From 899436d5ad79bc00a6abf65939907a6347c42522 Mon Sep 17 00:00:00 2001 From: Thierry Gosselin Date: Tue, 23 Apr 2024 18:06:53 -0400 Subject: [PATCH] # radiator 1.3.1 2024-04-23 * Updated DArT code that use COUNT files to check more for problematic markers usually stemming from merged project --- DESCRIPTION | 4 ++-- NEWS.md | 5 +++++ R/dart.R | 10 +++++----- README.md | 4 ++-- docs/404.html | 2 +- docs/LICENSE.html | 2 +- docs/articles/get_started.html | 4 ++-- docs/articles/index.html | 2 +- docs/articles/life_cycle.html | 4 ++-- docs/articles/rad_genomics_computer_setup.html | 10 +++++----- docs/authors.html | 2 +- docs/index.html | 8 ++++---- docs/news/index.html | 10 +++++++++- docs/pkgdown.yml | 2 +- docs/reference/Exposition_pipe_operator.html | 2 +- docs/reference/allele_count.html | 2 +- docs/reference/allele_frequencies.html | 2 +- docs/reference/assign_defaults.html | 2 +- docs/reference/bayescan_one.html | 2 +- docs/reference/betas_estimator.html | 2 +- docs/reference/blacklist_hw.html | 2 +- docs/reference/boxplot_stats.html | 2 +- docs/reference/calibrate_alleles.html | 2 +- docs/reference/change_pop_names.html | 2 +- docs/reference/check_args_class.html | 2 +- docs/reference/check_dart.html | 2 +- docs/reference/check_header_source_vcf.html | 2 +- docs/reference/check_pop_levels.html | 2 +- docs/reference/clean_dart_colnames.html | 2 +- docs/reference/clean_dart_locus.html | 2 +- docs/reference/clean_ind_names.html | 2 +- docs/reference/clean_markers_names.html | 2 +- docs/reference/clean_pop_names.html | 2 +- docs/reference/compound_assignment_pipe_operator.html | 2 +- docs/reference/compute_maf.html | 2 +- docs/reference/count_monomorphic.html | 2 +- docs/reference/dart2gds.html | 2 +- docs/reference/data_info.html | 2 +- docs/reference/detect_all_missing.html | 2 +- docs/reference/detect_allele_problems.html | 2 +- docs/reference/detect_biallelic_markers.html | 2 +- docs/reference/detect_biallelic_problems.html | 2 +- docs/reference/detect_dart_format.html | 2 +- docs/reference/detect_duplicate_genomes.html | 2 +- docs/reference/detect_genomic_format.html | 2 +- docs/reference/detect_het_outliers.html | 2 +- docs/reference/detect_microsatellites.html | 2 +- docs/reference/detect_mixed_genomes.html | 2 +- docs/reference/detect_paralogs.html | 2 +- docs/reference/detect_ref_genome.html | 2 +- docs/reference/diagnostic_maf.html | 2 +- docs/reference/distance2tibble.html | 2 +- docs/reference/distance_individuals.html | 2 +- docs/reference/erase_genotypes.html | 2 +- docs/reference/estimate_m.html | 2 +- docs/reference/extract_coverage.html | 2 +- docs/reference/extract_dart_target_id.html | 2 +- docs/reference/extract_data_source.html | 2 +- docs/reference/extract_dots.html | 2 +- docs/reference/extract_genotypes_metadata.html | 2 +- docs/reference/extract_individuals_metadata.html | 2 +- docs/reference/extract_individuals_vcf.html | 2 +- docs/reference/extract_info_vcf.html | 2 +- docs/reference/extract_markers_metadata.html | 2 +- docs/reference/filter_blacklist_genotypes.html | 2 +- docs/reference/filter_common_markers.html | 2 +- docs/reference/filter_coverage.html | 2 +- docs/reference/filter_dart_reproducibility.html | 2 +- docs/reference/filter_fis.html | 2 +- docs/reference/filter_genotyping.html | 2 +- docs/reference/filter_het.html | 2 +- docs/reference/filter_hwe.html | 2 +- docs/reference/filter_individuals.html | 2 +- docs/reference/filter_ld.html | 4 ++-- docs/reference/filter_monomorphic.html | 2 +- docs/reference/filter_rad.html | 2 +- docs/reference/filter_snp_number.html | 2 +- docs/reference/filter_snp_position_read.html | 2 +- docs/reference/filter_whitelist.html | 2 +- docs/reference/folder_prefix.html | 2 +- docs/reference/folder_short.html | 2 +- docs/reference/gds2tidy.html | 2 +- docs/reference/generate_filename.html | 2 +- docs/reference/generate_folder.html | 2 +- docs/reference/generate_geno_freq_boundaries.html | 2 +- docs/reference/generate_hzar.html | 2 +- docs/reference/generate_markers_metadata.html | 2 +- docs/reference/generate_squeleton_folders.html | 2 +- docs/reference/generate_strata.html | 2 +- docs/reference/generate_whitelist.html | 2 +- docs/reference/genome_similarity.html | 2 +- docs/reference/genomic_converter.html | 4 ++-- docs/reference/gt2array.html | 2 +- docs/reference/haplotype_reconstruction.html | 2 +- docs/reference/hwe_analysis.html | 2 +- docs/reference/ibdg_fh.html | 2 +- docs/reference/import_dart.html | 2 +- docs/reference/ind_total_reads.html | 2 +- docs/reference/index.html | 2 +- docs/reference/individuals2strata.html | 2 +- docs/reference/join_strata.html | 2 +- docs/reference/ld2df.html | 2 +- docs/reference/ld_boxplot.html | 2 +- docs/reference/ld_missing.html | 2 +- docs/reference/ld_pruning.html | 2 +- docs/reference/list_filters.html | 2 +- docs/reference/markers_genotyped_helper.html | 2 +- docs/reference/merge_dart.html | 2 +- docs/reference/message_func_call.html | 2 +- docs/reference/missing_per_pop.html | 2 +- docs/reference/n.html | 2 +- docs/reference/not_common_markers.html | 2 +- docs/reference/parallel_core_opt.html | 2 +- docs/reference/parse_gds_metadata.html | 2 +- docs/reference/pi.html | 2 +- docs/reference/pi_pop.html | 2 +- docs/reference/pi_rad.html | 2 +- docs/reference/pipe.html | 2 +- docs/reference/plot_bayescan.html | 2 +- docs/reference/plot_boxplot_coverage.html | 2 +- docs/reference/plot_boxplot_diversity.html | 2 +- docs/reference/plot_coverage_imbalance_diagnostic.html | 2 +- docs/reference/plot_density_distribution_coverage.html | 2 +- docs/reference/plot_density_distribution_het.html | 2 +- docs/reference/plot_density_distribution_maf.html | 2 +- docs/reference/plot_distribution_diversity.html | 2 +- docs/reference/plot_het_outliers.html | 2 +- docs/reference/plot_snp_number_loci.html | 2 +- docs/reference/plot_snp_position_read.html | 2 +- docs/reference/plot_upset.html | 2 +- docs/reference/private_alleles.html | 2 +- docs/reference/private_haplotypes.html | 2 +- docs/reference/radiator_common_arguments.html | 2 +- docs/reference/radiator_dots.html | 2 +- docs/reference/radiator_folder.html | 2 +- docs/reference/radiator_function_header.html | 2 +- docs/reference/radiator_gds.html | 2 +- docs/reference/radiator_gds_skeleton.html | 2 +- docs/reference/radiator_packages_dep.html | 2 +- docs/reference/radiator_parameters.html | 2 +- docs/reference/radiator_pkg_install.html | 2 +- docs/reference/radiator_question.html | 2 +- docs/reference/radiator_results_message.html | 2 +- docs/reference/radiator_snakecase.html | 2 +- docs/reference/radiator_split_tibble.html | 2 +- docs/reference/radiator_tic.html | 2 +- docs/reference/radiator_toc.html | 2 +- docs/reference/read_blacklist_genotypes.html | 2 +- docs/reference/read_blacklist_id.html | 2 +- docs/reference/read_dart.html | 2 +- docs/reference/read_plink.html | 2 +- docs/reference/read_rad.html | 2 +- docs/reference/read_strata.html | 2 +- docs/reference/read_vcf.html | 2 +- docs/reference/read_whitelist.html | 2 +- docs/reference/remove_duplicates.html | 2 +- docs/reference/replace_by_na.html | 2 +- docs/reference/reset_filters.html | 2 +- docs/reference/run_bayescan.html | 2 +- docs/reference/separate_gt.html | 2 +- docs/reference/separate_markers.html | 2 +- docs/reference/sex_markers_plot.html | 2 +- docs/reference/sexy_markers.html | 2 +- docs/reference/simulate_genos_from_posterior.html | 2 +- docs/reference/split_tibble_rows.html | 2 +- docs/reference/split_vcf.html | 2 +- docs/reference/strata_haplo.html | 2 +- docs/reference/subsampling_data.html | 2 +- docs/reference/summarise_genotypes.html | 2 +- docs/reference/summarize_sex.html | 2 +- docs/reference/summary_gds.html | 2 +- docs/reference/summary_rad.html | 2 +- docs/reference/summary_strata.html | 2 +- docs/reference/switch_allele_count.html | 2 +- docs/reference/switch_genotypes.html | 2 +- docs/reference/sync_gds.html | 2 +- docs/reference/tibble_stats.html | 2 +- docs/reference/tidy2gds.html | 2 +- docs/reference/tidy2wide.html | 2 +- docs/reference/tidy_dart_metadata.html | 2 +- docs/reference/tidy_fstat.html | 2 +- docs/reference/tidy_genepop.html | 2 +- docs/reference/tidy_genind.html | 2 +- docs/reference/tidy_genlight.html | 2 +- docs/reference/tidy_genomic_data.html | 2 +- docs/reference/tidy_gtypes.html | 2 +- docs/reference/tidy_plink.html | 2 +- docs/reference/tidy_vcf.html | 2 +- docs/reference/tidy_wide.html | 2 +- docs/reference/update_bl_individuals.html | 2 +- docs/reference/update_bl_markers.html | 2 +- docs/reference/update_filter_parameter.html | 2 +- docs/reference/update_radiator_gds.html | 2 +- docs/reference/vcf_strata.html | 2 +- docs/reference/write_arlequin.html | 2 +- docs/reference/write_bayescan.html | 2 +- docs/reference/write_betadiv.html | 2 +- docs/reference/write_colony.html | 2 +- docs/reference/write_dadi.html | 2 +- docs/reference/write_fasta.html | 2 +- docs/reference/write_faststructure.html | 2 +- docs/reference/write_fineradstructure.html | 2 +- docs/reference/write_gds.html | 2 +- docs/reference/write_genepop.html | 2 +- docs/reference/write_genepopedit.html | 2 +- docs/reference/write_genind.html | 2 +- docs/reference/write_genlight.html | 2 +- docs/reference/write_gsi_sim.html | 2 +- docs/reference/write_gtypes.html | 2 +- docs/reference/write_hapmap.html | 2 +- docs/reference/write_hierfstat.html | 2 +- docs/reference/write_hzar.html | 2 +- docs/reference/write_ldna.html | 2 +- docs/reference/write_maverick.html | 2 +- docs/reference/write_pcadapt.html | 2 +- docs/reference/write_plink.html | 2 +- docs/reference/write_rad.html | 2 +- docs/reference/write_related.html | 2 +- docs/reference/write_rubias.html | 2 +- docs/reference/write_snprelate.html | 2 +- docs/reference/write_stockr.html | 2 +- docs/reference/write_structure.html | 2 +- docs/reference/write_vcf.html | 2 +- 223 files changed, 252 insertions(+), 239 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0271cef4..9cb0a2fa 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: radiator Type: Package Title: RADseq Data Exploration, Manipulation and Visualization using R -Version: 1.3.0 -Date: 2024-02-22 +Version: 1.3.1 +Date: 2024-04-23 Encoding: UTF-8 Authors@R: c( person("Thierry", "Gosselin", email = "thierrygosselin@icloud.com", role = c("aut", "cre")), diff --git a/NEWS.md b/NEWS.md index 0cb72bf0..83d60712 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# radiator 1.3.1 2024-04-23 + +* 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 diff --git a/R/dart.R b/R/dart.R index b6266964..45e33c4f 100644 --- a/R/dart.R +++ b/R/dart.R @@ -882,8 +882,8 @@ import_dart <- function( target.id = strata.df$INDIVIDUALS, verbose = TRUE) - # Check for problematic DArT 2 rows ------------------------------------------ - if (dart.format == "2rows") { + # Check for problematic DArT 2 rows and counts -------------------------------- + if (dart.format == "2rows" || dart.format == "counts") { n.markers <- length(unique(data$MARKERS)) if (n.markers != nrow(data) / 2) { message("\n\nProblem with DArT file") @@ -1269,7 +1269,7 @@ dart2gds <- function( dplyr::mutate( dplyr::across( .cols = c(READ_DEPTH, ALLELE_REF_DEPTH, ALLELE_ALT_DEPTH), - .fns = replace_by_na, what = 0L + .fns = ~ replace_by_na(data = ., what = 0L) ) ) } else { @@ -1277,7 +1277,7 @@ dart2gds <- function( dplyr::mutate( dplyr::across( .cols = "ALLELE_REF_DEPTH", - .fns = switch_allele_count, dart.group = FALSE + .fns = ~ switch_allele_count(x = ., dart.group = FALSE, ref = TRUE) ) ) %>% dplyr::mutate( @@ -1290,7 +1290,7 @@ dart2gds <- function( # genotypes array ---------------------------------------------------------- - if (gt.vcf) { + if (gt.vcf) { genotypes.meta %<>% dplyr::mutate( GT_VCF = dplyr::case_when( diff --git a/README.md b/README.md index f180b335..a33f2e95 100644 --- a/README.md +++ b/README.md @@ -7,8 +7,8 @@ state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![minimal R version](https://img.shields.io/badge/R%3E%3D-NA-6666ff.svg)](https://cran.r-project.org/) -[![packageversion](https://img.shields.io/badge/Package%20version-1.3.0-orange.svg)](commits/master) -[![Last-changedate](https://img.shields.io/badge/last%20change-2024--02--25-brightgreen.svg)](/commits/master) +[![packageversion](https://img.shields.io/badge/Package%20version-1.3.1-orange.svg)](commits/master) +[![Last-changedate](https://img.shields.io/badge/last%20change-2024--04--23-brightgreen.svg)](/commits/master) [![R-CMD-check](https://github.com/thierrygosselin/radiator/workflows/R-CMD-check/badge.svg)](https://github.com/thierrygosselin/radiator/actions) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3687060.svg)](https://doi.org/10.5281/zenodo.3687060) diff --git a/docs/404.html b/docs/404.html index ab513ab2..06caca96 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 019837ee..4f901a64 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html index db0fb3b0..d3e9ebdc 100644 --- a/docs/articles/get_started.html +++ b/docs/articles/get_started.html @@ -33,7 +33,7 @@ radiator - 1.2.9 + 1.3.1 @@ -91,7 +91,7 @@

