From 3a8cb4f3232ed995230e7f92467a49892b71580d Mon Sep 17 00:00:00 2001 From: Thierry Gosselin Date: Wed, 5 Jun 2024 11:38:49 -0400 Subject: [PATCH] # radiator 1.3.4 2024-06-05 * 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 --- DESCRIPTION | 4 ++-- NEWS.md | 6 ++++++ 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 | 4 ++-- docs/authors.html | 2 +- docs/index.html | 6 +++--- docs/news/index.html | 7 ++++++- 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 | 11 +++++++++-- 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 | 2 +- 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 | 2 +- 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 +- .../reference/plot_coverage_imbalance_diagnostic.html | 2 +- .../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 +- man/extract_coverage.Rd | 7 ++++++- man/markers_het.Rd | 2 +- 224 files changed, 254 insertions(+), 231 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3de71f6f..1cad5abe 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: radiator Type: Package Title: RADseq Data Exploration, Manipulation and Visualization using R -Version: 1.3.3 -Date: 2024-05-15 +Version: 1.3.4 +Date: 2024-06-05 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 4859f5d3..c2a52460 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# radiator 1.3.4 2024-06-05 + +* 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 + + # radiator 1.3.3 2024-05-15 * Fix issue #188 related to coverage in DArT 1row and 2rows format diff --git a/README.md b/README.md index 47736ef4..10fd3403 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,8 @@ [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) -[![packageversion](https://img.shields.io/badge/Package%20version-1.3.3-orange.svg)](commits/master) -[![Last-changedate](https://img.shields.io/badge/last%20change-2024--05--15-brightgreen.svg)](/commits/master) +[![packageversion](https://img.shields.io/badge/Package%20version-1.3.4-orange.svg)](commits/master) +[![Last-changedate](https://img.shields.io/badge/last%20change-2024--06--05-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 e00b54f1..3620659c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 79e2f890..59373bf2 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html index 4fc5288f..ecb6bdac 100644 --- a/docs/articles/get_started.html +++ b/docs/articles/get_started.html @@ -33,7 +33,7 @@ radiator - 1.3.3 + 1.3.4 @@ -91,7 +91,7 @@

Get Started

Thierry Gosselin

-

2024-05-15

+

2024-06-05

Source: vignettes/get_started.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index f9ba5fad..a271d546 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/articles/life_cycle.html b/docs/articles/life_cycle.html index 7f5b8100..27bd6f88 100644 --- a/docs/articles/life_cycle.html +++ b/docs/articles/life_cycle.html @@ -33,7 +33,7 @@ radiator - 1.3.3 + 1.3.4 @@ -91,7 +91,7 @@

Life Cycle

Thierry Gosselin

-

2024-05-15

+

2024-06-05

Source: vignettes/life_cycle.Rmd diff --git a/docs/articles/rad_genomics_computer_setup.html b/docs/articles/rad_genomics_computer_setup.html index 7511b10a..60ddacb2 100644 --- a/docs/articles/rad_genomics_computer_setup.html +++ b/docs/articles/rad_genomics_computer_setup.html @@ -33,7 +33,7 @@ radiator - 1.3.3 + 1.3.4 @@ -90,7 +90,7 @@

RADseq Genomics in R

computer setup

-

2024-05-15

+

2024-06-05

Source: vignettes/rad_genomics_computer_setup.Rmd diff --git a/docs/authors.html b/docs/authors.html index 72d0627b..b256eb29 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/index.html b/docs/index.html index 510d9ab7..6fa0528e 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ radiator - 1.3.3 + 1.3.4 @@ -177,8 +177,8 @@

Dev status

diff --git a/docs/news/index.html b/docs/news/index.html index 3392e5c0..781ef5fc 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 @@ -66,6 +66,11 @@

