From a2d63d5a8b180b8c7bc0b9dbee637c8d22d27c06 Mon Sep 17 00:00:00 2001 From: Thierry Gosselin Date: Wed, 15 May 2024 10:06:05 -0400 Subject: [PATCH] # radiator 1.3.3 2024-05-15 * Fix issue #188 related to coverage in DArT 1row and 2rows format --- DESCRIPTION | 4 +- NEWS.md | 7 + R/gds.R | 40 +- README.md | 4 +- docs/404.html | 6 +- docs/LICENSE.html | 6 +- docs/articles/get_started.html | 8 +- docs/articles/index.html | 6 +- docs/articles/life_cycle.html | 8 +- .../articles/rad_genomics_computer_setup.html | 352 +++++++++--------- docs/authors.html | 8 +- docs/index.html | 11 +- docs/news/index.html | 16 +- docs/pkgdown.yml | 6 +- docs/reference/Exposition_pipe_operator.html | 6 +- docs/reference/allele_count.html | 6 +- docs/reference/allele_frequencies.html | 6 +- docs/reference/assign_defaults.html | 6 +- docs/reference/bayescan_one.html | 6 +- docs/reference/betas_estimator.html | 6 +- docs/reference/blacklist_hw.html | 6 +- docs/reference/boxplot_stats.html | 6 +- docs/reference/calibrate_alleles.html | 6 +- docs/reference/change_pop_names.html | 6 +- docs/reference/check_args_class.html | 6 +- docs/reference/check_dart.html | 6 +- docs/reference/check_header_source_vcf.html | 6 +- docs/reference/check_pop_levels.html | 6 +- docs/reference/clean_dart_colnames.html | 6 +- docs/reference/clean_dart_locus.html | 6 +- docs/reference/clean_ind_names.html | 6 +- docs/reference/clean_markers_names.html | 6 +- docs/reference/clean_pop_names.html | 6 +- .../compound_assignment_pipe_operator.html | 6 +- docs/reference/compute_maf.html | 6 +- docs/reference/count_monomorphic.html | 6 +- docs/reference/dart2gds.html | 6 +- docs/reference/data_info.html | 6 +- docs/reference/detect_all_missing.html | 6 +- docs/reference/detect_allele_problems.html | 6 +- docs/reference/detect_biallelic_markers.html | 6 +- docs/reference/detect_biallelic_problems.html | 6 +- docs/reference/detect_dart_format.html | 6 +- docs/reference/detect_duplicate_genomes.html | 11 +- docs/reference/detect_genomic_format.html | 6 +- docs/reference/detect_het_outliers.html | 6 +- docs/reference/detect_microsatellites.html | 6 +- docs/reference/detect_mixed_genomes.html | 6 +- docs/reference/detect_paralogs.html | 6 +- docs/reference/detect_ref_genome.html | 6 +- docs/reference/diagnostic_maf.html | 6 +- docs/reference/distance2tibble.html | 6 +- docs/reference/distance_individuals.html | 6 +- docs/reference/erase_genotypes.html | 6 +- docs/reference/estimate_m.html | 6 +- docs/reference/extract_coverage.html | 8 +- docs/reference/extract_dart_target_id.html | 6 +- docs/reference/extract_data_source.html | 6 +- docs/reference/extract_dots.html | 6 +- .../reference/extract_genotypes_metadata.html | 6 +- .../extract_individuals_metadata.html | 6 +- docs/reference/extract_individuals_vcf.html | 6 +- docs/reference/extract_info_vcf.html | 6 +- docs/reference/extract_markers_metadata.html | 6 +- .../reference/filter_blacklist_genotypes.html | 6 +- docs/reference/filter_common_markers.html | 6 +- docs/reference/filter_coverage.html | 6 +- .../filter_dart_reproducibility.html | 6 +- docs/reference/filter_fis.html | 6 +- docs/reference/filter_genotyping.html | 6 +- docs/reference/filter_het.html | 6 +- docs/reference/filter_hwe.html | 6 +- docs/reference/filter_individuals.html | 11 +- docs/reference/filter_ld.html | 6 +- docs/reference/filter_monomorphic.html | 6 +- docs/reference/filter_rad.html | 6 +- docs/reference/filter_snp_number.html | 6 +- docs/reference/filter_snp_position_read.html | 6 +- docs/reference/filter_whitelist.html | 6 +- docs/reference/folder_prefix.html | 6 +- docs/reference/folder_short.html | 6 +- docs/reference/gds2tidy.html | 6 +- docs/reference/generate_filename.html | 6 +- docs/reference/generate_folder.html | 6 +- .../generate_geno_freq_boundaries.html | 6 +- docs/reference/generate_hzar.html | 6 +- docs/reference/generate_markers_metadata.html | 6 +- .../reference/generate_squeleton_folders.html | 6 +- docs/reference/generate_strata.html | 6 +- docs/reference/generate_whitelist.html | 6 +- docs/reference/genome_similarity.html | 6 +- docs/reference/genomic_converter.html | 8 +- docs/reference/gt2array.html | 6 +- docs/reference/haplotype_reconstruction.html | 6 +- docs/reference/hwe_analysis.html | 6 +- docs/reference/ibdg_fh.html | 6 +- docs/reference/import_dart.html | 6 +- docs/reference/ind_total_reads.html | 6 +- docs/reference/index.html | 21 +- docs/reference/individuals2strata.html | 6 +- docs/reference/join_strata.html | 6 +- docs/reference/ld2df.html | 6 +- docs/reference/ld_boxplot.html | 6 +- docs/reference/ld_missing.html | 6 +- docs/reference/ld_pruning.html | 6 +- docs/reference/list_filters.html | 6 +- docs/reference/markers_genotyped_helper.html | 6 +- docs/reference/merge_dart.html | 6 +- docs/reference/message_func_call.html | 6 +- docs/reference/missing_per_pop.html | 6 +- docs/reference/n.html | 6 +- docs/reference/not_common_markers.html | 6 +- docs/reference/parallel_core_opt.html | 6 +- docs/reference/parse_gds_metadata.html | 6 +- docs/reference/pi.html | 6 +- docs/reference/pi_pop.html | 6 +- docs/reference/pi_rad.html | 6 +- docs/reference/pipe.html | 6 +- docs/reference/plot_bayescan.html | 6 +- docs/reference/plot_boxplot_coverage.html | 6 +- docs/reference/plot_boxplot_diversity.html | 6 +- .../plot_coverage_imbalance_diagnostic.html | 6 +- .../plot_density_distribution_coverage.html | 6 +- .../plot_density_distribution_het.html | 11 +- .../plot_density_distribution_maf.html | 11 +- .../plot_distribution_diversity.html | 6 +- docs/reference/plot_het_outliers.html | 6 +- docs/reference/plot_snp_number_loci.html | 6 +- docs/reference/plot_snp_position_read.html | 6 +- docs/reference/plot_upset.html | 6 +- docs/reference/private_alleles.html | 6 +- docs/reference/private_haplotypes.html | 6 +- docs/reference/radiator_common_arguments.html | 23 +- docs/reference/radiator_dots.html | 18 +- docs/reference/radiator_folder.html | 6 +- docs/reference/radiator_function_header.html | 6 +- docs/reference/radiator_gds.html | 6 +- docs/reference/radiator_gds_skeleton.html | 6 +- docs/reference/radiator_packages_dep.html | 6 +- docs/reference/radiator_parameters.html | 6 +- docs/reference/radiator_pkg_install.html | 6 +- docs/reference/radiator_question.html | 6 +- docs/reference/radiator_results_message.html | 6 +- docs/reference/radiator_snakecase.html | 6 +- docs/reference/radiator_split_tibble.html | 6 +- docs/reference/radiator_tic.html | 6 +- docs/reference/radiator_toc.html | 6 +- docs/reference/read_blacklist_genotypes.html | 6 +- docs/reference/read_blacklist_id.html | 6 +- docs/reference/read_dart.html | 6 +- docs/reference/read_plink.html | 6 +- docs/reference/read_rad.html | 6 +- docs/reference/read_strata.html | 6 +- docs/reference/read_vcf.html | 6 +- docs/reference/read_whitelist.html | 6 +- docs/reference/remove_duplicates.html | 6 +- docs/reference/replace_by_na.html | 6 +- docs/reference/reset_filters.html | 6 +- docs/reference/run_bayescan.html | 6 +- docs/reference/separate_gt.html | 6 +- docs/reference/separate_markers.html | 6 +- docs/reference/sex_markers_plot.html | 9 +- docs/reference/sexy_markers.html | 30 +- .../simulate_genos_from_posterior.html | 6 +- docs/reference/split_tibble_rows.html | 6 +- docs/reference/split_vcf.html | 6 +- docs/reference/strata_haplo.html | 6 +- docs/reference/subsampling_data.html | 6 +- docs/reference/summarise_genotypes.html | 6 +- docs/reference/summarize_sex.html | 6 +- docs/reference/summary_gds.html | 6 +- docs/reference/summary_rad.html | 6 +- docs/reference/summary_strata.html | 6 +- docs/reference/switch_allele_count.html | 6 +- docs/reference/switch_genotypes.html | 6 +- docs/reference/sync_gds.html | 6 +- docs/reference/tibble_stats.html | 6 +- docs/reference/tidy2gds.html | 6 +- docs/reference/tidy2wide.html | 6 +- docs/reference/tidy_dart_metadata.html | 6 +- docs/reference/tidy_fstat.html | 6 +- docs/reference/tidy_genepop.html | 6 +- docs/reference/tidy_genind.html | 6 +- docs/reference/tidy_genlight.html | 6 +- docs/reference/tidy_genomic_data.html | 6 +- docs/reference/tidy_gtypes.html | 6 +- docs/reference/tidy_plink.html | 6 +- docs/reference/tidy_vcf.html | 6 +- docs/reference/tidy_wide.html | 6 +- docs/reference/update_bl_individuals.html | 6 +- docs/reference/update_bl_markers.html | 6 +- docs/reference/update_filter_parameter.html | 6 +- docs/reference/update_radiator_gds.html | 6 +- docs/reference/vcf_strata.html | 6 +- docs/reference/write_arlequin.html | 6 +- docs/reference/write_bayescan.html | 11 +- docs/reference/write_betadiv.html | 6 +- docs/reference/write_colony.html | 6 +- docs/reference/write_dadi.html | 6 +- docs/reference/write_fasta.html | 6 +- docs/reference/write_faststructure.html | 6 +- docs/reference/write_fineradstructure.html | 6 +- docs/reference/write_gds.html | 6 +- docs/reference/write_genepop.html | 6 +- docs/reference/write_genepopedit.html | 6 +- docs/reference/write_genind.html | 6 +- docs/reference/write_genlight.html | 6 +- docs/reference/write_gsi_sim.html | 6 +- docs/reference/write_gtypes.html | 11 +- docs/reference/write_hapmap.html | 6 +- docs/reference/write_hierfstat.html | 6 +- docs/reference/write_hzar.html | 6 +- docs/reference/write_ldna.html | 6 +- docs/reference/write_maverick.html | 6 +- docs/reference/write_pcadapt.html | 11 +- docs/reference/write_plink.html | 6 +- docs/reference/write_rad.html | 6 +- docs/reference/write_related.html | 6 +- docs/reference/write_rubias.html | 6 +- docs/reference/write_snprelate.html | 6 +- docs/reference/write_stockr.html | 6 +- docs/reference/write_structure.html | 6 +- docs/reference/write_vcf.html | 6 +- man/extract_coverage.Rd | 2 +- 224 files changed, 936 insertions(+), 912 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ec54efc4..3de71f6f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: radiator Type: Package Title: RADseq Data Exploration, Manipulation and Visualization using R -Version: 1.3.2 -Date: 2024-04-30 +Version: 1.3.3 +Date: 2024-05-15 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 030d939f..4859f5d3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# radiator 1.3.3 2024-05-15 + +* Fix issue #188 related to coverage in DArT 1row and 2rows format + + + + # radiator 1.3.2 2024-04-30 * works with R 4.3.4 diff --git a/R/gds.R b/R/gds.R index d876eeb6..6ea89f9f 100644 --- a/R/gds.R +++ b/R/gds.R @@ -971,7 +971,7 @@ extract_genotypes_metadata <- function( #' baddly generated. It will say you have Read and allele Depth info, but you don't. #' Default: \code{stacks.haplo.check = FALSE}. #' @param dart.check (optional, logical) DArT have different reporting for coverage -#' information. +#' information. Will no longer report the average coverage stats from 1 and 2-rows DArT format. #' Default: \code{dart.check = FALSE}. # @keywords internal #' @export @@ -1000,15 +1000,21 @@ check_coverage <- function(gds, genotypes.metadata.check = FALSE, stacks.haplo.c # DArT count and 1 and 2 rows have different information... if (dart.check && "dart" %in% data.source) { if (any(c("2rows", "1row") %in% data.source)) { - got.coverage <- extract_markers_metadata( - gds, - markers.meta.select = c("AVG_COUNT_REF", "AVG_COUNT_SNP"), - whitelist = TRUE - ) - if (!is.null(got.coverage)) { - got.coverage <- c("AVG_COUNT_REF", "AVG_COUNT_SNP") - return(got.coverage) - } + # got.coverage <- extract_markers_metadata( + # gds, + # markers.meta.select = c("AVG_COUNT_REF", "AVG_COUNT_SNP"), + # whitelist = TRUE + # ) + # if (!is.null(got.coverage)) { + # got.coverage <- c("AVG_COUNT_REF", "AVG_COUNT_SNP") + # return(got.coverage) + # } + message("Coverage statistics information for 2rows and 1row DArT format is ignored") + message("\nradiator cannot generate coverage statistics from source\npotential blacklisted individuals bias the statistics generated by DArT") + message("\nrequest DArT count format from DArT") + + got.coverage <- NULL + return(got.coverage) }#End DART 1row and 2 rows } @@ -2162,7 +2168,7 @@ generate_stats <- function( # subsample = variant.select # exhaustive = FALSE # force.stats = TRUE - # # path.folder = NULL + # path.folder = NULL # plot = TRUE # digits = 6 # # file.date = NULL @@ -2562,7 +2568,7 @@ generate_stats <- function( } if (individuals) { - # changing the margin doesnt work with seqarray, the GDS needs to be optimized by sample + # changing the margin doesn't work with seqarray, the GDS needs to be optimized by sample # this operation is very costly in both time and disk space. # faster to do matrix calculations by rows and sums # Note to myself: the huge speed gain by using other packages robustbse, Rfast, etc. @@ -2791,11 +2797,11 @@ generate_stats <- function( # NOTE TO MYSELF need to work on including that one with DArT files...-------- #DArT 1 row and 2rows -------------------------------------------------------- # if ("dart" %in% data.source && any(c("2rows", "1row") %in% data.source)) { - # depth <- extract_markers_metadata( - # gds, - # markers.meta.select = c("AVG_COUNT_REF", "AVG_COUNT_SNP"), - # whitelist = TRUE - # ) + # depth <- extract_markers_metadata( + # gds, + # markers.meta.select = c("AVG_COUNT_REF", "AVG_COUNT_SNP"), + # whitelist = TRUE + # ) # markers <- ind <- FALSE # # if (is.null(depth)) return(NULL) diff --git a/README.md b/README.md index c93f379f..47736ef4 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-1.3.2-orange.svg)](commits/master) -[![Last-changedate](https://img.shields.io/badge/last%20change-2024--04--30-brightgreen.svg)](/commits/master) +[![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) [![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 06caca96..e00b54f1 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found (404) • radiator - + @@ -32,7 +32,7 @@ radiator - 1.3.1 + 1.3.3 @@ -109,7 +109,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 4f901a64..79e2f890 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -1,5 +1,5 @@ -GNU General Public License • radiatorGNU General Public License • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -277,7 +277,7 @@