Get Started

Thierry Gosselin

-

2024-01-25

+

2024-04-23

Source: vignettes/get_started.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index c5f1080f..29137612 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/articles/life_cycle.html b/docs/articles/life_cycle.html index 4de7b3c7..3f500905 100644 --- a/docs/articles/life_cycle.html +++ b/docs/articles/life_cycle.html @@ -33,7 +33,7 @@ radiator - 1.2.9 + 1.3.1 @@ -91,7 +91,7 @@

Life Cycle

Thierry Gosselin

-

2024-01-25

+

2024-04-23

Source: vignettes/life_cycle.Rmd diff --git a/docs/articles/rad_genomics_computer_setup.html b/docs/articles/rad_genomics_computer_setup.html index 97e26139..d991720e 100644 --- a/docs/articles/rad_genomics_computer_setup.html +++ b/docs/articles/rad_genomics_computer_setup.html @@ -33,7 +33,7 @@ radiator - 1.2.9 + 1.3.1 @@ -90,7 +90,7 @@

RADseq Genomics in R

computer setup

-

2024-01-25

+

2024-04-23

Source: vignettes/rad_genomics_computer_setup.Rmd @@ -721,7 +721,7 @@

cd .. sudo rm -R lz4* 
cd ~/Downloads
-curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.2.tar.gz | tar xf -
+curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
 cd zstd*
 make 
 sudo make install
@@ -992,14 +992,14 @@ 

 
To install pcaMethods, from
 bioconductor:

 
-BiocManager::install("pcaMethods")

+BiocManager::install("pcaMethods")

fastsimcoal2

To install fastsimcoal2 -v.2.6.0.3, to use in grur::simulate_rad:

+v.2.6.0.3, to use in grur::simulate_rad:

LINUX

diff --git a/docs/authors.html b/docs/authors.html index 8df7e0ba..2e704015 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1
diff --git a/docs/index.html b/docs/index.html index 516d823f..8071d1a2 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ radiator - 1.2.9 + 1.3.1
@@ -111,7 +111,7 @@

Installationdevtools::package_info(pkgs = "SeqArray") # to verify version # If manually installing SeqArray is necessary -BiocManager::install("SeqArray") +BiocManager::install("SeqArray")

Web site with additional info: https://thierrygosselin.github.io/radiator/

diff --git a/docs/news/index.html b/docs/news/index.html index 0462f12a..332602d9 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 @@ -66,6 +66,14 @@

Changelog

Source: NEWS.md +
+

radiator 1.3.1 2024-04-23

+
  • Updated DArT code that use COUNT files to check more for problematic markers usually stemming from merged project
    • +
+
+