Changelog

Source: NEWS.md +
+

radiator 1.3.4 2024-06-05

+

radiator 1.3.3 2024-05-15

diff --git a/docs/reference/allele_count.html b/docs/reference/allele_count.html index 565376ec..f34a0bbf 100644 --- a/docs/reference/allele_count.html +++ b/docs/reference/allele_count.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/allele_frequencies.html b/docs/reference/allele_frequencies.html index d58b50db..3ef7bd15 100644 --- a/docs/reference/allele_frequencies.html +++ b/docs/reference/allele_frequencies.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/assign_defaults.html b/docs/reference/assign_defaults.html index 8ea10f07..040659d9 100644 --- a/docs/reference/assign_defaults.html +++ b/docs/reference/assign_defaults.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/bayescan_one.html b/docs/reference/bayescan_one.html index 8a6f12a7..61dfbf1f 100644 --- a/docs/reference/bayescan_one.html +++ b/docs/reference/bayescan_one.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/betas_estimator.html b/docs/reference/betas_estimator.html index b4db4eeb..74a8698d 100644 --- a/docs/reference/betas_estimator.html +++ b/docs/reference/betas_estimator.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/blacklist_hw.html b/docs/reference/blacklist_hw.html index 237ff851..93cee9bb 100644 --- a/docs/reference/blacklist_hw.html +++ b/docs/reference/blacklist_hw.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/boxplot_stats.html b/docs/reference/boxplot_stats.html index c488e1c2..31aad607 100644 --- a/docs/reference/boxplot_stats.html +++ b/docs/reference/boxplot_stats.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/calibrate_alleles.html b/docs/reference/calibrate_alleles.html index 690ede22..1a4455e7 100644 --- a/docs/reference/calibrate_alleles.html +++ b/docs/reference/calibrate_alleles.html @@ -24,7 +24,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/change_pop_names.html b/docs/reference/change_pop_names.html index 47c61e5a..b690e7e8 100644 --- a/docs/reference/change_pop_names.html +++ b/docs/reference/change_pop_names.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/check_args_class.html b/docs/reference/check_args_class.html index dffc37e6..c51c69c9 100644 --- a/docs/reference/check_args_class.html +++ b/docs/reference/check_args_class.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/check_dart.html b/docs/reference/check_dart.html index 7a6b21a6..b84e8644 100644 --- a/docs/reference/check_dart.html +++ b/docs/reference/check_dart.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/check_header_source_vcf.html b/docs/reference/check_header_source_vcf.html index bb585c73..4f8954f4 100644 --- a/docs/reference/check_header_source_vcf.html +++ b/docs/reference/check_header_source_vcf.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/check_pop_levels.html b/docs/reference/check_pop_levels.html index f50fc651..bc4c7c45 100644 --- a/docs/reference/check_pop_levels.html +++ b/docs/reference/check_pop_levels.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/clean_dart_colnames.html b/docs/reference/clean_dart_colnames.html index 883b4ffc..b3153cf4 100644 --- a/docs/reference/clean_dart_colnames.html +++ b/docs/reference/clean_dart_colnames.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/clean_dart_locus.html b/docs/reference/clean_dart_locus.html index bcf4cf4e..5501a63e 100644 --- a/docs/reference/clean_dart_locus.html +++ b/docs/reference/clean_dart_locus.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/clean_ind_names.html b/docs/reference/clean_ind_names.html index 71478aea..72026c05 100644 --- a/docs/reference/clean_ind_names.html +++ b/docs/reference/clean_ind_names.html @@ -22,7 +22,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/clean_markers_names.html b/docs/reference/clean_markers_names.html index 397d0bdc..aef61a15 100644 --- a/docs/reference/clean_markers_names.html +++ b/docs/reference/clean_markers_names.html @@ -23,7 +23,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/clean_pop_names.html b/docs/reference/clean_pop_names.html index 94dd1e30..97119315 100644 --- a/docs/reference/clean_pop_names.html +++ b/docs/reference/clean_pop_names.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/compound_assignment_pipe_operator.html b/docs/reference/compound_assignment_pipe_operator.html index f640917c..1769835e 100644 --- a/docs/reference/compound_assignment_pipe_operator.html +++ b/docs/reference/compound_assignment_pipe_operator.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/compute_maf.html b/docs/reference/compute_maf.html index 6b834ca0..7e57f537 100644 --- a/docs/reference/compute_maf.html +++ b/docs/reference/compute_maf.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/count_monomorphic.html b/docs/reference/count_monomorphic.html index 0c38d811..5b655ca5 100644 --- a/docs/reference/count_monomorphic.html +++ b/docs/reference/count_monomorphic.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/dart2gds.html b/docs/reference/dart2gds.html index 251edeea..cefb65dd 100644 --- a/docs/reference/dart2gds.html +++ b/docs/reference/dart2gds.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/data_info.html b/docs/reference/data_info.html index 936c40f2..0d740e53 100644 --- a/docs/reference/data_info.html +++ b/docs/reference/data_info.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_all_missing.html b/docs/reference/detect_all_missing.html index 84cf31f5..0f65a14b 100644 --- a/docs/reference/detect_all_missing.html +++ b/docs/reference/detect_all_missing.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_allele_problems.html b/docs/reference/detect_allele_problems.html index 88683e0e..8cdcbd02 100644 --- a/docs/reference/detect_allele_problems.html +++ b/docs/reference/detect_allele_problems.html @@ -25,7 +25,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_biallelic_markers.html b/docs/reference/detect_biallelic_markers.html index 5f2b50e3..b74a6d64 100644 --- a/docs/reference/detect_biallelic_markers.html +++ b/docs/reference/detect_biallelic_markers.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_biallelic_problems.html b/docs/reference/detect_biallelic_problems.html index 8f0c0ee6..fa11f77c 100644 --- a/docs/reference/detect_biallelic_problems.html +++ b/docs/reference/detect_biallelic_problems.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_dart_format.html b/docs/reference/detect_dart_format.html index f52c93ab..8fd774d3 100644 --- a/docs/reference/detect_dart_format.html +++ b/docs/reference/detect_dart_format.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_duplicate_genomes.html b/docs/reference/detect_duplicate_genomes.html index e6abab3e..2d0c882f 100644 --- a/docs/reference/detect_duplicate_genomes.html +++ b/docs/reference/detect_duplicate_genomes.html @@ -22,7 +22,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_genomic_format.html b/docs/reference/detect_genomic_format.html index 4b0d6ee4..e3829776 100644 --- a/docs/reference/detect_genomic_format.html +++ b/docs/reference/detect_genomic_format.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_het_outliers.html b/docs/reference/detect_het_outliers.html index ca7342c0..7eb53d3b 100644 --- a/docs/reference/detect_het_outliers.html +++ b/docs/reference/detect_het_outliers.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_microsatellites.html b/docs/reference/detect_microsatellites.html index b60d6b7b..2a7c706a 100644 --- a/docs/reference/detect_microsatellites.html +++ b/docs/reference/detect_microsatellites.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_mixed_genomes.html b/docs/reference/detect_mixed_genomes.html index e11a9aef..6d0820e6 100644 --- a/docs/reference/detect_mixed_genomes.html +++ b/docs/reference/detect_mixed_genomes.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_paralogs.html b/docs/reference/detect_paralogs.html index 205aab75..17609ea2 100644 --- a/docs/reference/detect_paralogs.html +++ b/docs/reference/detect_paralogs.html @@ -22,7 +22,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/detect_ref_genome.html b/docs/reference/detect_ref_genome.html index 4676fd68..8376ba98 100644 --- a/docs/reference/detect_ref_genome.html +++ b/docs/reference/detect_ref_genome.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/diagnostic_maf.html b/docs/reference/diagnostic_maf.html index b6b327e7..915fd234 100644 --- a/docs/reference/diagnostic_maf.html +++ b/docs/reference/diagnostic_maf.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/distance2tibble.html b/docs/reference/distance2tibble.html index 157cfb52..98ccaeb0 100644 --- a/docs/reference/distance2tibble.html +++ b/docs/reference/distance2tibble.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/distance_individuals.html b/docs/reference/distance_individuals.html index fe9f0c8d..a69729f0 100644 --- a/docs/reference/distance_individuals.html +++ b/docs/reference/distance_individuals.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/erase_genotypes.html b/docs/reference/erase_genotypes.html index aeb4a710..5f4fc712 100644 --- a/docs/reference/erase_genotypes.html +++ b/docs/reference/erase_genotypes.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/estimate_m.html b/docs/reference/estimate_m.html index 351c19f0..fb0a9590 100644 --- a/docs/reference/estimate_m.html +++ b/docs/reference/estimate_m.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/extract_coverage.html b/docs/reference/extract_coverage.html index 2ab35ee5..b9f7cc2d 100644 --- a/docs/reference/extract_coverage.html +++ b/docs/reference/extract_coverage.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 @@ -91,7 +91,8 @@

check_coverage

ad = TRUE, coverage.stats = c("sum", "mean", "median", "iqr"), subsample.info = 1, - verbose = TRUE + verbose = TRUE, + parallel.core = TRUE ) @@ -151,6 +152,12 @@

Arguments

the function is a little more chatty during execution. Default: verbose = TRUE.