How to Apply These Terms
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html index dfebac0e..4fc5288f 100644 --- a/docs/articles/get_started.html +++ b/docs/articles/get_started.html @@ -6,7 +6,7 @@ Get Started • radiator - + @@ -33,7 +33,7 @@ radiator - 1.3.1 + 1.3.3 @@ -91,7 +91,7 @@

Get Started

Thierry Gosselin

-

2024-04-24

+

2024-05-15

Source: vignettes/get_started.Rmd @@ -304,7 +304,7 @@

Overview

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/articles/index.html b/docs/articles/index.html index 29137612..f9ba5fad 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,5 +1,5 @@ -Articles • radiatorArticles • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -85,7 +85,7 @@

All vignettes

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/articles/life_cycle.html b/docs/articles/life_cycle.html index 78af7636..7f5b8100 100644 --- a/docs/articles/life_cycle.html +++ b/docs/articles/life_cycle.html @@ -6,7 +6,7 @@ Life Cycle • radiator - + @@ -33,7 +33,7 @@ radiator - 1.3.1 + 1.3.3 @@ -91,7 +91,7 @@

Life Cycle

Thierry Gosselin

-

2024-04-24

+

2024-05-15

Source: vignettes/life_cycle.Rmd @@ -148,7 +148,7 @@

2024-04-24

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/articles/rad_genomics_computer_setup.html b/docs/articles/rad_genomics_computer_setup.html index 834f4399..7511b10a 100644 --- a/docs/articles/rad_genomics_computer_setup.html +++ b/docs/articles/rad_genomics_computer_setup.html @@ -6,7 +6,7 @@ RADseq Genomics in R • radiator - + @@ -33,7 +33,7 @@ radiator - 1.3.1 + 1.3.3 @@ -90,7 +90,7 @@

RADseq Genomics in R

computer setup

-

2024-04-24

+

2024-05-15

Source: vignettes/rad_genomics_computer_setup.Rmd @@ -680,9 +680,21 @@

Error related to install.packages("adegenet")
+

Error: HTTP status was 404 Not Found +

+

This error is sometimes poping after a new R upgrade. Try installing +the problematic package differently.

