version 2.2.0

ChangeLog

@@ -1,3 +1,21 @@
+Changes from Version 2.1.2 to 2.2.0 [September 06 2023]
+
+* Major modifications:
+** reimplementation of the compute.fstats function to improve memory usage and increase speed (> 1 order of magnitude).
+
+* Adding two new functions:
+** randomallele.pca to perform PCA on pooldata (or countdata) objects after randomly sampling one read or count per population and SNP to make the representation unaffected by differences in pool (pop) sample size and/or read coverage (or Pool-Seq data).
+** pooldata2diyabc to convert a pooldata object into DIYABC genotype data file
+
+* Other modifications
+** adding computation of pairwise-population divergence (1-Q2) in compute.fstats
+** adding option return.F2.blockjackknife.samples in compute.fstats to export estimates of all pairwise F2 for each block-jackknife blocks. The obtained array is compatible with functions from the admixtools2 package
+** adding option output.pairwise.fst and output.pairwise.div to the compute.fstats function
+** reimplementation of the compute.F4ratio function to estimate F4 ratio from F2 and F2 block-jackknife samples (rather than F4)
+** fixing minor bug in vcf2pooldata to allow proper parsing of vcf generated with snpEff
+** correction of roxygen issue
+** update and editing of the vignette
+
 Changes from Version 2.1.1 to 2.1.2 [March 22 2023]
 
 * Fixing a bug in the pooldata2genobaypass and pooldata2genoselestim export function (the last subset is now printed when using thinning option)

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: poolfstat
 Maintainer: Mathieu Gautier <mathieu.gautier@inrae.fr>
 Author: Mathieu Gautier
-Version: 2.1.2
+Version: 2.2.0
 License: GPL (>= 2)
 Title: Computing f-Statistics and Building Admixture Graphs Based on
         Allele Count or Pool-Seq Read Count Data
@@ -12,8 +12,8 @@ Imports: Rcpp (>= 1.0.5), methods, data.table, utils, foreach,
         Matrix,RcppProgress, progress, nnls
 Depends: R (>= 3.0)
 Encoding: UTF-8
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 NeedsCompilation: yes
-Packaged: 2023-03-22 21:34:52 UTC; mathieu
+Packaged: 2023-09-06 15:12:50 UTC; mathieu
 Repository: CRAN
-Date/Publication: 2023-03-22 22:00:02 UTC
+Date/Publication: 2023-09-06 15:50:06 UTC