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
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e93b37fa..b1ccb46f 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,5 +5,5 @@ articles: get_started: get_started.html life_cycle: life_cycle.html rad_genomics_computer_setup: rad_genomics_computer_setup.html -last_built: 2024-01-25T22:34Z +last_built: 2024-04-23T22:04Z diff --git a/docs/reference/Exposition_pipe_operator.html b/docs/reference/Exposition_pipe_operator.html index c7ca60dc..7e585840 100644 --- a/docs/reference/Exposition_pipe_operator.html +++ b/docs/reference/Exposition_pipe_operator.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1
diff --git a/docs/reference/allele_count.html b/docs/reference/allele_count.html index 6ef8a83a..6bcd42ca 100644 --- a/docs/reference/allele_count.html +++ b/docs/reference/allele_count.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/allele_frequencies.html b/docs/reference/allele_frequencies.html index e852a16e..3b863a1b 100644 --- a/docs/reference/allele_frequencies.html +++ b/docs/reference/allele_frequencies.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/assign_defaults.html b/docs/reference/assign_defaults.html index ffbefd40..d6b31fda 100644 --- a/docs/reference/assign_defaults.html +++ b/docs/reference/assign_defaults.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/bayescan_one.html b/docs/reference/bayescan_one.html index 6ee5132e..a8adae0b 100644 --- a/docs/reference/bayescan_one.html +++ b/docs/reference/bayescan_one.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/betas_estimator.html b/docs/reference/betas_estimator.html index f16fb672..c1fdc4a1 100644 --- a/docs/reference/betas_estimator.html +++ b/docs/reference/betas_estimator.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/blacklist_hw.html b/docs/reference/blacklist_hw.html index 854679a3..1c47c918 100644 --- a/docs/reference/blacklist_hw.html +++ b/docs/reference/blacklist_hw.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/boxplot_stats.html b/docs/reference/boxplot_stats.html index 11631add..b5b179e9 100644 --- a/docs/reference/boxplot_stats.html +++ b/docs/reference/boxplot_stats.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/calibrate_alleles.html b/docs/reference/calibrate_alleles.html index aa55feff..0f867bc4 100644 --- a/docs/reference/calibrate_alleles.html +++ b/docs/reference/calibrate_alleles.html @@ -24,7 +24,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/change_pop_names.html b/docs/reference/change_pop_names.html index 47eb2947..a09c11c8 100644 --- a/docs/reference/change_pop_names.html +++ b/docs/reference/change_pop_names.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/check_args_class.html b/docs/reference/check_args_class.html index 19ec0fb6..aebc64ce 100644 --- a/docs/reference/check_args_class.html +++ b/docs/reference/check_args_class.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/check_dart.html b/docs/reference/check_dart.html index ed7ad0b2..a93d4ee6 100644 --- a/docs/reference/check_dart.html +++ b/docs/reference/check_dart.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/check_header_source_vcf.html b/docs/reference/check_header_source_vcf.html index 34be8c9a..327b5485 100644 --- a/docs/reference/check_header_source_vcf.html +++ b/docs/reference/check_header_source_vcf.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/check_pop_levels.html b/docs/reference/check_pop_levels.html index c4c3ada4..eb4f0879 100644 --- a/docs/reference/check_pop_levels.html +++ b/docs/reference/check_pop_levels.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/clean_dart_colnames.html b/docs/reference/clean_dart_colnames.html index 89c81c8b..caaf9324 100644 --- a/docs/reference/clean_dart_colnames.html +++ b/docs/reference/clean_dart_colnames.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/clean_dart_locus.html b/docs/reference/clean_dart_locus.html index 71ffe955..d36c600d 100644 --- a/docs/reference/clean_dart_locus.html +++ b/docs/reference/clean_dart_locus.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/clean_ind_names.html b/docs/reference/clean_ind_names.html index dd9dddba..f6566a96 100644 --- a/docs/reference/clean_ind_names.html +++ b/docs/reference/clean_ind_names.html @@ -22,7 +22,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/clean_markers_names.html b/docs/reference/clean_markers_names.html index cd5c6b3f..1a6e9aed 100644 --- a/docs/reference/clean_markers_names.html +++ b/docs/reference/clean_markers_names.html @@ -23,7 +23,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/clean_pop_names.html b/docs/reference/clean_pop_names.html index dd3b07fa..296e6aba 100644 --- a/docs/reference/clean_pop_names.html +++ b/docs/reference/clean_pop_names.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/compound_assignment_pipe_operator.html b/docs/reference/compound_assignment_pipe_operator.html index 35fa17f7..5a529ad4 100644 --- a/docs/reference/compound_assignment_pipe_operator.html +++ b/docs/reference/compound_assignment_pipe_operator.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/compute_maf.html b/docs/reference/compute_maf.html index 8095396d..1c34155f 100644 --- a/docs/reference/compute_maf.html +++ b/docs/reference/compute_maf.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/count_monomorphic.html b/docs/reference/count_monomorphic.html index 98ac08f2..e55d510e 100644 --- a/docs/reference/count_monomorphic.html +++ b/docs/reference/count_monomorphic.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/dart2gds.html b/docs/reference/dart2gds.html index a7a80d94..3dea5ec0 100644 --- a/docs/reference/dart2gds.html +++ b/docs/reference/dart2gds.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/data_info.html b/docs/reference/data_info.html index 677b06bf..a97edb43 100644 --- a/docs/reference/data_info.html +++ b/docs/reference/data_info.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_all_missing.html b/docs/reference/detect_all_missing.html index 6853216d..690c591f 100644 --- a/docs/reference/detect_all_missing.html +++ b/docs/reference/detect_all_missing.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_allele_problems.html b/docs/reference/detect_allele_problems.html index 401bdf8e..0145712b 100644 --- a/docs/reference/detect_allele_problems.html +++ b/docs/reference/detect_allele_problems.html @@ -25,7 +25,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_biallelic_markers.html b/docs/reference/detect_biallelic_markers.html index 71b7ab29..ac7683dc 100644 --- a/docs/reference/detect_biallelic_markers.html +++ b/docs/reference/detect_biallelic_markers.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_biallelic_problems.html b/docs/reference/detect_biallelic_problems.html index 655c3252..68a5ac6d 100644 --- a/docs/reference/detect_biallelic_problems.html +++ b/docs/reference/detect_biallelic_problems.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_dart_format.html b/docs/reference/detect_dart_format.html index 8060a2b8..b6ba0b20 100644 --- a/docs/reference/detect_dart_format.html +++ b/docs/reference/detect_dart_format.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_duplicate_genomes.html b/docs/reference/detect_duplicate_genomes.html index f3d8c562..9e4f22d2 100644 --- a/docs/reference/detect_duplicate_genomes.html +++ b/docs/reference/detect_duplicate_genomes.html @@ -24,7 +24,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_genomic_format.html b/docs/reference/detect_genomic_format.html index c40388ff..14d3d237 100644 --- a/docs/reference/detect_genomic_format.html +++ b/docs/reference/detect_genomic_format.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_het_outliers.html b/docs/reference/detect_het_outliers.html index c7068998..702bf5f5 100644 --- a/docs/reference/detect_het_outliers.html +++ b/docs/reference/detect_het_outliers.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_microsatellites.html b/docs/reference/detect_microsatellites.html index 20916f18..f7e5e99a 100644 --- a/docs/reference/detect_microsatellites.html +++ b/docs/reference/detect_microsatellites.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_mixed_genomes.html b/docs/reference/detect_mixed_genomes.html index 543c81d8..e5ccc7e0 100644 --- a/docs/reference/detect_mixed_genomes.html +++ b/docs/reference/detect_mixed_genomes.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_paralogs.html b/docs/reference/detect_paralogs.html index df2c3c41..e7e11d51 100644 --- a/docs/reference/detect_paralogs.html +++ b/docs/reference/detect_paralogs.html @@ -22,7 +22,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/detect_ref_genome.html b/docs/reference/detect_ref_genome.html index 83342564..05ee8f5e 100644 --- a/docs/reference/detect_ref_genome.html +++ b/docs/reference/detect_ref_genome.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/diagnostic_maf.html b/docs/reference/diagnostic_maf.html index b4308a07..dcecdbf8 100644 --- a/docs/reference/diagnostic_maf.html +++ b/docs/reference/diagnostic_maf.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/distance2tibble.html b/docs/reference/distance2tibble.html index ef565d6c..36fdf555 100644 --- a/docs/reference/distance2tibble.html +++ b/docs/reference/distance2tibble.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/distance_individuals.html b/docs/reference/distance_individuals.html index 3f978f8b..a423ff06 100644 --- a/docs/reference/distance_individuals.html +++ b/docs/reference/distance_individuals.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/erase_genotypes.html b/docs/reference/erase_genotypes.html index f89b92b9..d0cc71f7 100644 --- a/docs/reference/erase_genotypes.html +++ b/docs/reference/erase_genotypes.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/estimate_m.html b/docs/reference/estimate_m.html index f10203cb..1f2c1701 100644 --- a/docs/reference/estimate_m.html +++ b/docs/reference/estimate_m.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/extract_coverage.html b/docs/reference/extract_coverage.html index fc3ff0f9..e2f7194e 100644 --- a/docs/reference/extract_coverage.html +++ b/docs/reference/extract_coverage.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/extract_dart_target_id.html b/docs/reference/extract_dart_target_id.html index 57112023..a6fa5518 100644 --- a/docs/reference/extract_dart_target_id.html +++ b/docs/reference/extract_dart_target_id.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/extract_data_source.html b/docs/reference/extract_data_source.html index ce9600ee..56378c60 100644 --- a/docs/reference/extract_data_source.html +++ b/docs/reference/extract_data_source.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/extract_dots.html b/docs/reference/extract_dots.html index 3ebdd57e..26b971f3 100644 --- a/docs/reference/extract_dots.html +++ b/docs/reference/extract_dots.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/extract_genotypes_metadata.html b/docs/reference/extract_genotypes_metadata.html index 5b56dc6a..2c89293f 100644 --- a/docs/reference/extract_genotypes_metadata.html +++ b/docs/reference/extract_genotypes_metadata.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/extract_individuals_metadata.html b/docs/reference/extract_individuals_metadata.html index 38d40810..bb8154cf 100644 --- a/docs/reference/extract_individuals_metadata.html +++ b/docs/reference/extract_individuals_metadata.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/extract_individuals_vcf.html b/docs/reference/extract_individuals_vcf.html index 65dd92b4..44dffcf8 100644 --- a/docs/reference/extract_individuals_vcf.html +++ b/docs/reference/extract_individuals_vcf.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/extract_info_vcf.html b/docs/reference/extract_info_vcf.html index e8c9c2f7..8635e625 100644 --- a/docs/reference/extract_info_vcf.html +++ b/docs/reference/extract_info_vcf.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/extract_markers_metadata.html b/docs/reference/extract_markers_metadata.html index 5485a632..8d87be81 100644 --- a/docs/reference/extract_markers_metadata.html +++ b/docs/reference/extract_markers_metadata.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_blacklist_genotypes.html b/docs/reference/filter_blacklist_genotypes.html index d5ca8a81..161e4acc 100644 --- a/docs/reference/filter_blacklist_genotypes.html +++ b/docs/reference/filter_blacklist_genotypes.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_common_markers.html b/docs/reference/filter_common_markers.html index 0263d775..0a86c22c 100644 --- a/docs/reference/filter_common_markers.html +++ b/docs/reference/filter_common_markers.html @@ -24,7 +24,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_coverage.html b/docs/reference/filter_coverage.html index 341d4288..3c226460 100644 --- a/docs/reference/filter_coverage.html +++ b/docs/reference/filter_coverage.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_dart_reproducibility.html b/docs/reference/filter_dart_reproducibility.html index 5c26a904..4e2442e7 100644 --- a/docs/reference/filter_dart_reproducibility.html +++ b/docs/reference/filter_dart_reproducibility.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_fis.html b/docs/reference/filter_fis.html index 2abd7f3b..ff88ecfd 100644 --- a/docs/reference/filter_fis.html +++ b/docs/reference/filter_fis.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_genotyping.html b/docs/reference/filter_genotyping.html index 2b715a8c..0da88aad 100644 --- a/docs/reference/filter_genotyping.html +++ b/docs/reference/filter_genotyping.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_het.html b/docs/reference/filter_het.html index a872953e..d420ca35 100644 --- a/docs/reference/filter_het.html +++ b/docs/reference/filter_het.html @@ -37,7 +37,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_hwe.html b/docs/reference/filter_hwe.html index 90304440..4cc14942 100644 --- a/docs/reference/filter_hwe.html +++ b/docs/reference/filter_hwe.html @@ -35,7 +35,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_individuals.html b/docs/reference/filter_individuals.html index a822c975..8fefca43 100644 --- a/docs/reference/filter_individuals.html +++ b/docs/reference/filter_individuals.html @@ -28,7 +28,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_ld.html b/docs/reference/filter_ld.html index e9fec3cf..20912083 100644 --- a/docs/reference/filter_ld.html +++ b/docs/reference/filter_ld.html @@ -37,7 +37,7 @@ radiator - 1.2.9 + 1.3.1 @@ -255,7 +255,7 @@