+ +
parallel.core
+

(optional) The number of core used for parallel +execution during import. +Default: parallel.core = parallel::detectCores() - 1.

+ diff --git a/docs/reference/extract_dart_target_id.html b/docs/reference/extract_dart_target_id.html index f9378b36..06366fd6 100644 --- a/docs/reference/extract_dart_target_id.html +++ b/docs/reference/extract_dart_target_id.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/extract_data_source.html b/docs/reference/extract_data_source.html index bfb91775..7dc8faee 100644 --- a/docs/reference/extract_data_source.html +++ b/docs/reference/extract_data_source.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/extract_dots.html b/docs/reference/extract_dots.html index 4bc3de01..fd0bcd1e 100644 --- a/docs/reference/extract_dots.html +++ b/docs/reference/extract_dots.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/extract_genotypes_metadata.html b/docs/reference/extract_genotypes_metadata.html index c04158be..7aa9273e 100644 --- a/docs/reference/extract_genotypes_metadata.html +++ b/docs/reference/extract_genotypes_metadata.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/extract_individuals_metadata.html b/docs/reference/extract_individuals_metadata.html index 8d096840..fe976fb9 100644 --- a/docs/reference/extract_individuals_metadata.html +++ b/docs/reference/extract_individuals_metadata.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/extract_individuals_vcf.html b/docs/reference/extract_individuals_vcf.html index af261215..d04c486a 100644 --- a/docs/reference/extract_individuals_vcf.html +++ b/docs/reference/extract_individuals_vcf.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/extract_info_vcf.html b/docs/reference/extract_info_vcf.html index 36643ea8..8de76c91 100644 --- a/docs/reference/extract_info_vcf.html +++ b/docs/reference/extract_info_vcf.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/extract_markers_metadata.html b/docs/reference/extract_markers_metadata.html index a7dd8bab..1f8a248a 100644 --- a/docs/reference/extract_markers_metadata.html +++ b/docs/reference/extract_markers_metadata.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_blacklist_genotypes.html b/docs/reference/filter_blacklist_genotypes.html index 288991d3..b3ed14f2 100644 --- a/docs/reference/filter_blacklist_genotypes.html +++ b/docs/reference/filter_blacklist_genotypes.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_common_markers.html b/docs/reference/filter_common_markers.html index 8e2f8e42..4061c425 100644 --- a/docs/reference/filter_common_markers.html +++ b/docs/reference/filter_common_markers.html @@ -24,7 +24,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_coverage.html b/docs/reference/filter_coverage.html index 8ea5b2cc..69113610 100644 --- a/docs/reference/filter_coverage.html +++ b/docs/reference/filter_coverage.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_dart_reproducibility.html b/docs/reference/filter_dart_reproducibility.html index e5af3849..740bb150 100644 --- a/docs/reference/filter_dart_reproducibility.html +++ b/docs/reference/filter_dart_reproducibility.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_fis.html b/docs/reference/filter_fis.html index c9e99f7f..2c8d1bb7 100644 --- a/docs/reference/filter_fis.html +++ b/docs/reference/filter_fis.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_genotyping.html b/docs/reference/filter_genotyping.html index 6e5d2357..2598e08d 100644 --- a/docs/reference/filter_genotyping.html +++ b/docs/reference/filter_genotyping.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_het.html b/docs/reference/filter_het.html index 4c7dd8ed..97efdfe0 100644 --- a/docs/reference/filter_het.html +++ b/docs/reference/filter_het.html @@ -37,7 +37,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_hwe.html b/docs/reference/filter_hwe.html index c0e1080d..dddcfd84 100644 --- a/docs/reference/filter_hwe.html +++ b/docs/reference/filter_hwe.html @@ -35,7 +35,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_individuals.html b/docs/reference/filter_individuals.html index e803b995..9ee1f4dd 100644 --- a/docs/reference/filter_individuals.html +++ b/docs/reference/filter_individuals.html @@ -26,7 +26,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_ld.html b/docs/reference/filter_ld.html index 952131bf..4f8fe3ee 100644 --- a/docs/reference/filter_ld.html +++ b/docs/reference/filter_ld.html @@ -37,7 +37,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_monomorphic.html b/docs/reference/filter_monomorphic.html index 83349936..42dcb9a9 100644 --- a/docs/reference/filter_monomorphic.html +++ b/docs/reference/filter_monomorphic.html @@ -29,7 +29,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_rad.html b/docs/reference/filter_rad.html index 9a213313..12726db3 100644 --- a/docs/reference/filter_rad.html +++ b/docs/reference/filter_rad.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_snp_number.html b/docs/reference/filter_snp_number.html index 50b840ea..175f1517 100644 --- a/docs/reference/filter_snp_number.html +++ b/docs/reference/filter_snp_number.html @@ -25,7 +25,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_snp_position_read.html b/docs/reference/filter_snp_position_read.html index bdee4aca..f748cf14 100644 --- a/docs/reference/filter_snp_position_read.html +++ b/docs/reference/filter_snp_position_read.html @@ -23,7 +23,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/filter_whitelist.html b/docs/reference/filter_whitelist.html index 41bcfaf2..f7b87531 100644 --- a/docs/reference/filter_whitelist.html +++ b/docs/reference/filter_whitelist.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/folder_prefix.html b/docs/reference/folder_prefix.html index f22a8a69..860196b6 100644 --- a/docs/reference/folder_prefix.html +++ b/docs/reference/folder_prefix.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/folder_short.html b/docs/reference/folder_short.html index 54236246..5e88a9f1 100644 --- a/docs/reference/folder_short.html +++ b/docs/reference/folder_short.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/gds2tidy.html b/docs/reference/gds2tidy.html index e0cfeea9..406a219b 100644 --- a/docs/reference/gds2tidy.html +++ b/docs/reference/gds2tidy.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/generate_filename.html b/docs/reference/generate_filename.html index c3c42a0a..1aa02089 100644 --- a/docs/reference/generate_filename.html +++ b/docs/reference/generate_filename.