[Adephylo-commits] r2 - in pkg: . inst

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Nov 20 11:15:05 CET 2008 

Author: jombart
Date: 2008-11-20 11:15:05 +0100 (Thu, 20 Nov 2008)
New Revision: 2

Added:
   pkg/ChangeLog
   pkg/DESCRIPTION
   pkg/TITLE
   pkg/TODO
   pkg/data/
   pkg/inst/
   pkg/inst/CITATION
   pkg/inst/files/
   pkg/misc/
Log:
First add of files.


Added: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	                        (rev 0)
+++ pkg/ChangeLog	2008-11-20 10:15:05 UTC (rev 2)
@@ -0,0 +1,173 @@
+			CHANGES IN ADEGENET VERSION 1.2-1
+
+
+NEW FEATURES
+
+	o documentation of scaleGen provides an example of usefulness of
+	an appropriate scaling in PCA
+
+BUG FIXES
+
+	o fixed the recognition of NAs in df2genind
+
+	o fixed the call to inherits in spca (returned value changes in R-devel)
+
+
+
+			CHANGES IN ADEGENET VERSION 1.2-0
+
+
+NEW FEATURES
+
+	o implement different levels of ploidy in genind / genpop
+	objects. Make necessary adaptations throughout the package.
+
+	o put some stop where needed when ploidy!=2 is not handled.
+
+	o implement a "sep" argument in df2genind.
+
+	o implement accessor for genind/genpop: nLoc.
+
+	o implement "scaleGen" for genind/genpop, which allows for
+	different types of scaling.
+
+	o added several coercion methods, from genind/genpop to
+	data.frame, matrix and ktab objects.
+
+	o implemented propTyped, a function giving the proportion of
+	non-missing data in different ways.
+
+BUG FIXES
+
+	o missing data indicated in summary corrected (loci with more
+	alleles had more weight in the computations).
+
+
+
+			CHANGES IN ADEGENET VERSION 1.1-2
+
+
+NEW FEATURES
+
+	o significant improvement in the speed of genind2df (more than
+	twice as fast as before).
+
+	o function propShared added: computes the proportion of shared
+	alleles among a set of genotypes (core computations in C).
+
+	o A warning is issued when NAs exist in the input of sPCA.
+
+	o improvement of the validity checking for genind/genpop:
+	validObject now detects duplicates in any kind of names (ind.names,
+	pop.names, etc.) and prints the corresponding items.
+
+
+
+BUG FIXES
+
+	o genind2df does now handles the pop argument correctly.
+
+	o df2genind does no longer bug when there is an entirely non-typed
+	locus.
+
+
+
+			CHANGES IN ADEGENET VERSION 1.1-1
+
+
+NEW FEATURES
+
+	o I/O: df2genind no longer fails when entirely non-type
+	individuals exist.
+
+	o Monmonier: optimize.monmonier now computes the 'best'
+	boundary only once instead of twice. The whole code was re-thought
+	and optimized for speed. Monmonier's boundaries can now form
+	loops. Instead of stoping at a given threshold, it is also
+	possible to ask for a given length of boundary (argument
+	bd.length).
+
+	o The function chooseCN has a new option to return a list of
+	spatial weights defined as the inverse of spatial distances, at a
+	given exponent.
+
+	o A wrapper for glob.varcomp has been implemented for genind
+	objects, through the new function fstat.
+
+	o The elements of the @other slot are now proceeded wisely when
+	objects are subsetted using the '[' operator.
+
+
+BUG FIXES
+
+	o I/O: df2genind no longer fails when entirely non-type
+	individuals exist.
+
+	o monmonier no longer fails when coordinates are drawn from a
+	regular grid. The matched call of the returned object has been
+	fixed.
+
+
+
+			CHANGES IN ADEGENET VERSION 1.1-0
+
+NEW FEATURES
+	o Data representation: S4 classes in replacement of old S3
+	classes.
+
+	o Spatial genetics: the spatial Principal Component Analysis
+	(Jombart et al, 2008, Heredity), two multivariate spatial
+	tests, and new functionalities for Monmonier's algorithm.
+
+	o I/O: functions to import data are now 'read' functions;
+	available for formats of GENETIX, Fstat, Genepop, STRUCTURE and
+	from data.frames of genotypes. Export from genind to data.frame of
+	genotypes.
+
+	o Data: five new simulated geo-referenced datasets
+
+	o Simulations: a hybridize function, which creates hybrids from
+	two parent datasets. Can output to STRUCTURE format.
+
+	o Data manipulation: new function to separate data by
+	population. Accessors to genind and genpop object like with
+	matrices using 'foo[ chosenGenotypes, chosenAlleles]'.
+
+
+
+			CHANGES IN ADEGENET VERSION 1.0-2
+
+NEW FEATURES
+
+	o adegenetWeb is a simple function opening the adegenet website in
+	the default web browser.
+
+	o sim2pop is a dataset obtained by simulation using the software
+	Easypop. It contains 130 georeferenced genotypes sampled from two
+	distinct populations.
+
+	o monmonier documentation was improved by adding a genetic
+	example, using sim2pop data.
+
+BUG FIXES
+
+	o some bugs corrected in optimize.monmonier
+
+
+			CHANGES IN ADEGENET VERSION 1.0-1
+
+NEW FEATURES
+
+	o chooseCN is a simple interactive tool for choosing and building
+	a connection network from spatial coordinates. This tool is called
+	by monmonier function.
+
+	o monmonier, optimize.monmonier, plot.monmonier and print.monmonier
+	implement the Monmonier algorithm. While not restrained to genetic
+	data analysis, this method can be used to find genetic boundaries
+	among individuals or populations based on their allelic
+	frequencies and spatial coordinates. 
+
+BUG FIXES
+
+	o several bugs fixed in I/O functions