Examples

require(SNPRelate) #To install SNPRelate: install.packages("BiocManager") -BiocManager::install ("SNPRelate") +BiocManager::install ("SNPRelate") library(radiator) data <- radiator::read_vcf(data = "my.vcf", strata = "my.strata.tsv", verbose = TRUE) diff --git a/docs/reference/filter_monomorphic.html b/docs/reference/filter_monomorphic.html index 4d9633cd..93257372 100644 --- a/docs/reference/filter_monomorphic.html +++ b/docs/reference/filter_monomorphic.html @@ -29,7 +29,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_rad.html b/docs/reference/filter_rad.html index 151e0e34..e5362d09 100644 --- a/docs/reference/filter_rad.html +++ b/docs/reference/filter_rad.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_snp_number.html b/docs/reference/filter_snp_number.html index 220a029e..7705958e 100644 --- a/docs/reference/filter_snp_number.html +++ b/docs/reference/filter_snp_number.html @@ -25,7 +25,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_snp_position_read.html b/docs/reference/filter_snp_position_read.html index 7c29f7e7..bca08dbe 100644 --- a/docs/reference/filter_snp_position_read.html +++ b/docs/reference/filter_snp_position_read.html @@ -23,7 +23,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/filter_whitelist.html b/docs/reference/filter_whitelist.html index 706bf52f..a7729b2f 100644 --- a/docs/reference/filter_whitelist.html +++ b/docs/reference/filter_whitelist.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/folder_prefix.html b/docs/reference/folder_prefix.html index a9b55f9e..528db784 100644 --- a/docs/reference/folder_prefix.html +++ b/docs/reference/folder_prefix.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/folder_short.html b/docs/reference/folder_short.html index 9cb0c18e..a8cff0a1 100644 --- a/docs/reference/folder_short.html +++ b/docs/reference/folder_short.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/gds2tidy.html b/docs/reference/gds2tidy.html index 0cb18c11..3b80f9c8 100644 --- a/docs/reference/gds2tidy.html +++ b/docs/reference/gds2tidy.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/generate_filename.html b/docs/reference/generate_filename.html index be584f3b..664cfa6c 100644 --- a/docs/reference/generate_filename.html +++ b/docs/reference/generate_filename.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/generate_folder.html b/docs/reference/generate_folder.html index 058244a6..201ae808 100644 --- a/docs/reference/generate_folder.html +++ b/docs/reference/generate_folder.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/generate_geno_freq_boundaries.html b/docs/reference/generate_geno_freq_boundaries.html index 4cb75fee..e30b3d3b 100644 --- a/docs/reference/generate_geno_freq_boundaries.html +++ b/docs/reference/generate_geno_freq_boundaries.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/generate_hzar.html b/docs/reference/generate_hzar.html index 84288060..520713b0 100644 --- a/docs/reference/generate_hzar.html +++ b/docs/reference/generate_hzar.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/generate_markers_metadata.html b/docs/reference/generate_markers_metadata.html index 068b3b67..eee683c3 100644 --- a/docs/reference/generate_markers_metadata.html +++ b/docs/reference/generate_markers_metadata.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/generate_squeleton_folders.html b/docs/reference/generate_squeleton_folders.html index ed3ec2ac..33d8914b 100644 --- a/docs/reference/generate_squeleton_folders.html +++ b/docs/reference/generate_squeleton_folders.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/generate_strata.html b/docs/reference/generate_strata.html index 7c32e29d..b6274262 100644 --- a/docs/reference/generate_strata.html +++ b/docs/reference/generate_strata.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/generate_whitelist.html b/docs/reference/generate_whitelist.html index 06a38f14..4d84be68 100644 --- a/docs/reference/generate_whitelist.html +++ b/docs/reference/generate_whitelist.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/genome_similarity.html b/docs/reference/genome_similarity.html index b17ee5cd..c6ef4036 100644 --- a/docs/reference/genome_similarity.html +++ b/docs/reference/genome_similarity.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/genomic_converter.html b/docs/reference/genomic_converter.html index 6e601ff7..fa82c724 100644 --- a/docs/reference/genomic_converter.html +++ b/docs/reference/genomic_converter.html @@ -31,7 +31,7 @@ radiator - 1.2.9 + 1.3.1 @@ -356,7 +356,7 @@

