[Adephylo-commits] r3 - pkg

Thu Nov 20 11:34:36 CET 2008

Author: jombart
Date: 2008-11-20 11:34:36 +0100 (Thu, 20 Nov 2008)
New Revision: 3

Modified:
   pkg/ChangeLog
   pkg/DESCRIPTION
   pkg/TITLE
   pkg/TODO
Log:
Changed basic files for adephylo.


Modified: pkg/ChangeLog
===================================================================

--- pkg/ChangeLog	2008-11-20 10:15:05 UTC (rev 2)
+++ pkg/ChangeLog	2008-11-20 10:34:36 UTC (rev 3)
@@ -1,173 +1,7 @@
-			CHANGES IN ADEGENET VERSION 1.2-1
+			CHANGES IN ADEPHYLO VERSION 1.0-0
 
 
 NEW FEATURES
 
-	o documentation of scaleGen provides an example of usefulness of
-	an appropriate scaling in PCA
+	o 
 
-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

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-11-20 10:15:05 UTC (rev 2)
+++ pkg/DESCRIPTION	2008-11-20 10:34:36 UTC (rev 3)
@@ -1,12 +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
+Package: adephylo
+Version: 1.0-0
+Date: 2008/11/20
+Title: adephylo: multivariate analysis for the comparative method.
+Author: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>, Stephane Dray <dray at biomserv.univ-lyon1.fr>
 Maintainer: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>
-Suggests: ade4, genetics, hierfstat, spdep, tripack
+Suggests: ade4, ape, phylobase
 Depends: methods
-Description: Classes and functions for genetic data analysis within the multivariate framework.
+Description: Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
 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
+Collate: zzz.R

Modified: pkg/TITLE
===================================================================
--- pkg/TITLE	2008-11-20 10:15:05 UTC (rev 2)
+++ pkg/TITLE	2008-11-20 10:34:36 UTC (rev 3)
@@ -1 +1 @@
-adegenet: a R package for the multivariate analysis of genetic markers.
\ No newline at end of file
+adephylo: multivariate analysis for the comparative method.
\ No newline at end of file

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-11-20 10:15:05 UTC (rev 2)
+++ pkg/TODO	2008-11-20 10:34:36 UTC (rev 3)
@@ -14,7 +14,7 @@
 #
 # Delete fixed things each new release.
 #
-# T.J. 2008
+# T. Jombart, 2008
 #
 ######################
 
@@ -26,25 +26,23 @@
 
 # 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)
+* make a vignette
 
 
 # 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)
+* plot methods from phylobase ('old' version)
+* proximities like Abouheif, etc.
+* orthogram
+* ppca
+* put some sample datasets from ade4
 
 
+
 # TESTING:
 ==========
 * 
@@ -54,31 +52,14 @@
 # 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.).
+* re-implement all phylogenetic methods from ade4 in adephylo
+* implement several phylogenetic proximities
+* implement an orthobasis for phylogenies
+* write a comprehensive tutorial, going through adephylo, ade4, ape, phylobase, etc. 
 
-

