NEWS.md

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

radiator 1.3.2 2024-04-30

• works with R 4.3.4
• Fix issue #186 related some particular DArT files
• Fix issue #187 related to sexy_markers and VCF files

radiator 1.3.1 2024-04-24

• works with R 4.3.3
• Updated DArT code that use COUNT files to check more for problematic markers usually stemming from merged projects

radiator 1.3.0 2024-02-22

• Bug fix using coverage and DArT data

radiator 1.2.9 2024-01-25

• Bug fix stemming from genalex files and genind conversion

radiator 1.2.8 2023-04-03

• Several bug fix while reading VCF from ipyrad

radiator 1.2.7 2023-03-20

• Additional checks during DArT file reading.

radiator 1.2.6 2023-03-13

• Bug fix with pcadapt, bayescan, genlight output thanks to @jcaccavo. Confusion between POP_ID and STRATA remained for some less used functions while the migration towards STRATA only inside radiator.

radiator 1.2.5 2023-01-20

• huge work on filter_ma that now incorporate Minor Allele Frequency (MAF), Minor Allele Count (MAC) and Minor Allele Depth (MAD).

radiator 1.2.4 2022-11-17

• 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

radiator 1.2.3 2022-10-30

• bug fix with reading VCF, the new update works with SeqArray (>= 1.36.0)
• work on Tidy VCF.

radiator 1.2.2 2021-12-20

• bug fix when using arlequin output file
• bug fix using DArT data

radiator 1.2.1 2021-10-28

• 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

radiator 1.2.0 2021-06-16

• 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

radiator 1.1.9 2020-12-14

• 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

radiator 1.1.8 2020-10-17

• 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

radiator 1.1.7 2020-08-21

• PLINK files: fix a couple of bugs reading the tped
• removed tidyr::gather and tidyr::spread dependencies (they are deprecated)
• DArT data in 1-row format was not working properly with latest data.table melt function. Changed to tidyr::pivot_long.

radiator 1.1.6 2020-06-23

• updated radiator so that it work with latest release of SeqArray (v.1.28.1), that introduced breaking changes.

radiator 1.1.5 2020-03-07

• fineRADstructure rules have changed, I'm no longer doing gymnastic to make the population work with genomic_converter or write_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.

radiator 1.1.4 2020-02-04

• read_plink and tidy_plink: new rules to get the best out of PLINK tped and bed files.

radiator 1.1.3 2020-01-21

• detect_microsatellites: new radiator function that detect microsatellites using GMATA.

radiator 1.1.0 2019-05-31

• 2 new output formats: genepopedit and rubias
• 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 after detect_mixed_genomes, filter_hwe and sexy_markers.
• sexy_markers: couple of bug fixed. More testing with the different genomic format.

radiator 1.0.0 2019-05-01

• There is still documentation and vignette to fix, but this is the release that will be submitted to CRAN
• Major SeqArray and GDS integration
• Imputation module was removed from radiator and now lives exclusively in package grur
• filter_dart is deprecated. Please use filter_rad, the ONE function to rule them all;)
• Worked on travis
• pkgdown website
• vignettes
• better function doc

radiator 0.0.21 2018-11-14

• snp.ld: using missing data now works by chromosome/scaffold.

radiator 0.0.20 2018-11-12

• tidy_vcf, tidy_genomic_data and genomic_converter: works better with ipyrad vcf's

radiator 0.0.19 2018-11-07

• tidy_vcf, tidy_genomic_data and genomic_converter: works better with freebayes and stacks vcf

radiator 0.0.18 2018-10-23

• tidy_vcf, tidy_genomic_data and genomic_converter: work without strata/pop grouping
• snp_ld: new argument ld.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.

radiator 0.0.17 2018-10-04

• tidy_vcf, tidy_genomic_data and genomic_converter: way faster with huge VCF
• tidy_vcf and write_seqarray: work better with vcf generated by Stacks
• write_ldna: new function that generates a LDna input file from a tidy data frame.

radiator 0.0.16 2018-09-04

• tidy_vcf, tidy_genomic_data and genomic_converter: way faster with huge VCF
• write_fineradstructure: fix bug when data was from DArT

radiator 0.0.15 2018-08-17

• genomic_converter, tidy_genomic_data: bug fix when individuals are integers
• fis_summary: arguments updated

radiator 0.0.14 2018-08-04

• filter_dart and filter_rad: can now opt out of HWE filtering.
• filter_hwe: user can opt to see figures but skip filtering

radiator 0.0.13 2018-07-09

• 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

radiator 0.0.12 2018-06-21

• transferred write_gsi_sim from assigner to radiator
• 2 write functions: write_snprelate and write_seqarray

radiator 0.0.11 2018-04-26

• 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.coverage
  • filter.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.

radiator 0.0.10 2018-03-06

• New output file: stockr This output file format enables to run the data in the stockR package from Scott Fisher at CSIRO in Hobart.

radiator 0.0.9 2018-03-01

• 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.

radiator 0.0.8 2018-02-08

• New output file: fineRADstructure

radiator 0.0.7 2018-02-06

• 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

radiator 0.0.6 2017-10-02

• tidy_genomic_data and genomic_converter: bug fix and improvements.
• write_snprelate and it's associated output from genomic_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 inside tidy_genomic_data and genomic_converter to minimize short linkage disequilibrium as a new option snp.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.

radiator 0.0.5 2017-09-20

• tidy_dart and filter_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 and genomic_converter can now accept DArT data directly.
• several typos where fix. Thanks to @IdoBar for this.

radiator 0.0.4 2017-09-07

• new function: run_bayescan to run BayeScan ... with radiator
• new separate write functions also included in genomic_converter: write_bayescan, write_pcadapt and write_hzar.

radiator 0.0.3 2017-07-18

• small mod
• writting in specific folder
• writting specific plot

radiator 0.0.2 2017-07-15

• Work on different functions to prep for official package launch

radiator 0.0.1 2017-06-18

• First commit

thierrygosselin/radiator documentation built on May 5, 2024, 5:12 a.m.