Examples

radiator::detect_genomic_format(data = "populations.snps.vcf") # The simplest form of the function: -require(strataG) # for the gtypes format... +require(strataG) # for the gtypes format... snowcrab <- genomic_converter( data = "populations.snps.vcf", strata = "snowcrab.strata.tsv", output = c("genlight", "genepop", "gtypes")) diff --git a/docs/reference/gt2array.html b/docs/reference/gt2array.html index c68f2a0a..f68e906e 100644 --- a/docs/reference/gt2array.html +++ b/docs/reference/gt2array.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/haplotype_reconstruction.html b/docs/reference/haplotype_reconstruction.html index 042b0707..cf011e5e 100644 --- a/docs/reference/haplotype_reconstruction.html +++ b/docs/reference/haplotype_reconstruction.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/hwe_analysis.html b/docs/reference/hwe_analysis.html index 662e573e..e6a87236 100644 --- a/docs/reference/hwe_analysis.html +++ b/docs/reference/hwe_analysis.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/ibdg_fh.html b/docs/reference/ibdg_fh.html index a739a5dd..41f86bfe 100644 --- a/docs/reference/ibdg_fh.html +++ b/docs/reference/ibdg_fh.html @@ -48,7 +48,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/import_dart.html b/docs/reference/import_dart.html index 7df5fa33..045b26b5 100644 --- a/docs/reference/import_dart.html +++ b/docs/reference/import_dart.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/ind_total_reads.html b/docs/reference/ind_total_reads.html index e4856a9f..219b763a 100644 --- a/docs/reference/ind_total_reads.html +++ b/docs/reference/ind_total_reads.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index 8c2b4483..bd9be9f0 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/individuals2strata.html b/docs/reference/individuals2strata.html index 3da9c00b..f65e5c44 100644 --- a/docs/reference/individuals2strata.html +++ b/docs/reference/individuals2strata.html @@ -25,7 +25,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/join_strata.html b/docs/reference/join_strata.html index 642b51a7..25aacfa1 100644 --- a/docs/reference/join_strata.html +++ b/docs/reference/join_strata.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/ld2df.html b/docs/reference/ld2df.html index 00ab870f..a18c8640 100644 --- a/docs/reference/ld2df.html +++ b/docs/reference/ld2df.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/ld_boxplot.html b/docs/reference/ld_boxplot.html index 0323626c..4367f28a 100644 --- a/docs/reference/ld_boxplot.html +++ b/docs/reference/ld_boxplot.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/ld_missing.html b/docs/reference/ld_missing.html index a12de27d..5c7b5ebb 100644 --- a/docs/reference/ld_missing.html +++ b/docs/reference/ld_missing.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/ld_pruning.html b/docs/reference/ld_pruning.html index 4dd037cc..040815ce 100644 --- a/docs/reference/ld_pruning.html +++ b/docs/reference/ld_pruning.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/list_filters.html b/docs/reference/list_filters.html index 731e7ee2..c7c048e0 100644 --- a/docs/reference/list_filters.html +++ b/docs/reference/list_filters.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/markers_genotyped_helper.html b/docs/reference/markers_genotyped_helper.html index 46ad13ba..3c9df84c 100644 --- a/docs/reference/markers_genotyped_helper.html +++ b/docs/reference/markers_genotyped_helper.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/merge_dart.html b/docs/reference/merge_dart.html index 42381bfd..cb9c47dd 100644 --- a/docs/reference/merge_dart.html +++ b/docs/reference/merge_dart.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/message_func_call.html b/docs/reference/message_func_call.html index 2e976d79..71e6fd17 100644 --- a/docs/reference/message_func_call.html +++ b/docs/reference/message_func_call.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/missing_per_pop.html b/docs/reference/missing_per_pop.html index b25f4e39..7f6547ff 100644 --- a/docs/reference/missing_per_pop.html +++ b/docs/reference/missing_per_pop.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/n.html b/docs/reference/n.html index 817bd35e..241b72f8 100644 --- a/docs/reference/n.html +++ b/docs/reference/n.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/not_common_markers.html b/docs/reference/not_common_markers.html index 11e968d8..38474933 100644 --- a/docs/reference/not_common_markers.html +++ b/docs/reference/not_common_markers.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/parallel_core_opt.html b/docs/reference/parallel_core_opt.html index 50367cd8..c90d8951 100644 --- a/docs/reference/parallel_core_opt.html +++ b/docs/reference/parallel_core_opt.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/parse_gds_metadata.html b/docs/reference/parse_gds_metadata.html index a740a025..0d7ab646 100644 --- a/docs/reference/parse_gds_metadata.html +++ b/docs/reference/parse_gds_metadata.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/pi.html b/docs/reference/pi.html index 9b4c76ae..85ae2ceb 100644 --- a/docs/reference/pi.html +++ b/docs/reference/pi.html @@ -26,7 +26,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/pi_pop.html b/docs/reference/pi_pop.html index 029ecb95..94dd9b17 100644 --- a/docs/reference/pi_pop.html +++ b/docs/reference/pi_pop.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/pi_rad.html b/docs/reference/pi_rad.html index 0a2f9b06..7f101caa 100644 --- a/docs/reference/pi_rad.html +++ b/docs/reference/pi_rad.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html index 9a1b0cb5..57a5bcc1 100644 --- a/docs/reference/pipe.html +++ b/docs/reference/pipe.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_bayescan.html b/docs/reference/plot_bayescan.html index e29730fd..89023923 100644 --- a/docs/reference/plot_bayescan.html +++ b/docs/reference/plot_bayescan.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_boxplot_coverage.html b/docs/reference/plot_boxplot_coverage.html index 6b369683..84b023bf 100644 --- a/docs/reference/plot_boxplot_coverage.html +++ b/docs/reference/plot_boxplot_coverage.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_boxplot_diversity.html b/docs/reference/plot_boxplot_diversity.html index 951b2d9d..cd6e5688 100644 --- a/docs/reference/plot_boxplot_diversity.html +++ b/docs/reference/plot_boxplot_diversity.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_coverage_imbalance_diagnostic.html b/docs/reference/plot_coverage_imbalance_diagnostic.html index 5fe0d472..a4406f9a 100644 --- a/docs/reference/plot_coverage_imbalance_diagnostic.html +++ b/docs/reference/plot_coverage_imbalance_diagnostic.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_density_distribution_coverage.html b/docs/reference/plot_density_distribution_coverage.html index 139f2e91..1146cb10 100644 --- a/docs/reference/plot_density_distribution_coverage.html +++ b/docs/reference/plot_density_distribution_coverage.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_density_distribution_het.html b/docs/reference/plot_density_distribution_het.html index 485cebd8..6f0eb5a9 100644 --- a/docs/reference/plot_density_distribution_het.html +++ b/docs/reference/plot_density_distribution_het.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_density_distribution_maf.html b/docs/reference/plot_density_distribution_maf.html index 2f48811b..cc65f468 100644 --- a/docs/reference/plot_density_distribution_maf.html +++ b/docs/reference/plot_density_distribution_maf.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_distribution_diversity.html b/docs/reference/plot_distribution_diversity.html index 94f81d2c..2d82b11a 100644 --- a/docs/reference/plot_distribution_diversity.html +++ b/docs/reference/plot_distribution_diversity.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_het_outliers.html b/docs/reference/plot_het_outliers.html index 89e40d0d..e233c5f8 100644 --- a/docs/reference/plot_het_outliers.html +++ b/docs/reference/plot_het_outliers.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_snp_number_loci.html b/docs/reference/plot_snp_number_loci.html index 01ab203e..8f307c78 100644 --- a/docs/reference/plot_snp_number_loci.html +++ b/docs/reference/plot_snp_number_loci.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_snp_position_read.html b/docs/reference/plot_snp_position_read.html index 9b146d12..60991367 100644 --- a/docs/reference/plot_snp_position_read.html +++ b/docs/reference/plot_snp_position_read.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/plot_upset.html b/docs/reference/plot_upset.html index 35be6e8d..87e84ff1 100644 --- a/docs/reference/plot_upset.html +++ b/docs/reference/plot_upset.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/private_alleles.html b/docs/reference/private_alleles.html index 8136e51a..1ac8a329 100644 --- a/docs/reference/private_alleles.html +++ b/docs/reference/private_alleles.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/private_haplotypes.html b/docs/reference/private_haplotypes.html index a63654e2..70872333 100644 --- a/docs/reference/private_haplotypes.html +++ b/docs/reference/private_haplotypes.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_common_arguments.html b/docs/reference/radiator_common_arguments.html index e2cf4ba0..d9f1b8fc 100644 --- a/docs/reference/radiator_common_arguments.html +++ b/docs/reference/radiator_common_arguments.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_dots.html b/docs/reference/radiator_dots.html index 8f5fe3c1..9c01f70b 100644 --- a/docs/reference/radiator_dots.html +++ b/docs/reference/radiator_dots.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_folder.html b/docs/reference/radiator_folder.html index 6a14af6e..fd38cd2d 100644 --- a/docs/reference/radiator_folder.html +++ b/docs/reference/radiator_folder.