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/generate_folder.html b/docs/reference/generate_folder.html index 807918d8..7b999775 100644 --- a/docs/reference/generate_folder.html +++ b/docs/reference/generate_folder.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/generate_geno_freq_boundaries.html b/docs/reference/generate_geno_freq_boundaries.html index c67920ed..f1f93dac 100644 --- a/docs/reference/generate_geno_freq_boundaries.html +++ b/docs/reference/generate_geno_freq_boundaries.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/generate_hzar.html b/docs/reference/generate_hzar.html index 571ab833..46736484 100644 --- a/docs/reference/generate_hzar.html +++ b/docs/reference/generate_hzar.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/generate_markers_metadata.html b/docs/reference/generate_markers_metadata.html index 17b90f9a..cff386d9 100644 --- a/docs/reference/generate_markers_metadata.html +++ b/docs/reference/generate_markers_metadata.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/generate_squeleton_folders.html b/docs/reference/generate_squeleton_folders.html index 10e1da37..015475f9 100644 --- a/docs/reference/generate_squeleton_folders.html +++ b/docs/reference/generate_squeleton_folders.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/generate_strata.html b/docs/reference/generate_strata.html index 5d5aff18..38c59989 100644 --- a/docs/reference/generate_strata.html +++ b/docs/reference/generate_strata.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/generate_whitelist.html b/docs/reference/generate_whitelist.html index e4db730f..bc9392d1 100644 --- a/docs/reference/generate_whitelist.html +++ b/docs/reference/generate_whitelist.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/genome_similarity.html b/docs/reference/genome_similarity.html index 5ac856a7..866bbe25 100644 --- a/docs/reference/genome_similarity.html +++ b/docs/reference/genome_similarity.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/genomic_converter.html b/docs/reference/genomic_converter.html index dce77f29..2c671c2b 100644 --- a/docs/reference/genomic_converter.html +++ b/docs/reference/genomic_converter.html @@ -31,7 +31,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/gt2array.html b/docs/reference/gt2array.html index c79214dd..63c4beda 100644 --- a/docs/reference/gt2array.html +++ b/docs/reference/gt2array.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/haplotype_reconstruction.html b/docs/reference/haplotype_reconstruction.html index 52be66a6..f5a412b2 100644 --- a/docs/reference/haplotype_reconstruction.html +++ b/docs/reference/haplotype_reconstruction.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/hwe_analysis.html b/docs/reference/hwe_analysis.html index 6165b475..b6a96971 100644 --- a/docs/reference/hwe_analysis.html +++ b/docs/reference/hwe_analysis.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/ibdg_fh.html b/docs/reference/ibdg_fh.html index 84dead9c..0ccf1a3e 100644 --- a/docs/reference/ibdg_fh.html +++ b/docs/reference/ibdg_fh.html @@ -48,7 +48,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/import_dart.html b/docs/reference/import_dart.html index a4f02264..17148602 100644 --- a/docs/reference/import_dart.html +++ b/docs/reference/import_dart.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/ind_total_reads.html b/docs/reference/ind_total_reads.html index 605e8e8e..48a77ab6 100644 --- a/docs/reference/ind_total_reads.html +++ b/docs/reference/ind_total_reads.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/index.html b/docs/reference/index.html index 46de0e9f..70645831 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/individuals2strata.html b/docs/reference/individuals2strata.html index 208a8235..3bc19983 100644 --- a/docs/reference/individuals2strata.html +++ b/docs/reference/individuals2strata.html @@ -25,7 +25,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/join_strata.html b/docs/reference/join_strata.html index f1dc86a2..9de248a4 100644 --- a/docs/reference/join_strata.html +++ b/docs/reference/join_strata.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/ld2df.html b/docs/reference/ld2df.html index 05e0b3e0..44ecc60a 100644 --- a/docs/reference/ld2df.html +++ b/docs/reference/ld2df.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/ld_boxplot.html b/docs/reference/ld_boxplot.html index 30ce41f2..08172eac 100644 --- a/docs/reference/ld_boxplot.html +++ b/docs/reference/ld_boxplot.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/ld_missing.html b/docs/reference/ld_missing.html index 17338a95..281c0539 100644 --- a/docs/reference/ld_missing.html +++ b/docs/reference/ld_missing.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/ld_pruning.html b/docs/reference/ld_pruning.html index acff0396..a06bfd52 100644 --- a/docs/reference/ld_pruning.html +++ b/docs/reference/ld_pruning.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/list_filters.html b/docs/reference/list_filters.html index 0c0fce32..5ca12fc1 100644 --- a/docs/reference/list_filters.html +++ b/docs/reference/list_filters.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/markers_genotyped_helper.html b/docs/reference/markers_genotyped_helper.html index aede1ab0..cd407929 100644 --- a/docs/reference/markers_genotyped_helper.html +++ b/docs/reference/markers_genotyped_helper.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/merge_dart.html b/docs/reference/merge_dart.html index 51313a01..8723034d 100644 --- a/docs/reference/merge_dart.html +++ b/docs/reference/merge_dart.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/message_func_call.html b/docs/reference/message_func_call.html index b0a90bd4..eaaca50c 100644 --- a/docs/reference/message_func_call.html +++ b/docs/reference/message_func_call.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/missing_per_pop.html b/docs/reference/missing_per_pop.html index f734e751..1346923f 100644 --- a/docs/reference/missing_per_pop.html +++ b/docs/reference/missing_per_pop.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/n.html b/docs/reference/n.html index 650b55af..5b50b0f3 100644 --- a/docs/reference/n.html +++ b/docs/reference/n.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/not_common_markers.html b/docs/reference/not_common_markers.html index 52702221..6ba27e6d 100644 --- a/docs/reference/not_common_markers.html +++ b/docs/reference/not_common_markers.