version 3.1.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rehh
 Maintainer: Alexander Klassmann <[email protected]>
 Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
-Version: 3.1.1
+Version: 3.1.2
 License: GPL (>= 2)
 Title: Searching for Footprints of Selection using 'Extended Haplotype
         Homozygosity' Based Tests
@@ -22,15 +22,19 @@ Description: Population genetic data such as 'Single Nucleotide
         visualization and interpretation of these statistics. 
         Due to changes in the API, albeit mostly minor, 
         versions 3.X are not compatible with versions 2.0.X.
+        Note: optionally, vcf files can be imported using package vcfR. That package
+        is currently removed from CRAN, but can still be installed from 
+        <https://github.com/knausb/vcfR> following instructions there.
 Depends: R (>= 2.10)
 Imports: methods, rehh.data
-Suggests: ape, bookdown, gap, knitr, qqman, rmarkdown, testthat, vcfR
+Suggests: ape, bookdown, data.table, gap, knitr, qqman, rmarkdown,
+        R.utils, testthat, vcfR
 VignetteBuilder: knitr
 NeedsCompilation: yes
-Packaged: 2020-06-19 09:14:17 UTC; alex
+Packaged: 2020-07-17 09:16:17 UTC; alex
 RoxygenNote: 7.1.0
 URL: https://CRAN.R-project.org/package=rehh,
         https://gitlab.com/oneoverx/rehh
 BugReports: https://gitlab.com/oneoverx/rehh/issues
 Repository: CRAN
-Date/Publication: 2020-06-19 10:00:02 UTC
+Date/Publication: 2020-07-17 10:30:03 UTC