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_function_header.html b/docs/reference/radiator_function_header.html index 67ca06f3..35429f6d 100644 --- a/docs/reference/radiator_function_header.html +++ b/docs/reference/radiator_function_header.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_gds.html b/docs/reference/radiator_gds.html index 6aeb9999..578aa681 100644 --- a/docs/reference/radiator_gds.html +++ b/docs/reference/radiator_gds.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_gds_skeleton.html b/docs/reference/radiator_gds_skeleton.html index 28707fcd..a78cfc55 100644 --- a/docs/reference/radiator_gds_skeleton.html +++ b/docs/reference/radiator_gds_skeleton.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_packages_dep.html b/docs/reference/radiator_packages_dep.html index 59249957..46f362aa 100644 --- a/docs/reference/radiator_packages_dep.html +++ b/docs/reference/radiator_packages_dep.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_parameters.html b/docs/reference/radiator_parameters.html index c0fdbf0a..b06bdaac 100644 --- a/docs/reference/radiator_parameters.html +++ b/docs/reference/radiator_parameters.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_pkg_install.html b/docs/reference/radiator_pkg_install.html index 3bbbe630..42de9716 100644 --- a/docs/reference/radiator_pkg_install.html +++ b/docs/reference/radiator_pkg_install.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_question.html b/docs/reference/radiator_question.html index 2308c00d..46468b97 100644 --- a/docs/reference/radiator_question.html +++ b/docs/reference/radiator_question.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_results_message.html b/docs/reference/radiator_results_message.html index 566b515e..641a55df 100644 --- a/docs/reference/radiator_results_message.html +++ b/docs/reference/radiator_results_message.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_snakecase.html b/docs/reference/radiator_snakecase.html index 8c170033..4fc158a6 100644 --- a/docs/reference/radiator_snakecase.html +++ b/docs/reference/radiator_snakecase.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_split_tibble.html b/docs/reference/radiator_split_tibble.html index 70dcc12d..962743d9 100644 --- a/docs/reference/radiator_split_tibble.html +++ b/docs/reference/radiator_split_tibble.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_tic.html b/docs/reference/radiator_tic.html index fdf970cb..99347514 100644 --- a/docs/reference/radiator_tic.html +++ b/docs/reference/radiator_tic.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/radiator_toc.html b/docs/reference/radiator_toc.html index 227dfd42..bc6b2b2f 100644 --- a/docs/reference/radiator_toc.html +++ b/docs/reference/radiator_toc.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/read_blacklist_genotypes.html b/docs/reference/read_blacklist_genotypes.html index 73e8058f..4901fe12 100644 --- a/docs/reference/read_blacklist_genotypes.html +++ b/docs/reference/read_blacklist_genotypes.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/read_blacklist_id.html b/docs/reference/read_blacklist_id.html index 2227c425..8dbe68d5 100644 --- a/docs/reference/read_blacklist_id.html +++ b/docs/reference/read_blacklist_id.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/read_dart.html b/docs/reference/read_dart.html index 9e674c44..3f0d188f 100644 --- a/docs/reference/read_dart.html +++ b/docs/reference/read_dart.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/read_plink.html b/docs/reference/read_plink.html index 7c64075a..77336fe2 100644 --- a/docs/reference/read_plink.html +++ b/docs/reference/read_plink.html @@ -24,7 +24,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/read_rad.html b/docs/reference/read_rad.html index 47af3c6f..40dab71c 100644 --- a/docs/reference/read_rad.html +++ b/docs/reference/read_rad.html @@ -24,7 +24,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/read_strata.html b/docs/reference/read_strata.html index b8c9d0fa..147738eb 100644 --- a/docs/reference/read_strata.html +++ b/docs/reference/read_strata.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/read_vcf.html b/docs/reference/read_vcf.html index 3f770389..fa3b6d0d 100644 --- a/docs/reference/read_vcf.html +++ b/docs/reference/read_vcf.html @@ -27,7 +27,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/read_whitelist.html b/docs/reference/read_whitelist.html index 22ba457d..a4d664c2 100644 --- a/docs/reference/read_whitelist.html +++ b/docs/reference/read_whitelist.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/remove_duplicates.html b/docs/reference/remove_duplicates.html index 96aedd96..9b409e38 100644 --- a/docs/reference/remove_duplicates.html +++ b/docs/reference/remove_duplicates.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/replace_by_na.html b/docs/reference/replace_by_na.html index 562f3d91..c9f77a20 100644 --- a/docs/reference/replace_by_na.html +++ b/docs/reference/replace_by_na.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/reset_filters.html b/docs/reference/reset_filters.html index 63f97338..dbb492d7 100644 --- a/docs/reference/reset_filters.html +++ b/docs/reference/reset_filters.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/run_bayescan.html b/docs/reference/run_bayescan.html index 1660c19e..ff3c0de0 100644 --- a/docs/reference/run_bayescan.html +++ b/docs/reference/run_bayescan.html @@ -31,7 +31,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/separate_gt.html b/docs/reference/separate_gt.html index 16f15eb7..df80123a 100644 --- a/docs/reference/separate_gt.html +++ b/docs/reference/separate_gt.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/separate_markers.html b/docs/reference/separate_markers.html index f8b0259e..b209bfd0 100644 --- a/docs/reference/separate_markers.html +++ b/docs/reference/separate_markers.html @@ -23,7 +23,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/sex_markers_plot.html b/docs/reference/sex_markers_plot.html index c2af7d88..4f8e71c0 100644 --- a/docs/reference/sex_markers_plot.html +++ b/docs/reference/sex_markers_plot.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/sexy_markers.html b/docs/reference/sexy_markers.html index b14bc5c4..80804e96 100644 --- a/docs/reference/sexy_markers.html +++ b/docs/reference/sexy_markers.html @@ -22,7 +22,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/simulate_genos_from_posterior.html b/docs/reference/simulate_genos_from_posterior.html index 14bfc198..499054d1 100644 --- a/docs/reference/simulate_genos_from_posterior.html +++ b/docs/reference/simulate_genos_from_posterior.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/split_tibble_rows.html b/docs/reference/split_tibble_rows.html index bdd41d7d..3f0e2d4a 100644 --- a/docs/reference/split_tibble_rows.html +++ b/docs/reference/split_tibble_rows.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/split_vcf.html b/docs/reference/split_vcf.html index 818a0322..a43e07de 100644 --- a/docs/reference/split_vcf.html +++ b/docs/reference/split_vcf.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/strata_haplo.html b/docs/reference/strata_haplo.html index c4e0436a..e8b9e3cd 100644 --- a/docs/reference/strata_haplo.html +++ b/docs/reference/strata_haplo.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/subsampling_data.html b/docs/reference/subsampling_data.html index a1c35b0c..60a1a87c 100644 --- a/docs/reference/subsampling_data.html +++ b/docs/reference/subsampling_data.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/summarise_genotypes.html b/docs/reference/summarise_genotypes.html index 4edf20ed..b9959c59 100644 --- a/docs/reference/summarise_genotypes.html +++ b/docs/reference/summarise_genotypes.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/summarize_sex.html b/docs/reference/summarize_sex.html index d339935c..14b66900 100644 --- a/docs/reference/summarize_sex.html +++ b/docs/reference/summarize_sex.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/summary_gds.html b/docs/reference/summary_gds.html index 21a07d48..3abfb279 100644 --- a/docs/reference/summary_gds.html +++ b/docs/reference/summary_gds.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/summary_rad.html b/docs/reference/summary_rad.html index 4c49ffaf..5cc5e1b1 100644 --- a/docs/reference/summary_rad.html +++ b/docs/reference/summary_rad.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/summary_strata.html b/docs/reference/summary_strata.html index d60edb6f..45c4d16a 100644 --- a/docs/reference/summary_strata.html +++ b/docs/reference/summary_strata.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/switch_allele_count.html b/docs/reference/switch_allele_count.html index 3ed26731..7fa300d3 100644 --- a/docs/reference/switch_allele_count.html +++ b/docs/reference/switch_allele_count.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/switch_genotypes.html b/docs/reference/switch_genotypes.html index 90a19f7c..c13b7296 100644 --- a/docs/reference/switch_genotypes.html +++ b/docs/reference/switch_genotypes.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/sync_gds.html b/docs/reference/sync_gds.html index a79c0a17..c604aa3f 100644 --- a/docs/reference/sync_gds.html +++ b/docs/reference/sync_gds.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tibble_stats.html b/docs/reference/tibble_stats.html index 2fce076b..8846956f 100644 --- a/docs/reference/tibble_stats.html +++ b/docs/reference/tibble_stats.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy2gds.html b/docs/reference/tidy2gds.html index dc918ec2..4cac68bc 100644 --- a/docs/reference/tidy2gds.html +++ b/docs/reference/tidy2gds.