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/parallel_core_opt.html b/docs/reference/parallel_core_opt.html index 5988fc0e..f47a74b4 100644 --- a/docs/reference/parallel_core_opt.html +++ b/docs/reference/parallel_core_opt.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/parse_gds_metadata.html b/docs/reference/parse_gds_metadata.html index ad2f807e..5adb957c 100644 --- a/docs/reference/parse_gds_metadata.html +++ b/docs/reference/parse_gds_metadata.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/pi.html b/docs/reference/pi.html index ac69dca4..dca393ca 100644 --- a/docs/reference/pi.html +++ b/docs/reference/pi.html @@ -26,7 +26,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/pi_pop.html b/docs/reference/pi_pop.html index 60944089..bf51afa8 100644 --- a/docs/reference/pi_pop.html +++ b/docs/reference/pi_pop.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/pi_rad.html b/docs/reference/pi_rad.html index aacecefd..01e38d49 100644 --- a/docs/reference/pi_rad.html +++ b/docs/reference/pi_rad.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html index 0585be18..f9deeb3f 100644 --- a/docs/reference/pipe.html +++ b/docs/reference/pipe.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_bayescan.html b/docs/reference/plot_bayescan.html index 492e4e8e..9b825746 100644 --- a/docs/reference/plot_bayescan.html +++ b/docs/reference/plot_bayescan.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_boxplot_coverage.html b/docs/reference/plot_boxplot_coverage.html index 17fbd811..96c2c302 100644 --- a/docs/reference/plot_boxplot_coverage.html +++ b/docs/reference/plot_boxplot_coverage.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_boxplot_diversity.html b/docs/reference/plot_boxplot_diversity.html index f1f295cf..37465750 100644 --- a/docs/reference/plot_boxplot_diversity.html +++ b/docs/reference/plot_boxplot_diversity.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_coverage_imbalance_diagnostic.html b/docs/reference/plot_coverage_imbalance_diagnostic.html index 44bc273b..dbf6299f 100644 --- a/docs/reference/plot_coverage_imbalance_diagnostic.html +++ b/docs/reference/plot_coverage_imbalance_diagnostic.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_density_distribution_coverage.html b/docs/reference/plot_density_distribution_coverage.html index 0937fe36..53d862f6 100644 --- a/docs/reference/plot_density_distribution_coverage.html +++ b/docs/reference/plot_density_distribution_coverage.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_density_distribution_het.html b/docs/reference/plot_density_distribution_het.html index 592c36af..428ecc0c 100644 --- a/docs/reference/plot_density_distribution_het.html +++ b/docs/reference/plot_density_distribution_het.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_density_distribution_maf.html b/docs/reference/plot_density_distribution_maf.html index 750b900c..666d57e1 100644 --- a/docs/reference/plot_density_distribution_maf.html +++ b/docs/reference/plot_density_distribution_maf.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_distribution_diversity.html b/docs/reference/plot_distribution_diversity.html index 410c85b0..7790f744 100644 --- a/docs/reference/plot_distribution_diversity.html +++ b/docs/reference/plot_distribution_diversity.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_het_outliers.html b/docs/reference/plot_het_outliers.html index ae00754d..a108a532 100644 --- a/docs/reference/plot_het_outliers.html +++ b/docs/reference/plot_het_outliers.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_snp_number_loci.html b/docs/reference/plot_snp_number_loci.html index f51e58a9..9ce9a822 100644 --- a/docs/reference/plot_snp_number_loci.html +++ b/docs/reference/plot_snp_number_loci.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_snp_position_read.html b/docs/reference/plot_snp_position_read.html index 3d03575c..2dcbf6dd 100644 --- a/docs/reference/plot_snp_position_read.html +++ b/docs/reference/plot_snp_position_read.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/plot_upset.html b/docs/reference/plot_upset.html index aa1218d7..cb52c6bc 100644 --- a/docs/reference/plot_upset.html +++ b/docs/reference/plot_upset.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/private_alleles.html b/docs/reference/private_alleles.html index 7ac1d578..ec6b6f9f 100644 --- a/docs/reference/private_alleles.html +++ b/docs/reference/private_alleles.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/private_haplotypes.html b/docs/reference/private_haplotypes.html index 1af437f0..7c2c60ea 100644 --- a/docs/reference/private_haplotypes.html +++ b/docs/reference/private_haplotypes.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_common_arguments.html b/docs/reference/radiator_common_arguments.html index 3e9357f3..60ef0e9e 100644 --- a/docs/reference/radiator_common_arguments.html +++ b/docs/reference/radiator_common_arguments.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_dots.html b/docs/reference/radiator_dots.html index 4a63653c..f469fad2 100644 --- a/docs/reference/radiator_dots.html +++ b/docs/reference/radiator_dots.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_folder.html b/docs/reference/radiator_folder.html index f956f508..56a8c2a9 100644 --- a/docs/reference/radiator_folder.html +++ b/docs/reference/radiator_folder.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_function_header.html b/docs/reference/radiator_function_header.html index c34ad494..4f2a84cd 100644 --- a/docs/reference/radiator_function_header.html +++ b/docs/reference/radiator_function_header.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_gds.html b/docs/reference/radiator_gds.html index 28716746..71e90e1c 100644 --- a/docs/reference/radiator_gds.html +++ b/docs/reference/radiator_gds.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_gds_skeleton.html b/docs/reference/radiator_gds_skeleton.html index 793c3f81..a6e87360 100644 --- a/docs/reference/radiator_gds_skeleton.html +++ b/docs/reference/radiator_gds_skeleton.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_packages_dep.html b/docs/reference/radiator_packages_dep.html index 8204a250..c09d106b 100644 --- a/docs/reference/radiator_packages_dep.html +++ b/docs/reference/radiator_packages_dep.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_parameters.html b/docs/reference/radiator_parameters.html index c22bcb3b..d346f70e 100644 --- a/docs/reference/radiator_parameters.html +++ b/docs/reference/radiator_parameters.