MD5

@@ -1,21 +1,21 @@
-15c16991b32edb45d348f678f4cc7817 *ChangeLog
-c72cb2ecc047c30e983ac2e0be2e6ac5 *DESCRIPTION
-3cc7968c037f63f90e481ee844401c80 *NAMESPACE
-02a0b04d9000854bce9ed55a9d813e39 *R/RcppExports.R
+0355fb21152ebebe0f4e8122cb5654e2 *ChangeLog
+44a400eda75a5e086caffd7631d2e0d9 *DESCRIPTION
+7f18daa8cbfc51a6c896a76fc057bd1a *NAMESPACE
+8d161664ab924629c5ae1094f937457f *R/RcppExports.R
 390f18fc42264d0f64bd94689cea4fea *R/add.leaf.R
 00299ca719357b9bfe0b190ce2e7093f *R/compare.fitted.fstats.R
-1651ed92d92e9f824944e982ab7adab1 *R/compute.F4ratio.R
-ef60c35697799aa6b9118ecf1a092212 *R/compute.fstats.R
-3df31db9d7b29d6904494e1a47afa672 *R/compute.pairwiseFST.R
+9c963be859c957058dcecb48b9e4b55d *R/compute.F4ratio.R
+34cc0bd57521116bf2ead5720bb0e7e1 *R/compute.fstats.R
+9fea490dd799112ef61bfeb14285d881 *R/compute.pairwiseFST.R
 23084d4b33486264bc80968eca535a85 *R/computeFST.R
 cd3a59851df8be0e7313410ca346c368 *R/countdata.subset.R
 21a24978fb7b5c8add9bed5fe2258574 *R/find.tree.popset.R
 ab41df2aaeae763897da026cbd5dd3ae *R/fit.graph.R
 87676f2cbe83e9fca809d3b81e48df0f *R/generate.graph.params.R
-1d74b12d4995398c8c957bbc776a1dc0 *R/generate.jacknife.blocks.R
-5f4a018fc1200ae95c7b6497e1dddadd *R/genobaypass2countdata.R
-33f9a94621bce23459403c4211f62aa4 *R/genobaypass2pooldata.R
-435b2f3b44a076501ebbf3f6ace41219 *R/genoselestim2pooldata.R
+90ac9dbba7f8b4d015a14b1f6ef518cf *R/generate.jacknife.blocks.R
+11f12c83682639173230b21bb8acd60d *R/genobaypass2countdata.R
+0677565d444de7d2ecb5b87765bccf35 *R/genobaypass2pooldata.R
+38afef0454229b3bd49e06d9e7b325a8 *R/genoselestim2pooldata.R
 f42a318247a5d7ccab9f8f8e83b4dd72 *R/genotreemix2countdata.R
 8a9c589604d79be9047b40ca80beb548 *R/graph.builder.R
 9824087879343fbbd2518b69c96e71a0 *R/graph.params2qpGraphFiles.R
@@ -25,31 +25,43 @@ f0a6815409dd92ba79c7a4e8ce05e640 *R/is.countdata.R
 7ea54d0db958a5c8c1b9dd6039ee678f *R/is.graph.params.R
 cd68d07429c34755376e9054ae8139c6 *R/is.pooldata.R
 8000f74e582416e7d7f8fc255330c6b5 *R/make.example.files.R
-724926a75d85a2bcab3ef28c11cbb6dc *R/out.objects.R
-1c955e259a43a5ab97d2dbc5c64a9aed *R/plot_fstats.R
+db87c82d1b745684bc086f4f5ac697c1 *R/out.objects.R
+f128df41bd042d119c1c0c445dad91bf *R/plot_fstats.R
 b95d25203844369c629325a138ce9b9f *R/pooldata.subset.R
+b4a4c1f95b79bc049c244a5d59ed6f46 *R/pooldata2diyabc.R
 acb2d54024c3ae13a21f7dfbe66bb3e6 *R/pooldata2genobaypass.R
 a15f9a418c018ced67144a5a3381ba71 *R/pooldata2genoselestim.R
-711f58f8b20ac27f39e57b114d7afe7e *R/poolfstat-package.R
+c105c00f06a09c638779c5f52909c144 *R/poolfstat-package.R
 44696321fe117359bf7e8a35ea76c24a *R/popsync2pooldata.R
+5b8d6d719b310fc2b014e74884ddf006 *R/randomallele.pca.R
 92bcc870506baca09da03b8d85f6459c *R/rooted.njtree.builder.R
-24f8150ef989263e3642f6d3ba85d68a *R/vcf2pooldata.R
+98dc0fdf37b362d098f3cd8f208938d0 *R/vcf2pooldata.R
 7760efc66b868ab15b24e9d572a4c3df *build/vignette.rds
 03affc875f6055d45e7eb0d233d45c33 *inst/CITATION
 fbabf191da0f6c0565583ceff32fbf8a *inst/doc/vignette.Rnw
-caf2ee4631190ba68d58ba606fe765f0 *inst/doc/vignette.pdf
+5264b8aa648313fcdca2c7d908a4bb87 *inst/doc/vignette.pdf
 639adddc62b922fde532126ca2f32d1c *inst/ex.sync.gz
 8ff7d9f354e64f5b79c583986c9cb7e0 *inst/ex.vcf.gz
 6f7933a26daebef7b718dab5ef9401e5 *man/add.leaf.Rd
+d26ece24a762a2512780054d029536c7 *man/bjack_cov.Rd
 008322c6fe4e9aa8ad53e18b188bc4b3 *man/compare.fitted.fstats.Rd
-60d89cab56fcd0432894970e16b31b94 *man/compute.f4ratio.Rd
-16149270ae39fb4e796406245e1fba5e *man/compute.fstats.Rd
+fb5a3aac926b7395c3d6f43776e83bcf *man/compute.f4ratio.Rd
+2f85fc8b53c02d95903079b31d160b86 *man/compute.fstats.Rd
 92e6f82623daa6d3954af4d2804b0fcf *man/compute.pairwiseFST.Rd
 f508d39fe942f7923ce42d2db9772dea *man/computeFST.Rd
 47af21b635b13c3b3d0545d2c4655b70 *man/compute_Ddenom.Rd
 35a2fb5c2de8034b5625d07a245141bd *man/compute_Ddenom_bjmeans.Rd
 2bc262fbb77aa37cfe2255671b531ce0 *man/compute_F2_bjmeans.Rd