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy2wide.html b/docs/reference/tidy2wide.html index aa311827..57a23746 100644 --- a/docs/reference/tidy2wide.html +++ b/docs/reference/tidy2wide.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_dart_metadata.html b/docs/reference/tidy_dart_metadata.html index e8b2d803..aa4a9d7d 100644 --- a/docs/reference/tidy_dart_metadata.html +++ b/docs/reference/tidy_dart_metadata.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_fstat.html b/docs/reference/tidy_fstat.html index ffe4968e..108e395e 100644 --- a/docs/reference/tidy_fstat.html +++ b/docs/reference/tidy_fstat.html @@ -25,7 +25,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_genepop.html b/docs/reference/tidy_genepop.html index a58e17f5..93bf51fd 100644 --- a/docs/reference/tidy_genepop.html +++ b/docs/reference/tidy_genepop.html @@ -25,7 +25,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_genind.html b/docs/reference/tidy_genind.html index 9603bc60..1acf7666 100644 --- a/docs/reference/tidy_genind.html +++ b/docs/reference/tidy_genind.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_genlight.html b/docs/reference/tidy_genlight.html index 29f30114..bb7f7c12 100644 --- a/docs/reference/tidy_genlight.html +++ b/docs/reference/tidy_genlight.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_genomic_data.html b/docs/reference/tidy_genomic_data.html index a30bcf68..62a0d781 100644 --- a/docs/reference/tidy_genomic_data.html +++ b/docs/reference/tidy_genomic_data.html @@ -26,7 +26,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_gtypes.html b/docs/reference/tidy_gtypes.html index c7e669ae..cf8901d8 100644 --- a/docs/reference/tidy_gtypes.html +++ b/docs/reference/tidy_gtypes.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_plink.html b/docs/reference/tidy_plink.html index 2a4dd617..77250c59 100644 --- a/docs/reference/tidy_plink.html +++ b/docs/reference/tidy_plink.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_vcf.html b/docs/reference/tidy_vcf.html index a61b6f45..2a5543b1 100644 --- a/docs/reference/tidy_vcf.html +++ b/docs/reference/tidy_vcf.html @@ -24,7 +24,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/tidy_wide.html b/docs/reference/tidy_wide.html index 97c5f296..66a44b5b 100644 --- a/docs/reference/tidy_wide.html +++ b/docs/reference/tidy_wide.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/update_bl_individuals.html b/docs/reference/update_bl_individuals.html index bccdece5..a1d79150 100644 --- a/docs/reference/update_bl_individuals.html +++ b/docs/reference/update_bl_individuals.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/update_bl_markers.html b/docs/reference/update_bl_markers.html index 9f754317..cf55b6ba 100644 --- a/docs/reference/update_bl_markers.html +++ b/docs/reference/update_bl_markers.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/update_filter_parameter.html b/docs/reference/update_filter_parameter.html index 04ee91f1..5f2e7de4 100644 --- a/docs/reference/update_filter_parameter.html +++ b/docs/reference/update_filter_parameter.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/update_radiator_gds.html b/docs/reference/update_radiator_gds.html index 96f45145..a372c4dd 100644 --- a/docs/reference/update_radiator_gds.html +++ b/docs/reference/update_radiator_gds.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/vcf_strata.html b/docs/reference/vcf_strata.html index c47e43ff..a9630309 100644 --- a/docs/reference/vcf_strata.html +++ b/docs/reference/vcf_strata.html @@ -18,7 +18,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_arlequin.html b/docs/reference/write_arlequin.html index 08c88747..00d84857 100644 --- a/docs/reference/write_arlequin.html +++ b/docs/reference/write_arlequin.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_bayescan.html b/docs/reference/write_bayescan.html index ae882403..8f8d1483 100644 --- a/docs/reference/write_bayescan.html +++ b/docs/reference/write_bayescan.html @@ -22,7 +22,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_betadiv.html b/docs/reference/write_betadiv.html index bd04afde..b809e396 100644 --- a/docs/reference/write_betadiv.html +++ b/docs/reference/write_betadiv.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_colony.html b/docs/reference/write_colony.html index ce30a269..e22c8eb0 100644 --- a/docs/reference/write_colony.html +++ b/docs/reference/write_colony.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_dadi.html b/docs/reference/write_dadi.html index 480de9d6..0436c0be 100644 --- a/docs/reference/write_dadi.html +++ b/docs/reference/write_dadi.html @@ -23,7 +23,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_fasta.html b/docs/reference/write_fasta.html index 91e5c392..9f17ee5f 100644 --- a/docs/reference/write_fasta.html +++ b/docs/reference/write_fasta.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_faststructure.html b/docs/reference/write_faststructure.html index a8dd6e70..02db9643 100644 --- a/docs/reference/write_faststructure.html +++ b/docs/reference/write_faststructure.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_fineradstructure.html b/docs/reference/write_fineradstructure.html index 374409f9..c7e40ff5 100644 --- a/docs/reference/write_fineradstructure.html +++ b/docs/reference/write_fineradstructure.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_gds.html b/docs/reference/write_gds.html index beee1f88..4f808b1f 100644 --- a/docs/reference/write_gds.html +++ b/docs/reference/write_gds.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_genepop.html b/docs/reference/write_genepop.html index cae51696..78f37767 100644 --- a/docs/reference/write_genepop.html +++ b/docs/reference/write_genepop.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_genepopedit.html b/docs/reference/write_genepopedit.html index 91fc015d..629242ef 100644 --- a/docs/reference/write_genepopedit.html +++ b/docs/reference/write_genepopedit.html @@ -32,7 +32,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_genind.html b/docs/reference/write_genind.html index 613e0772..a064abd3 100644 --- a/docs/reference/write_genind.html +++ b/docs/reference/write_genind.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_genlight.html b/docs/reference/write_genlight.html index 1e7eae04..49ab2047 100644 --- a/docs/reference/write_genlight.html +++ b/docs/reference/write_genlight.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_gsi_sim.html b/docs/reference/write_gsi_sim.html index 19b148b6..b4b42f00 100644 --- a/docs/reference/write_gsi_sim.html +++ b/docs/reference/write_gsi_sim.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_gtypes.html b/docs/reference/write_gtypes.html index 1aeedb5a..5d293893 100644 --- a/docs/reference/write_gtypes.html +++ b/docs/reference/write_gtypes.html @@ -21,7 +21,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_hapmap.html b/docs/reference/write_hapmap.html index d39fb589..f0c1d7c4 100644 --- a/docs/reference/write_hapmap.html +++ b/docs/reference/write_hapmap.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_hierfstat.html b/docs/reference/write_hierfstat.html index 87838b9d..a2158a19 100644 --- a/docs/reference/write_hierfstat.html +++ b/docs/reference/write_hierfstat.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_hzar.html b/docs/reference/write_hzar.html index c9c68b91..13c5d45d 100644 --- a/docs/reference/write_hzar.html +++ b/docs/reference/write_hzar.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_ldna.html b/docs/reference/write_ldna.html index 33cb0f89..db21284c 100644 --- a/docs/reference/write_ldna.html +++ b/docs/reference/write_ldna.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_maverick.html b/docs/reference/write_maverick.html index d37cb53e..4797384c 100644 --- a/docs/reference/write_maverick.html +++ b/docs/reference/write_maverick.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_pcadapt.html b/docs/reference/write_pcadapt.html index 3d5514ee..91513b7e 100644 --- a/docs/reference/write_pcadapt.html +++ b/docs/reference/write_pcadapt.html @@ -24,7 +24,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_plink.html b/docs/reference/write_plink.html index 7144d260..38314609 100644 --- a/docs/reference/write_plink.html +++ b/docs/reference/write_plink.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_rad.html b/docs/reference/write_rad.html index 2ad82a39..6571f03c 100644 --- a/docs/reference/write_rad.html +++ b/docs/reference/write_rad.html @@ -28,7 +28,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_related.html b/docs/reference/write_related.html index bac73f96..f8b61592 100644 --- a/docs/reference/write_related.html +++ b/docs/reference/write_related.html @@ -24,7 +24,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_rubias.html b/docs/reference/write_rubias.html index 077e3238..388f7faa 100644 --- a/docs/reference/write_rubias.html +++ b/docs/reference/write_rubias.html @@ -17,7 +17,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_snprelate.html b/docs/reference/write_snprelate.html index 052ac9b5..7a243f3e 100644 --- a/docs/reference/write_snprelate.html +++ b/docs/reference/write_snprelate.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_stockr.html b/docs/reference/write_stockr.html index f51a6bb5..d581eab8 100644 --- a/docs/reference/write_stockr.html +++ b/docs/reference/write_stockr.html @@ -19,7 +19,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_structure.html b/docs/reference/write_structure.html index 016d1c9c..cfe8408f 100644 --- a/docs/reference/write_structure.html +++ b/docs/reference/write_structure.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1 diff --git a/docs/reference/write_vcf.html b/docs/reference/write_vcf.html index 943bf215..7f0efb79 100644 --- a/docs/reference/write_vcf.html +++ b/docs/reference/write_vcf.html @@ -20,7 +20,7 @@ radiator - 1.2.9 + 1.3.1