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_pkg_install.html b/docs/reference/radiator_pkg_install.html index 1bdd53b5..da4afa13 100644 --- a/docs/reference/radiator_pkg_install.html +++ b/docs/reference/radiator_pkg_install.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_question.html b/docs/reference/radiator_question.html index 8832f01b..866811f5 100644 --- a/docs/reference/radiator_question.html +++ b/docs/reference/radiator_question.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_results_message.html b/docs/reference/radiator_results_message.html index 3d806023..ac45dcd1 100644 --- a/docs/reference/radiator_results_message.html +++ b/docs/reference/radiator_results_message.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_snakecase.html b/docs/reference/radiator_snakecase.html index bf64d00a..a957cc7c 100644 --- a/docs/reference/radiator_snakecase.html +++ b/docs/reference/radiator_snakecase.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_split_tibble.html b/docs/reference/radiator_split_tibble.html index 3b099191..b94c3d77 100644 --- a/docs/reference/radiator_split_tibble.html +++ b/docs/reference/radiator_split_tibble.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_tic.html b/docs/reference/radiator_tic.html index c249da60..d5138c6e 100644 --- a/docs/reference/radiator_tic.html +++ b/docs/reference/radiator_tic.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/radiator_toc.html b/docs/reference/radiator_toc.html index 76510cd7..00d8bea4 100644 --- a/docs/reference/radiator_toc.html +++ b/docs/reference/radiator_toc.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/read_blacklist_genotypes.html b/docs/reference/read_blacklist_genotypes.html index cd49840b..45c84543 100644 --- a/docs/reference/read_blacklist_genotypes.html +++ b/docs/reference/read_blacklist_genotypes.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/read_blacklist_id.html b/docs/reference/read_blacklist_id.html index 8bd6c308..17bd0c87 100644 --- a/docs/reference/read_blacklist_id.html +++ b/docs/reference/read_blacklist_id.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/read_dart.html b/docs/reference/read_dart.html index 7ffaf3f4..460c42b6 100644 --- a/docs/reference/read_dart.html +++ b/docs/reference/read_dart.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/read_plink.html b/docs/reference/read_plink.html index 20cefae1..57fecb34 100644 --- a/docs/reference/read_plink.html +++ b/docs/reference/read_plink.html @@ -24,7 +24,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/read_rad.html b/docs/reference/read_rad.html index 5f85d666..44c52659 100644 --- a/docs/reference/read_rad.html +++ b/docs/reference/read_rad.html @@ -24,7 +24,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/read_strata.html b/docs/reference/read_strata.html index 59858576..d9eb6450 100644 --- a/docs/reference/read_strata.html +++ b/docs/reference/read_strata.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/read_vcf.html b/docs/reference/read_vcf.html index 75b355f0..7e2e5c9c 100644 --- a/docs/reference/read_vcf.html +++ b/docs/reference/read_vcf.html @@ -27,7 +27,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/read_whitelist.html b/docs/reference/read_whitelist.html index b9942883..284160d3 100644 --- a/docs/reference/read_whitelist.html +++ b/docs/reference/read_whitelist.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/remove_duplicates.html b/docs/reference/remove_duplicates.html index 384cd95b..24322e7d 100644 --- a/docs/reference/remove_duplicates.html +++ b/docs/reference/remove_duplicates.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/replace_by_na.html b/docs/reference/replace_by_na.html index 6a4dda8e..445ecfc5 100644 --- a/docs/reference/replace_by_na.html +++ b/docs/reference/replace_by_na.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/reset_filters.html b/docs/reference/reset_filters.html index 458020b2..02b65ed3 100644 --- a/docs/reference/reset_filters.html +++ b/docs/reference/reset_filters.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/run_bayescan.html b/docs/reference/run_bayescan.html index c534bfb5..836bd611 100644 --- a/docs/reference/run_bayescan.html +++ b/docs/reference/run_bayescan.html @@ -31,7 +31,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/separate_gt.html b/docs/reference/separate_gt.html index 9eaebe4f..98c03ad7 100644 --- a/docs/reference/separate_gt.html +++ b/docs/reference/separate_gt.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/separate_markers.html b/docs/reference/separate_markers.html index cbd8734d..971ae215 100644 --- a/docs/reference/separate_markers.html +++ b/docs/reference/separate_markers.html @@ -23,7 +23,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/sex_markers_plot.html b/docs/reference/sex_markers_plot.html index a50121b0..51a4a87a 100644 --- a/docs/reference/sex_markers_plot.html +++ b/docs/reference/sex_markers_plot.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/sexy_markers.html b/docs/reference/sexy_markers.html index 666545ed..48937ad3 100644 --- a/docs/reference/sexy_markers.html +++ b/docs/reference/sexy_markers.html @@ -22,7 +22,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/simulate_genos_from_posterior.html b/docs/reference/simulate_genos_from_posterior.html index 8b9ec6f9..609cc892 100644 --- a/docs/reference/simulate_genos_from_posterior.html +++ b/docs/reference/simulate_genos_from_posterior.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/split_tibble_rows.html b/docs/reference/split_tibble_rows.html index b690e836..2d7ca63b 100644 --- a/docs/reference/split_tibble_rows.html +++ b/docs/reference/split_tibble_rows.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/split_vcf.html b/docs/reference/split_vcf.html index 66b27d42..5c14343d 100644 --- a/docs/reference/split_vcf.html +++ b/docs/reference/split_vcf.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/strata_haplo.html b/docs/reference/strata_haplo.html index 84b5281f..e20040bc 100644 --- a/docs/reference/strata_haplo.html +++ b/docs/reference/strata_haplo.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/subsampling_data.html b/docs/reference/subsampling_data.html index ae009819..d0e9413e 100644 --- a/docs/reference/subsampling_data.html +++ b/docs/reference/subsampling_data.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/summarise_genotypes.html b/docs/reference/summarise_genotypes.html index 109c2e28..0add851b 100644 --- a/docs/reference/summarise_genotypes.html +++ b/docs/reference/summarise_genotypes.