+1010bb16a929dd662b3d6d578213a6c2 *man/compute_F3fromF2.Rd
+347da20bf2f34e3133878122d8f6de91 *man/compute_F3fromF2samples.Rd
+959f76b173dc3e2f6dac4d462f0ce1e4 *man/compute_F4DfromF2samples.Rd
+453c703f08610ec638fbec63281330ff *man/compute_F4fromF2.Rd
+ab1eaa8d06150113ff07e6ea5cc2e0c2 *man/compute_F4fromF2samples.Rd
+0718f26c8a64aed49d31c8f73b674127 *man/compute_H1.Rd
+68aefba9733f7658928c9d120c541207 *man/compute_Q2.Rd
 383a1385a3e345a46c7765d85d3fd7d8 *man/compute_Q_bjmeans.Rd
+d7006f555fc7a30be9b1f0a5c6e2d01f *man/compute_QmatfromF2samples.Rd
+db0783f93a44e6c727a860e98299a836 *man/compute_blockDdenom.Rd
 c380161324d63b215fe7465193d1453b *man/countdata-class.Rd
 68e36a76380b0ce02c898293fa77518e *man/countdata.subset.Rd
 a7375a8fb9a682018a9300ac47e424c8 *man/extract_allele_names.Rd
@@ -59,12 +71,14 @@ ba9583ae7792d178f0ae101d05556063 *man/extract_vscan_counts.Rd
 da26e6ea66a17acb65574956ec34e661 *man/find_indelneighbor_idx.Rd
 44bfbb64633532def42a2e8b90be3eca *man/fit.graph.Rd
 85d968f26248329157ee2129fa3d5de8 *man/fitted.graph-class.Rd
-ee048684c529fb5d07c1277aa16eb5cd *man/fstats-class.Rd
+9d4b2d1e802b16ecb00d0dace1fef97c *man/fstats-class.Rd
 6739ef7c8af6e4ba843fdd2a28516256 *man/generate.graph.params.Rd
-c26148e19a122715ba97ad7b1a6e0bd0 *man/generate.jackknife.blocks.Rd
-678e1ab5a9716a5cf26521dec9d61a81 *man/genobaypass2countdata.Rd
-777b35ece89327c13d556cf422572f54 *man/genobaypass2pooldata.Rd
-0be9738a28c402de9ff920429a98a5b8 *man/genoselestim2pooldata.Rd
+4900d6405dca75fc1ddfe0d3f9820b34 *man/generate.jackknife.blocks.Rd
+e2c3431a1cd0960c067fba2f13189ff4 *man/generateF3names.Rd
+b13335b982a376e82bef892708bc88a2 *man/generateF4names.Rd
+0b87b569f963fb2b5e369850111af59d *man/genobaypass2countdata.Rd
+3e9f02789cac988a74f2efa64c1123bd *man/genobaypass2pooldata.Rd
+a1659663f83893bd31a2e9bb01b41514 *man/genoselestim2pooldata.Rd
 b581ea2ece8f1c594c908420fe6a9891 *man/genotreemix2countdata.Rd
 91310b852a1de6bb7e28b6625bfb2d07 *man/graph.builder.Rd
 40064bb6251107900beeff241e22ccf6 *man/graph.params-class.Rd
@@ -83,13 +97,16 @@ e4372d1ff8736981bee5ff5237bdd9b2 *man/plot-fitted.graph-method.Rd
 d4d082e53b5c664023b82ec03c08382c *man/plot-fstats-method.Rd
 37b4396e889caab9039c407750880fbf *man/plot-graph.params-method.Rd
 58796cac41f7147c8ada386170c2b206 *man/plot-pairwisefst-method.Rd
-4d2b0d0a9edf9fb095368aba97fe6e3a *man/plot_fstats.Rd
+05e291428efb143ffdfa841a048b3c83 *man/plot_fstats.Rd
 0ddd0a718feef78113473bd22d981203 *man/pooldata-class.Rd
 a87528739a7f077195c6b1cedc9de3a1 *man/pooldata.subset.Rd
+d1b2b033e5c585758393bdfa601a5861 *man/pooldata2diyabc.Rd
 03e3828b0391a7ecf281db14c79f00db *man/pooldata2genobaypass.Rd
 d89d39af626cc98933a1771dfc2fc769 *man/pooldata2genoselestim.Rd
-dac6e2d8cae65c97098a56cb6a1c299e *man/poolfstat.Rd
+f028369b799e588489b17da502795653 *man/poolfstat.Rd
+3f069f9f5957c9af9491b7c579688853 *man/poppair_idx.Rd
 3a9465eb3fa84397ef1aba7560c91b90 *man/popsync2pooldata.Rd
+f93c7b60bad695dd200dc9a503c064de *man/randomallele.pca.Rd
 8b4874f9041aa31c6e42cd577e63961c *man/rooted.njtree.builder.Rd
 5ec016849a3a6a76ef29704b8f2c0a65 *man/scan_allele_info.Rd
 cce2a9d822628109323e7ad163e3a4c2 *man/show-countdata-method.Rd
@@ -99,8 +116,8 @@ ea884c9a26c9391de77bd547f15d740c *man/show-fitted.graph-method.Rd
 dc44a0c721e8f8bfa3e2462d3f7df421 *man/show-pairwisefst-method.Rd
 38cba55d34edb3d10535316a049d557e *man/show-pooldata-method.Rd
 bcb6172e4918ab4e33eb79bfab2038e6 *man/vcf2pooldata.Rd
-7a88cfe27904af971396c318e0cf1cff *src/RcppExports.cpp
+fadcb4f06c5f67679b5fe33529a9dce1 *src/RcppExports.cpp
 4bb1027b38fba90878bbd0008bfa46b5 *src/extract_counts.cpp
-73170f36bc30ccb043e7915262db5ac1 *src/fast_block_averages.cpp
-e0e392ff82f5f62a4732fcbb6b73f65c *vignettes/poolfstat_vignette_6pops.pdf
+ecefb2aac8222522f817553ab8dac98d *src/fast_block_averages.cpp
+8656e03cb79112c08c9f5394f2e59e50 *vignettes/poolfstat_vignette_6pops.pdf
 fbabf191da0f6c0565583ceff32fbf8a *vignettes/vignette.Rnw