Added: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	                        (rev 0)
+++ pkg/DESCRIPTION	2008-11-20 10:15:05 UTC (rev 2)
@@ -0,0 +1,12 @@
+Package: adegenet
+Version: 1.2-2
+Date: 2008/07/30
+Title: adegenet: a R package for the multivariate analysis of genetic markers.
+Author: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>, with contributions from Peter Solymos
+Maintainer: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>
+Suggests: ade4, genetics, hierfstat, spdep, tripack
+Depends: methods
+Description: Classes and functions for genetic data analysis within the multivariate framework.
+License: GPL (>=2)
+LazyLoad: yes
+Collate: classes.R auxil.R genind2genpop.R propTyped.R basicMethods.R old2new.R makefreq.R chooseCN.R dist.genpop.R export.R setAs.R gstat.randtest.R HWE.R import.R monmonier.R coords.monmonier.R spca.R spca.rtests.R zzz.R hybridize.R fstat.R propShared.R scale.R colorplot.R loadingplot.R

Added: pkg/TITLE
===================================================================
--- pkg/TITLE	                        (rev 0)
+++ pkg/TITLE	2008-11-20 10:15:05 UTC (rev 2)
@@ -0,0 +1 @@
+adegenet: a R package for the multivariate analysis of genetic markers.
\ No newline at end of file

Added: pkg/TODO
===================================================================
--- pkg/TODO	                        (rev 0)
+++ pkg/TODO	2008-11-20 10:15:05 UTC (rev 2)
@@ -0,0 +1,84 @@
+#######################
+#
+# adegenet TODO list
+#
+#######################
+#
+# please list here all intended modifications
+# and all detected bugs
+#
+# please add a "-- done" or "-- fixed" tag when
+# you achieved something
+#
+# Inside a given section, priority goes decreasing.
+#
+# Delete fixed things each new release.
+#
+# T.J. 2008
+#
+######################
+
+
+
+# FOR NEXT STABLE VERSION
+=========================
+=========================
+
+# 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) -- fixed: was due to an error in the data file (wrong nloc); now read.genetix corrects that automatically and issues a warning. (TJ)
+* fix bug 1.2-2.03 (monmonier issue) -- fixed: was a non-detected code 2 due to intersection check with previously drawn segment (was not always removed). (TJ)
+* fix request 1.2-2.04 (implement adjusted heretozygosity in summary)
+
+# DOCUMENTATION ISSUES:
+=======================
+* make a tutorial for the sPCA -- done (TJ)
+
+
+# NEW IMPLEMENTATIONS:
+=====================
+* color plot for the sPCA results, based on RGB representation of Cavalli-Sforza -- done(TJ)
+* loadingplot for plotting loadings of one axis -- done (TJ)
+* adegenetTutorial function which opens the online tutorials -- done (TJ)
+* allow for the use of na.replace and scaleGen in spca function -- done (TJ)
+* add rupica dataset -- done (TJ)
+
+
+# TESTING:
+==========
+* 
+
+
+
+# LOW PRIORITY / MINOR ISSUES
+===========================
+===========================
+* in spca, when nfposi=0, the returned object actually contains what corresponds to nfposi=1. Comes from multispati in ade4. To correct in ade4.
+* use spcaIllus to illustrate global.rtest and local.rtest
+* check all examples and look for possible improvements
+* Implement a method to merge different markers for the same individuals
+* Build accessors for marker names, indiv names, pop names, spatial coords, ... -- done in part (nLoc) (TJ)
+* Return a spatial object from monmonier (class sp?)
+* implement classical Fst sensu Weir 1996
+* Implement different levels of ploidy in:
+- hybridize
+- read.structure
+- propShared
+* Permit specification of a matrix of spatial weights in spca (email A. Piotti).
+*
+
+
+# LONG TERM
+==========================
+==========================
+* import from geneticsBase -- wait for geneSet to be stable
+* export to geneticsBase -- same thing
+* see where code needs tuning, and use C/C++
+* implement global.rtest and local.rtest for genind/genpop objects
+* Implement dudi wrappers for genind / genpop objects -- one step (automatic coercion as data.frames) (TJ)
+* Check the formulae provided for Reynolds (consistent with Felsenstein's
+formulae, not straightforward reading the original article)
+* Implement wrappers for spatial function (Moran's I, Mantel's correlogram, etc.).
+
+

Added: pkg/inst/CITATION
===================================================================
--- pkg/inst/CITATION	                        (rev 0)
+++ pkg/inst/CITATION	2008-11-20 10:15:05 UTC (rev 2)
@@ -0,0 +1,13 @@
+citHeader("To cite the adegenet package:")
+
+citEntry(
+entry="Article",
+title = "adegenet: a R package for the multivariate analysis of genetic markers",
+journal= "Bioinformatics",
+year = "2008",
+author = "T. Jombart",
+volume = "24",
+pages = "1403-1405",
+doi = "10.1093/bioinformatics/btn129",
+textVersion = "Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405. doi: 10.1093/bioinformatics/btn129"
+)

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