MD5

@@ -1,6 +1,6 @@
-216ebef7dd3ed6d5d2f97e941d2cedba *DESCRIPTION
+4be95bfe5393b4ad0d988f9076587813 *DESCRIPTION
 479cda305f23caf8bd3f42caa2013c3e *NAMESPACE
-5a7c1e7859161a14aaab006e8eda8a47 *NEWS.md
+c3bdce8419097ef74d75dedfadbb2264 *NEWS.md
 d778a01442f62a331f42f43636d35c9a *R/as.newick.R
 791804c313fb1e1bc68e7c5b95ecc92d *R/calc_candidate_regions.R
 f64accc80d3c07213985e6eebd0969a7 *R/calc_ehh.R
@@ -9,7 +9,7 @@ adf2e4d9478c23d89b6a1f64cbb8e645 *R/calc_ehhs.R
 8652c8e385335d536e351d10ccba7767 *R/calc_haplen.R
 647a736449be2f7cb9ef08fc31691ad5 *R/calc_pairwise_haplen.R
 c0a7134ed354a1cc6e2d92cff7cb528b *R/calc_region_stats.R
-a1fb5440c3d353c9e0554d490fbe54d1 *R/data2haplohh.R
+aebc3fea50b8605b1d1aa3aaf21776bd *R/data2haplohh.R
 3caea4a19997c6f248290697f797b4a1 *R/distribplot.R
 ef5e101f1c8c4891d5991bf2fd0257b4 *R/extract_regions.R
 e5d4611c5eeb4e3f839683a3f665e214 *R/freqbinplot.R
@@ -30,16 +30,16 @@ e232bea3e5d1d83fdf560f24d01deb18 *R/scan_hh.R
 f31185006802c7467a9f6a8cc8c92fa8 *R/scan_hh_full.R
 d857d3be60093cc3900f1d221fd867fc *R/subset.haplohh.R
 9d53dfc94e3a08334b06091ab986217d *R/update_haplohh.R
-6b171b4a301acf569ba0e769e9d5a6c1 *build/vignette.rds
+8228a460ed62d771a05ec3e1e9a7cb59 *build/vignette.rds
 bbd50c8eb813216188dce7896d1490d3 *data/datalist
 91be48fb8754c805321891b9374459f3 *data/haplohh_cgu_bta12.RData
 8439f1531106aeabce40b21067a1ac5e *inst/CITATION
-0ee64a467d5c93db7b2be307e11f26e2 *inst/doc/examples.R
-b95272364cd9cf5b1878029bfd9806d9 *inst/doc/examples.Rmd
-a41208e8dab335f4f130ff7f93c36771 *inst/doc/examples.html
-ed76eaeccd8abfc4252be98087ee5fee *inst/doc/rehh.R
-b90310876f11661123cfb49c34426dd3 *inst/doc/rehh.Rmd
-2fb6867007e600d51503ee8943843580 *inst/doc/rehh.html
+ae04d6c09732f0e29be34d966896d3d4 *inst/doc/examples.R
+347ed7fd5246ab0a51b07eb65c551f51 *inst/doc/examples.Rmd
+a66b153a90d0c7ba1cfc0e6d7d993e13 *inst/doc/examples.html
+0aca4270ed980c2b91db059f72ce8512 *inst/doc/rehh.R
+0cb9f06cbea7141d8522641178da4b54 *inst/doc/rehh.Rmd
+4c42ce24a6e5e3c0f331df7518413c4d *inst/doc/rehh.html
 529c33971c081bacc8d00072aac22b20 *inst/extdata/bta12_cgu.vcf.gz
 1a13676197023c7796532d96aeff7f76 *inst/extdata/example1.hap
 98aedc74c294ec4769b8e3272200fbbe *inst/extdata/example1.map
@@ -57,7 +57,7 @@ c933fc808090cbc1cade18247471df48 *man/calc_furcation.Rd
 12a719a71c961a21e8de7f5146ac1dc2 *man/calc_haplen.Rd
 36e5218744298abe44f67dbfb6d4c599 *man/calc_pairwise_haplen.Rd
 2acaa7c3c89fcb46f3c7e4f370160986 *man/calc_region_stats.Rd
-db9874cb4175160771d2cd213a308712 *man/data2haplohh.Rd
+aae72c0cb9f1bffb913dd8b13d534125 *man/data2haplohh.Rd
 de43ae62050ec49c91c44138fe93b67c *man/distribplot.Rd
 d557df62cd52e701005da0a5f0d8ec7c *man/extract_regions.Rd
 17a00bb024774a6d4ef9491306f79872 *man/freqbinplot.Rd
@@ -76,7 +76,7 @@ b240d6b987257834ba5e9815aadfc537 *man/haplohh_cgu_bta12.Rd
 c7933322276a4b8fa37433e050766c4d *man/plot.furcation.Rd
 939fa1dcc75eacda1eef877ee99c9e7b *man/plot.haplen.Rd
 cd8682e4686cbe6130490e25a8e79301 *man/plot.haplohh.Rd
-2b1b8920146f7bbc54396addf3f03879 *man/rehh-package.Rd
+9d5eba020ec22ee48ef012d9f1a54d70 *man/rehh-package.Rd
 0b3af48394811f7b7e481ca6fd7c63fd *man/remove.example.files.Rd
 a67e3e8c460d7f55dde5243edf351c6c *man/scan_hh.Rd
 9894dd029348f74ae46e2fb658289e24 *man/scan_hh_full.Rd
@@ -121,14 +121,14 @@ d10abdbe610dee90be8e7c6a1baf28da *tests/testthat/furcation_F1205400.newick
 7f87b223f6153b8926956609ba293241 *tests/testthat/setup.R
 a177583dabfe62a659b2d0ff4e5829d8 *tests/testthat/teardown.R
 0f2d4d7ffafcef03cde572357aa3508e *tests/testthat/test_calc_candidate_regions.R
-d1aafcac0ed921cf02f6d7eba43eba30 *tests/testthat/test_data2haplohh.R
-82366eb2c263bc212b2b92f4cadeff53 *tests/testthat/test_error_messages.R
+b333feb96e38279b41a60f9fcb93dd65 *tests/testthat/test_data2haplohh.R
+a57d331f176ddaa7e7a19fb056cd2626 *tests/testthat/test_error_messages.R
 3c553b425c68132fe5a74a06fc85d3e4 *tests/testthat/test_examples.R
 6adc3c44917659c38b0adddbbf254f18 *tests/testthat/test_furcation.R
 83461c197932114fbb6185821cdae353 *tests/testthat/test_ihh2ihs.R
 09bd1fc643230fc24c90aac2c2d2f035 *tests/testthat/test_scan_full.R
-92ec3d02dd0aaf89127226ec51e4b0c7 *tests/testthat/test_scan_hh.R
-b95272364cd9cf5b1878029bfd9806d9 *vignettes/examples.Rmd
+06e74a8f326b2099d3ef7b77c1664a89 *tests/testthat/test_scan_hh.R
+347ed7fd5246ab0a51b07eb65c551f51 *vignettes/examples.Rmd
 80ac2e78110aa3e54fb5ce824bd5574f *vignettes/genetics.csl
-b90310876f11661123cfb49c34426dd3 *vignettes/rehh.Rmd
+0cb9f06cbea7141d8522641178da4b54 *vignettes/rehh.Rmd
 0ae5b0965175c9ae6cbc11dd9bf5adc5 *vignettes/vignette.bib

NEWS.md

@@ -1,3 +1,7 @@
+### rehh 3.1.2 (July 17, 2020)
+
+* added option to parse vcf files using package 'data.table' in order to avoid reliance on package 'vcfR' which is currently removed from CRAN (but still available on github: https://github.com/knausb/vcfR)
+
 ### rehh 3.1.1 (June 19, 2020)
 
 * option to use stepwise continuous EHH(S) curves for integration and plotting