- Fix the one column matrices in dplyr::filter warning.
- Fix the error when dplyr::select couldn't find the column STRATA.
- Open the
parallel.core
argument for some internal functions to help windows users with parallel processing problems in R. #188 - Work around for
.DynamicClusterCall
pushed greavess #189
- Fix issue #188 related to coverage in DArT 1row and 2rows format
- works with R 4.3.4
- Fix issue #186 related some particular DArT files
- Fix issue #187 related to sexy_markers and VCF files
- works with R 4.3.3
- Updated DArT code that use COUNT files to check more for problematic markers usually stemming from merged projects
- Bug fix using coverage and DArT data
- Bug fix stemming from genalex files and genind conversion
- Several bug fix while reading VCF from ipyrad
- Additional checks during DArT file reading.
- Bug fix with
pcadapt
,bayescan
,genlight
output thanks to @jcaccavo. Confusion betweenPOP_ID
andSTRATA
remained for some less used functions while the migration towardsSTRATA
only inside radiator.
- huge work on
filter_ma
that now incorporate Minor Allele Frequency (MAF), Minor Allele Count (MAC) and Minor Allele Depth (MAD).
- bug fix when using some tidy function from GDS, the connection was not closing properly
- work on genind, genlight, genepop, hierfstat, arlequin functions
- updated the vignette
- bug fix with reading VCF, the new update works with SeqArray (>= 1.36.0)
- work on Tidy VCF.
- bug fix when using arlequin output file
- bug fix using DArT data
- bug fix when using genepop file and
genomic_converter
- bug fix in
genomic_converter
when using genlight as input and PLINK as output file - More GATK VCF problems detections and warnings
- updated to work with R 4.1.0
- bug fix with some format during conversion when necessary genotype format wasn't found
- more safe results when importing VCF files with windows and parallel processing
- bug fix using plink files and future
- continue to test future backend and carrier
- bug fix when using microsatellites as input and some specific output format
- No longer using Travis CI and AppVeyor to test the package
- R-CMD-check: now using GitHub actions and rhub that test on the 3 OS.
- Taking advantage of future, furrr and carrier packages
- PLINK files: fix a couple of bugs reading the tped
- removed
tidyr::gather
andtidyr::spread
dependencies (they are deprecated) - DArT data in 1-row format was not working properly with latest
data.table
melt function. Changed totidyr::pivot_long
.
- updated radiator so that it work with latest release of SeqArray (v.1.28.1), that introduced breaking changes.
fineRADstructure
rules have changed, I'm no longer doing gymnastic to make the population work withgenomic_converter
orwrite_fineradstructure
, it's not up to the user to make sure the pop id starts with a letter. Some codes might now be broken because of this.
read_plink
andtidy_plink
: new rules to get the best out of PLINK tped and bed files.
detect_microsatellites
: new radiator function that detect microsatellites using GMATA.
- 2 new output formats:
genepopedit
andrubias
- 1 new detect function:
detect_paralogs
that copy the method described in McKinney et al. 2017. This function is the logical step to make available for users afterdetect_mixed_genomes
,filter_hwe
andsexy_markers
. sexy_markers
: couple of bug fixed. More testing with the different genomic format.
- There is still documentation and vignette to fix, but this is the release that will be submitted to CRAN
- Major
SeqArray
andGDS
integration - Imputation module was removed from
radiator
and now lives exclusively in packagegrur
filter_dart
is deprecated. Please usefilter_rad
, the ONE function to rule them all;)- Worked on travis
- pkgdown website
- vignettes
- better function doc
snp.ld
: using missing data now works by chromosome/scaffold.
tidy_vcf
,tidy_genomic_data
andgenomic_converter
: works better with ipyrad vcf's
tidy_vcf
,tidy_genomic_data
andgenomic_converter
: works better with freebayes and stacks vcf
tidy_vcf
,tidy_genomic_data
andgenomic_converter
: work without strata/pop groupingsnp_ld
: new argumentld.threshold
for long.distance linkage disequilibrium.write_vcf
: will now output ID as LOCUS_COL or LOCUS_(POS-1) if COL info is not provided.
tidy_vcf
,tidy_genomic_data
andgenomic_converter
: way faster with huge VCFtidy_vcf
andwrite_seqarray
: work better with vcf generated by Stackswrite_ldna
: new function that generates a LDna input file from a tidy data frame.
tidy_vcf
,tidy_genomic_data
andgenomic_converter
: way faster with huge VCFwrite_fineradstructure
: fix bug when data was from DArT
genomic_converter
,tidy_genomic_data
: bug fix when individuals are integersfis_summary
: arguments updated
filter_dart
andfilter_rad
: can now opt out of HWE filtering.filter_hwe
: user can opt to see figures but skip filtering
- working to make radiator work correctly with ggplot2 v.3.0.0
- radiator ready for R 3.5.1 "Feather Spray" released on 2018/07/05
- transferred
write_gsi_sim
from assigner to radiator - 2
write
functions:write_snprelate
andwrite_seqarray
- when individuals in strata file/object and data don't match, an error is generated
- to reduce
radiator
dependencies, several packages were moved in the Suggests field. filter_dart
: lots of new stuff. More appropriate filter arguments:filter.coverage
is deprecated in favour of: filter.markers.coveragefilter.ind.missing.geno
is deprecated in favour of:filter.markers.missing
erase.genotypes
: new argument tailored to handle coverage for DArT counts data.filter.individuals.missing
: allows to blacklist sample early in the filtering pipeline.
- New output file: stockr This output file format enables to run the data in the stockR package from Scott Fisher at CSIRO in Hobart.
- New output file: related This output file format enables to run the data in the related R package, which is essantially the R version of COANCESTRY fortran program developed by Jinliang Wang.
- New output file: fineRADstructure
- Better VCF parsing
radiator
is ready for stacks v.2 beta8- starting to re-introduce
data.table
to increase speed during melting or casting data frames
tidy_genomic_data
andgenomic_converter
: bug fix and improvements.write_snprelate
and it's associated output fromgenomic_converter
is no longer available because of difficulties students are having in installing the package, it's dependencies and/or using the output. The code remains available here, without support.radiator::snp.ld
: the module insidetidy_genomic_data
andgenomic_converter
to minimize short linkage disequilibrium as a new optionsnp.ld = "middle"
. For locus with > 2 SNPs/read the option allows to select at random one SNP between the first and the last SNP on the read. If the locus as <= 2 SNPs on the read, the first one is selected. Note that for that last option, the numbers are reported. Thanks to Ido Bar for the idea.
tidy_dart
andfilter_dart
:- big overhaul.
- importing 1 and 2 row genotypes (called sometimes binary format) is easier
and no longer require to prep the DArT file
(the function parse DArT data with
*
at the beginning of certain lines). - filtering is easier and now interactive for those who want.
- plots are generated automatically.
tidy_genomic_data
andgenomic_converter
can now accept DArT data directly.- several typos where fix. Thanks to @IdoBar for this.
- new function:
run_bayescan
to run BayeScan ... with radiator - new separate
write
functions also included ingenomic_converter
:write_bayescan
,write_pcadapt
andwrite_hzar
.
- small mod
- writting in specific folder
- writting specific plot
- Work on different functions to prep for official package launch
- First commit