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/summarize_sex.html b/docs/reference/summarize_sex.html index ff53f89d..693cb631 100644 --- a/docs/reference/summarize_sex.html +++ b/docs/reference/summarize_sex.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/summary_gds.html b/docs/reference/summary_gds.html index 13a224e6..55233e9a 100644 --- a/docs/reference/summary_gds.html +++ b/docs/reference/summary_gds.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/summary_rad.html b/docs/reference/summary_rad.html index 7972e1e3..d5523a7c 100644 --- a/docs/reference/summary_rad.html +++ b/docs/reference/summary_rad.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/summary_strata.html b/docs/reference/summary_strata.html index cda73c7c..e6c4b2a6 100644 --- a/docs/reference/summary_strata.html +++ b/docs/reference/summary_strata.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/switch_allele_count.html b/docs/reference/switch_allele_count.html index 6652c83f..c8f9e6a5 100644 --- a/docs/reference/switch_allele_count.html +++ b/docs/reference/switch_allele_count.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/switch_genotypes.html b/docs/reference/switch_genotypes.html index 8d2d3cc4..762b708d 100644 --- a/docs/reference/switch_genotypes.html +++ b/docs/reference/switch_genotypes.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/sync_gds.html b/docs/reference/sync_gds.html index 7e349b48..ebe527e2 100644 --- a/docs/reference/sync_gds.html +++ b/docs/reference/sync_gds.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tibble_stats.html b/docs/reference/tibble_stats.html index 635fbea2..bf32c3cd 100644 --- a/docs/reference/tibble_stats.html +++ b/docs/reference/tibble_stats.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy2gds.html b/docs/reference/tidy2gds.html index a9d5a8e3..c2e5b740 100644 --- a/docs/reference/tidy2gds.html +++ b/docs/reference/tidy2gds.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy2wide.html b/docs/reference/tidy2wide.html index 3a97c801..8fd58654 100644 --- a/docs/reference/tidy2wide.html +++ b/docs/reference/tidy2wide.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_dart_metadata.html b/docs/reference/tidy_dart_metadata.html index 1d0dbbc1..58a83da3 100644 --- a/docs/reference/tidy_dart_metadata.html +++ b/docs/reference/tidy_dart_metadata.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_fstat.html b/docs/reference/tidy_fstat.html index 7ed7c4b4..b28d279e 100644 --- a/docs/reference/tidy_fstat.html +++ b/docs/reference/tidy_fstat.html @@ -25,7 +25,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_genepop.html b/docs/reference/tidy_genepop.html index 03b6fcb7..d2f61ecb 100644 --- a/docs/reference/tidy_genepop.html +++ b/docs/reference/tidy_genepop.html @@ -25,7 +25,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_genind.html b/docs/reference/tidy_genind.html index 82e77677..73350613 100644 --- a/docs/reference/tidy_genind.html +++ b/docs/reference/tidy_genind.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_genlight.html b/docs/reference/tidy_genlight.html index 9bc79f91..18ef4e35 100644 --- a/docs/reference/tidy_genlight.html +++ b/docs/reference/tidy_genlight.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_genomic_data.html b/docs/reference/tidy_genomic_data.html index 51001696..c2181815 100644 --- a/docs/reference/tidy_genomic_data.html +++ b/docs/reference/tidy_genomic_data.html @@ -26,7 +26,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_gtypes.html b/docs/reference/tidy_gtypes.html index 80a269d0..f2e71c88 100644 --- a/docs/reference/tidy_gtypes.html +++ b/docs/reference/tidy_gtypes.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_plink.html b/docs/reference/tidy_plink.html index 615d100f..c4c3c96f 100644 --- a/docs/reference/tidy_plink.html +++ b/docs/reference/tidy_plink.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_vcf.html b/docs/reference/tidy_vcf.html index c62f87b1..140379e4 100644 --- a/docs/reference/tidy_vcf.html +++ b/docs/reference/tidy_vcf.html @@ -24,7 +24,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/tidy_wide.html b/docs/reference/tidy_wide.html index b06ad6c8..ea440e02 100644 --- a/docs/reference/tidy_wide.html +++ b/docs/reference/tidy_wide.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/update_bl_individuals.html b/docs/reference/update_bl_individuals.html index 25b42f8f..992f6399 100644 --- a/docs/reference/update_bl_individuals.html +++ b/docs/reference/update_bl_individuals.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/update_bl_markers.html b/docs/reference/update_bl_markers.html index 73bf184c..9a0d14af 100644 --- a/docs/reference/update_bl_markers.html +++ b/docs/reference/update_bl_markers.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/update_filter_parameter.html b/docs/reference/update_filter_parameter.html index 46256cac..0966161b 100644 --- a/docs/reference/update_filter_parameter.html +++ b/docs/reference/update_filter_parameter.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/update_radiator_gds.html b/docs/reference/update_radiator_gds.html index e8afd052..7245a4c1 100644 --- a/docs/reference/update_radiator_gds.html +++ b/docs/reference/update_radiator_gds.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/vcf_strata.html b/docs/reference/vcf_strata.html index 94c0861f..8f19ed9c 100644 --- a/docs/reference/vcf_strata.html +++ b/docs/reference/vcf_strata.html @@ -18,7 +18,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_arlequin.html b/docs/reference/write_arlequin.html index eb8797ca..323b789d 100644 --- a/docs/reference/write_arlequin.html +++ b/docs/reference/write_arlequin.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_bayescan.html b/docs/reference/write_bayescan.html index 478de974..914e42c6 100644 --- a/docs/reference/write_bayescan.html +++ b/docs/reference/write_bayescan.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_betadiv.html b/docs/reference/write_betadiv.html index b6161cd9..4ce07623 100644 --- a/docs/reference/write_betadiv.html +++ b/docs/reference/write_betadiv.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_colony.html b/docs/reference/write_colony.html index dc291d6b..f586eeac 100644 --- a/docs/reference/write_colony.html +++ b/docs/reference/write_colony.