NAMESPACE

@@ -3,11 +3,22 @@
 export(.compute_Ddenom)
 export(.compute_Ddenom_bjmeans)
 export(.compute_F2_bjmeans)
+export(.compute_F3fromF2)
+export(.compute_F3fromF2samples)
+export(.compute_F4DfromF2samples)
+export(.compute_F4fromF2)
+export(.compute_F4fromF2samples)
+export(.compute_H1)
+export(.compute_Q2)
 export(.compute_Q_bjmeans)
+export(.compute_QmatfromF2samples)
+export(.compute_blockDdenom)
 export(.extract_allele_names)
 export(.extract_nonvscan_counts)
 export(.extract_vscan_counts)
 export(.find_indelneighbor_idx)
+export(.generateF3names)
+export(.generateF4names)
 export(.scan_allele_info)
 export(add.leaf)
 export(compare.fitted.fstats)
@@ -19,6 +30,7 @@ export(countdata.subset)
 export(find.tree.popset)
 export(fit.graph)
 export(generate.graph.params)
+export(generate.jackknife.blocks)
 export(genobaypass2countdata)
 export(genobaypass2pooldata)
 export(genoselestim2pooldata)
@@ -35,9 +47,11 @@ export(is.pooldata)
 export(make.example.files)
 export(plot_fstats)
 export(pooldata.subset)
+export(pooldata2diyabc)
 export(pooldata2genobaypass)
 export(pooldata2genoselestim)
 export(popsync2pooldata)
+export(randomallele.pca)
 export(rooted.njtree.builder)
 export(vcf2pooldata)
 exportClasses(countdata)
@@ -84,6 +98,7 @@ importFrom(stats,optim)
 importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,reorder)
+importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(utils,combn)
 importFrom(utils,read.table)