[adegenet-commits] r924 - in pkg/inst/doc: . figs

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Jun 22 15:14:13 CEST 2011 

Author: jombart
Date: 2011-06-22 15:14:12 +0200 (Wed, 22 Jun 2011)
New Revision: 924

Added:
   pkg/inst/doc/figs/base-045.pdf
   pkg/inst/doc/figs/base-076.pdf
   pkg/inst/doc/figs/base-079.pdf
   pkg/inst/doc/figs/base-085.pdf
   pkg/inst/doc/figs/base-087.pdf
   pkg/inst/doc/figs/base-088.pdf
   pkg/inst/doc/figs/base-103.pdf
   pkg/inst/doc/figs/base-104.pdf
Modified:
   pkg/inst/doc/adegenet-spca.Rnw
   pkg/inst/doc/adegenet-spca.pdf
   pkg/inst/doc/adegenet-spca.tex
   pkg/inst/doc/figs/spca-008.pdf
   pkg/inst/doc/figs/spca-010.pdf
   pkg/inst/doc/figs/spca-024.pdf
   pkg/inst/doc/figs/spca-025.pdf
   pkg/inst/doc/figs/spca-030.pdf
   pkg/inst/doc/figs/spca-032.pdf
   pkg/inst/doc/figs/spca-034.pdf
   pkg/inst/doc/figs/spca-035.pdf
   pkg/inst/doc/figs/spca-043.pdf
   pkg/inst/doc/figs/spca-044.pdf
   pkg/inst/doc/figs/spca-045.pdf
   pkg/inst/doc/figs/spca-046.pdf
   pkg/inst/doc/figs/spca-047.pdf
   pkg/inst/doc/figs/spca-049.pdf
   pkg/inst/doc/figs/spca-boxplot.pdf
   pkg/inst/doc/figs/spca-colorplot.pdf
   pkg/inst/doc/figs/spca-globalrtest.pdf
   pkg/inst/doc/figs/spca-localrtest.pdf
   pkg/inst/doc/figs/spca-screeplot.pdf
   pkg/inst/doc/figs/spca-svaluedem.pdf
Log:
All vignettes ready now.


Modified: pkg/inst/doc/adegenet-spca.Rnw
===================================================================
--- pkg/inst/doc/adegenet-spca.Rnw	2011-06-21 15:34:20 UTC (rev 923)
+++ pkg/inst/doc/adegenet-spca.Rnw	2011-06-22 13:14:12 UTC (rev 924)
@@ -300,7 +300,7 @@
 
 \noindent The axes of the analysis, denoted $\m{v}$ in eq. (4) \cite{tjart04}
 are stored as columns inside the \texttt{\$c1} component.
-Each columns contains loadings for all the alleles:
+Each column contains loadings for all the alleles:
 <<>>=
 head(mySpca$c1)
 tail(mySpca$c1)
@@ -653,7 +653,7 @@
 <<results=hide, fig=TRUE>>=
 rupica.X <- scaleGen(rupica, method="binom")
 rupica.pca1 <- dudi.pca(rupica.X, cent=FALSE, scale=FALSE, scannf=FALSE, nf=2)
-barplot(rupica.pca1$eig, title="Rupica dataset - PCA eigenvalues",
+barplot(rupica.pca1$eig, main="Rupica dataset - PCA eigenvalues",
         col=heat.colors(length(rupica.pca1$eig)))
 @
 
@@ -674,7 +674,7 @@
 \\
 
 
-We can use \texttt{s.label} to display to two first components of the analysis.
+We can use \texttt{s.label} to display the two first components of the analysis.
 Kernel density estimation (\texttt{s.kde2d}) is used for a better
 assessment of the distribution of the genotypes onto the principal axes:
 <<fig=TRUE>>=
@@ -685,7 +685,6 @@
 
 \noindent This scatterplot shows that the only structure identified by PCA points to a few outliers.
 \texttt{loadingplot} confirms that this corresponds to the possession of a few original alleles:
-Using this function, reproduce this figure:
 <<fig=TRUE>>=
 loadingplot(rupica.pca1$c1^2)
 @
@@ -763,8 +762,7 @@
 title("rupica.graph")
 @
 
-Perform Moran's test for the first two PCs, and plot the results.
-The first test should be significant:
+We perform Moran's test for the first two PCs, and plot the results.
 <<fig=TRUE>>=
 pc1.mctest <- moran.mc(rupica.pca1$li[,1], rupica.graph, 999)
 plot(pc1.mctest)
@@ -818,7 +816,7 @@
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{spatial Principal Component Analysis}
+\subsection{Spatial Principal Component Analysis}
 %%%%%%%%%%%%%%%%%%%%%%%%%%
 
 We apply an sPCA to the \texttt{rupica} dataset, using the connection network used previously in

Modified: pkg/inst/doc/adegenet-spca.pdf
===================================================================
--- pkg/inst/doc/adegenet-spca.pdf	2011-06-21 15:34:20 UTC (rev 923)
+++ pkg/inst/doc/adegenet-spca.pdf	2011-06-22 13:14:12 UTC (rev 924)
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 924

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