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_dadi.html b/docs/reference/write_dadi.html index 373976e1..5add85bd 100644 --- a/docs/reference/write_dadi.html +++ b/docs/reference/write_dadi.html @@ -23,7 +23,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_fasta.html b/docs/reference/write_fasta.html index eb180aff..481d4206 100644 --- a/docs/reference/write_fasta.html +++ b/docs/reference/write_fasta.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_faststructure.html b/docs/reference/write_faststructure.html index 9bce50dc..cdc21ba5 100644 --- a/docs/reference/write_faststructure.html +++ b/docs/reference/write_faststructure.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_fineradstructure.html b/docs/reference/write_fineradstructure.html index a5103558..c14859fa 100644 --- a/docs/reference/write_fineradstructure.html +++ b/docs/reference/write_fineradstructure.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_gds.html b/docs/reference/write_gds.html index 030c0f4a..045fc68a 100644 --- a/docs/reference/write_gds.html +++ b/docs/reference/write_gds.html @@ -21,7 +21,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_genepop.html b/docs/reference/write_genepop.html index 0395c0bf..bd4bdb97 100644 --- a/docs/reference/write_genepop.html +++ b/docs/reference/write_genepop.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_genepopedit.html b/docs/reference/write_genepopedit.html index c7d58052..2c8a09e0 100644 --- a/docs/reference/write_genepopedit.html +++ b/docs/reference/write_genepopedit.html @@ -32,7 +32,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_genind.html b/docs/reference/write_genind.html index 6810055d..02d8e207 100644 --- a/docs/reference/write_genind.html +++ b/docs/reference/write_genind.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_genlight.html b/docs/reference/write_genlight.html index 494cac37..19ef5f61 100644 --- a/docs/reference/write_genlight.html +++ b/docs/reference/write_genlight.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_gsi_sim.html b/docs/reference/write_gsi_sim.html index 2b033be2..5760866d 100644 --- a/docs/reference/write_gsi_sim.html +++ b/docs/reference/write_gsi_sim.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_gtypes.html b/docs/reference/write_gtypes.html index c1ee7efa..0a92fd18 100644 --- a/docs/reference/write_gtypes.html +++ b/docs/reference/write_gtypes.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_hapmap.html b/docs/reference/write_hapmap.html index 753bb0ea..fe7b5937 100644 --- a/docs/reference/write_hapmap.html +++ b/docs/reference/write_hapmap.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_hierfstat.html b/docs/reference/write_hierfstat.html index 17de933b..d4df67f7 100644 --- a/docs/reference/write_hierfstat.html +++ b/docs/reference/write_hierfstat.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_hzar.html b/docs/reference/write_hzar.html index 65618a72..4c54df56 100644 --- a/docs/reference/write_hzar.html +++ b/docs/reference/write_hzar.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_ldna.html b/docs/reference/write_ldna.html index a6a96e0a..f5a5a518 100644 --- a/docs/reference/write_ldna.html +++ b/docs/reference/write_ldna.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_maverick.html b/docs/reference/write_maverick.html index cb547cf2..68607d2c 100644 --- a/docs/reference/write_maverick.html +++ b/docs/reference/write_maverick.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_pcadapt.html b/docs/reference/write_pcadapt.html index 43da45b5..e63a46fa 100644 --- a/docs/reference/write_pcadapt.html +++ b/docs/reference/write_pcadapt.html @@ -22,7 +22,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_plink.html b/docs/reference/write_plink.html index d5c324f3..c0c921e3 100644 --- a/docs/reference/write_plink.html +++ b/docs/reference/write_plink.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_rad.html b/docs/reference/write_rad.html index dee1bb78..e6f27696 100644 --- a/docs/reference/write_rad.html +++ b/docs/reference/write_rad.html @@ -28,7 +28,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_related.html b/docs/reference/write_related.html index 2a39deb6..486b1833 100644 --- a/docs/reference/write_related.html +++ b/docs/reference/write_related.html @@ -24,7 +24,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_rubias.html b/docs/reference/write_rubias.html index 7865aeb9..70e54123 100644 --- a/docs/reference/write_rubias.html +++ b/docs/reference/write_rubias.html @@ -17,7 +17,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_snprelate.html b/docs/reference/write_snprelate.html index 3e474925..cabf6579 100644 --- a/docs/reference/write_snprelate.html +++ b/docs/reference/write_snprelate.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_stockr.html b/docs/reference/write_stockr.html index 625f5a4c..2a4365cf 100644 --- a/docs/reference/write_stockr.html +++ b/docs/reference/write_stockr.html @@ -19,7 +19,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_structure.html b/docs/reference/write_structure.html index af11328f..bbe38255 100644 --- a/docs/reference/write_structure.html +++ b/docs/reference/write_structure.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/docs/reference/write_vcf.html b/docs/reference/write_vcf.html index 1a670d02..8b5c4cdb 100644 --- a/docs/reference/write_vcf.html +++ b/docs/reference/write_vcf.html @@ -20,7 +20,7 @@ radiator - 1.3.3 + 1.3.4 diff --git a/man/extract_coverage.Rd b/man/extract_coverage.Rd index 7975c130..d106fa06 100644 --- a/man/extract_coverage.Rd +++ b/man/extract_coverage.Rd @@ -20,7 +20,8 @@ extract_coverage( ad = TRUE, coverage.stats = c("sum", "mean", "median", "iqr"), subsample.info = 1, - verbose = TRUE + verbose = TRUE, + parallel.core = TRUE ) } \arguments{ @@ -56,6 +57,10 @@ The subsample proportion used (e.g. 0.3 or none the default).} \item{verbose}{(optional, logical) When \code{verbose = TRUE} the function is a little more chatty during execution. Default: \code{verbose = TRUE}.} + +\item{parallel.core}{(optional) The number of core used for parallel +execution during import. +Default: \code{parallel.core = parallel::detectCores() - 1}.} } \description{ Check that the coverage info is in the GDS. By default, it will diff --git a/man/markers_het.Rd b/man/markers_het.Rd index 7411a058..8ce84e98 100644 --- a/man/markers_het.Rd +++ b/man/markers_het.Rd @@ -4,7 +4,7 @@ \alias{markers_het} \title{markers_het} \usage{ -markers_het(gds) +markers_het(gds, parallel.core = TRUE) } \description{ Calculate markers het