span> <span class="citation_start_page">e961.</span>
<span class="citation_doi">doi:10.1371/journal.pntd.0000961<br>
@@ -480,7 +474,8 @@
diversity of <span style="font-style: italic;">Toxoplasma gondii</span>:
Example
-of the anthropized environment from French Guiana. <br>
+of
+the anthropized environment from French Guiana. <br>
Infection, Genetics and Evolution.<br>
</p>
<p class="intro">[39] MONTANO, V., FERRI, G., MARCARI, V., BATINI, C.,
@@ -511,7 +506,8 @@
reproduction in natural populations of the Australian carp gudgeon (<em>Hypseleotris</em>:
Eleotridae).
-Molecular Ecology.
+Molecular
+Ecology.
doi: 10.1111/j.1365-294X.2011.05206.x<br>
</p>
<p class="intro">[44] Kinziger, A. P., Nakamoto, R. J., Anderson, E. C.
@@ -564,7 +560,8 @@
spiny lobster (<span style="font-style: italic;">Palinurus elephas</span>).
Biological
-Journal of the Linnean Society. doi:
+Journal
+of the Linnean Society. doi:
10.1111/j.1095-8312.2011.01728.x<br>
</p>
[52]* Farjadian S, Sazzini M, Tofanelli S, Castrì L, Taglioli L,
@@ -650,7 +647,8 @@
Clout, M. N. and Towns, D. R. (eds.). <span style="font-style: italic;">Island
invasives:
-eradication and management</span>. 426 Gland, Switzerland.<br>
+eradication
+and management</span>. 426 Gland, Switzerland.<br>
<br>
[68] Monteil, C. L., Guilbaud, C., Glaux, C., Lafolie, F., Soubeyrand,
S. and Morris, C. E. (2011), Emigration of the plant pathogen
@@ -929,6 +927,11 @@
Togninia minima causing grapevine trunk diseases in Spain. European
Journal of Plant Pathology. 10.1007/s10658-012-0110-6<br>
</p>
+<p class="intro">[119] Colin J. Garroway, Jeff Bowman and Paul J.
+Wilson (2012) Complex social structure of southern flying squirrels is
+related to spatial proximity but not kinship. BEHAVIORAL ECOLOGY AND
+SOCIOBIOLOGY. DOI: 10.1007/s00265-012-1431-3<br>
+</p>
<p class="intro"><br>
</p>
<p class="intro">* adegenet not or wrongly cited, but actually used in
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