[adegenet-commits] r220 - branches/devel-unstable
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 23 13:33:11 CET 2009
Author: jombart
Date: 2009-01-23 13:33:11 +0100 (Fri, 23 Jan 2009)
New Revision: 220
Removed:
branches/devel-unstable/ChangeLog
branches/devel-unstable/DESCRIPTION
branches/devel-unstable/R/
branches/devel-unstable/README
branches/devel-unstable/TITLE
branches/devel-unstable/TODO
branches/devel-unstable/data/
branches/devel-unstable/inst/
branches/devel-unstable/man/
branches/devel-unstable/misc/
branches/devel-unstable/src/
Log:
Removed branch devel
Deleted: branches/devel-unstable/ChangeLog
===================================================================
--- branches/devel-unstable/ChangeLog 2009-01-21 17:41:29 UTC (rev 219)
+++ branches/devel-unstable/ChangeLog 2009-01-23 12:33:11 UTC (rev 220)
@@ -1,173 +0,0 @@
- 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
Deleted: branches/devel-unstable/DESCRIPTION
===================================================================
--- branches/devel-unstable/DESCRIPTION 2009-01-21 17:41:29 UTC (rev 219)
+++ branches/devel-unstable/DESCRIPTION 2009-01-23 12:33:11 UTC (rev 220)
@@ -1,12 +0,0 @@
-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
Deleted: branches/devel-unstable/README
===================================================================
--- branches/devel-unstable/README 2009-01-21 17:41:29 UTC (rev 219)
+++ branches/devel-unstable/README 2009-01-23 12:33:11 UTC (rev 220)
@@ -1,11 +0,0 @@
-1. Put any C/Fortran code in src/
-2. If you have compiled code, add a .First.lib() function in R/
- to load the shared library
-3. Edit the help file skeletons in man/.
-4. Run R CMD build to create INDEX and data/00Index
-5. (Optionally) edit INDEX and data/O0Index
-6. Run R CMD check to check the package
-7. Run R CMD build to make the package file
-
-
- Read "Writing R Extensions" for more information.
Deleted: branches/devel-unstable/TITLE
===================================================================
--- branches/devel-unstable/TITLE 2009-01-21 17:41:29 UTC (rev 219)
+++ branches/devel-unstable/TITLE 2009-01-23 12:33:11 UTC (rev 220)
@@ -1 +0,0 @@
-adegenet: a R package for the multivariate analysis of genetic markers.
\ No newline at end of file
Deleted: branches/devel-unstable/TODO
===================================================================
--- branches/devel-unstable/TODO 2009-01-21 17:41:29 UTC (rev 219)
+++ branches/devel-unstable/TODO 2009-01-23 12:33:11 UTC (rev 220)
@@ -1,111 +0,0 @@
-#######################
-#
-# adegenet TODO list
-#
-#######################
-#
-# please list here all intended modifications
-# and all detected bugs
-#
-# please add a "-- done" or "-- fixed" tag when
-# you achieved something
-# '*' indicates stuff to do
-# 'o' indicates done stuff
-#
-# Inside a given section, priority goes decreasing.
-#
-# Delete fixed things each new release.
-#
-# T.J. 2008
-#
-######################
-
-
-
-# FOR NEXT STABLE VERSION
-=========================
-=========================
-
-# CODE ISSUES:
-==============
-o fix bug 1.2-2.01 (read.structure issue) -- fixed: was due to the default of "onerowperind" argument.
-o 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)
-o 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)
-o fix bug 1.2-2.05 (monmonier is such a pain is the ass) -- fixed, done and done (TJ)
-o !! comment the if(DEBUG) in monmonier when it is fixed -- done
-* make the package work after all changes (pass the check)
-
-
-# DOCUMENTATION ISSUES:
-=======================
-* make a tutorial for the sPCA -- done (TJ)
-* explain new changes inside the tutorial (handling of AFLP/RAPD...)
-
-
-# NEW IMPLEMENTATIONS:
-=====================
-o color plot for the sPCA results, based on RGB representation of Cavalli-Sforza -- done(TJ)
-o loadingplot for plotting loadings of one axis -- done (TJ)
-o adegenetTutorial function which opens the online tutorials -- done (TJ)
-o allow for the use of na.replace and scaleGen in spca function -- done (TJ)
-o add rupica dataset -- done (TJ)
-o enable reading data from URL (import2genind, read.[...]).
-* implement handling of presence/absence data
-* add a type argument to genind/genpop objects
-* make all the required subsequent changes in the package:
-- class definition and checks
-- constructors
-- basic methods
-- spca
-- distances
-- propShared
-- input/output
-- HWE
-- Fstat
-- old2new
-- scaleGen
-- genind2genpop
-- gstat.randtest
-- propTyped
-- hybridize
-- repool
-
-
-# TESTING:
-==========
-* test reading from url files.
-
-
-
-# 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 ? Or wait for EP to do it...
-* Implement different levels of ploidy in:
-- hybridize
-- read.structure
-- propShared
-o Permit specification of a matrix of spatial weights in spca (email A. Piotti) -- done (TJ)
-*
-
-
-# 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
-o 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.).
-
-
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