+

Instead of:

+
+BiocManager::install("SeqArray")
+

Try:

+
+remotes::install_local(path = "SeqArray_latest.tar.gz")
+
+

Error: C stacks usage

-
Error: C stack usage  7971092 is too close to the limit
+
Error: C stack usage  7971092 is too close to the limit

So far, I haven’t found the cure to this computer-specific problem.

Potential solutions:

@@ -713,35 +725,35 @@

Better to install and compile them from source to enable OpenMP. Install in the terminal zstd and lz4:

-
cd ~/Downloads
-curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.9.4.tar.gz | tar xf -
-cd lz4*
-make 
-sudo make install
-cd .. 
-sudo rm -R lz4*
-
cd ~/Downloads
-curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
-cd zstd*
-make 
-sudo make install
-cd .. 
-sudo rm -R zstd*
+
cd ~/Downloads
+curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.9.4.tar.gz | tar xf -
+cd lz4*
+make 
+sudo make install
+cd .. 
+sudo rm -R lz4*
+
cd ~/Downloads
+curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
+cd zstd*
+make 
+sudo make install
+cd .. 
+sudo rm -R zstd*

fstcore, fst and data.table requires these R Makevars specifications. If you have other lines, comment (#) before saving and installing from source:

-
-usethis::edit_r_makevars()
-
#fstcore fst data.table
-CC=/usr/local/bin/gcc -fopenmp
-CXX=/usr/local/bin/g++ -fopenmp
-CXX11=/usr/local/bin/g++ -fopenmp
-CXX14=/usr/local/bin/g++ -fopenmp
-CXX17=/usr/local/bin/g++ -fopenmp
-CXX1X=/usr/local/bin/g++ -fopenmp
-CXX98=/usr/local/bin/g++ -fopenmp
+usethis::edit_r_makevars()
+
#fstcore fst data.table
+CC=/usr/local/bin/gcc -fopenmp
+CXX=/usr/local/bin/g++ -fopenmp
+CXX11=/usr/local/bin/g++ -fopenmp
+CXX14=/usr/local/bin/g++ -fopenmp
+CXX17=/usr/local/bin/g++ -fopenmp
+CXX1X=/usr/local/bin/g++ -fopenmp
+CXX98=/usr/local/bin/g++ -fopenmp
+
 install.packages("fstcore", type = "source")
 install.packages("fst", type = "source")
 install.packages("data.table", type = "source")
@@ -754,9 +766,9 @@

Download

Download the latest github release of Allan Strand’s rmetasim

-
cd ~/Downloads
-curl -L -O https://github.com/stranda/rmetasim/archive/master.zip
-unzip master.zip
+
cd ~/Downloads
+curl -L -O https://github.com/stranda/rmetasim/archive/master.zip
+unzip master.zip

Modify the number of loci: MAXLOCI @@ -767,7 +779,7 @@

Modify the number of loci: MAXLOCIrmetasim-master/src/const.h. Navigate to lane 33 and change the integer to the desired maximum number of loci. Or do this in the Terminal:

-
sed -i -e 's/#define MAXLOCI               10001/#define MAXLOCI               20000/g' rmetasim-master/src/const.h
+
sed -i -e 's/#define MAXLOCI               10001/#define MAXLOCI               20000/g' rmetasim-master/src/const.h

Makevars configuration @@ -775,29 +787,29 @@

Makevars configuration
+
 
macOS

 
This latest os requires extra lines:

-
CC=/usr/local/bin/clang
-CXX=/usr/local/bin/clang++
-CXX1X=/usr/local/bin/clang++
-FLIBS=-L/usr/local/lib
-LDFLAGS=-L/usr/local/lib
-SHLIB_OPENMP_CFLAGS= -fopenmp
-SHLIB_OPENMP_FCFLAGS= -fopenmp
-SHLIB_OPENMP_FFLAGS= -fopenmp
-SHLIB_OPENMP_CXXFLAGS= -fopenmp
-CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

+
CC=/usr/local/bin/clang
+CXX=/usr/local/bin/clang++
+CXX1X=/usr/local/bin/clang++
+FLIBS=-L/usr/local/lib
+LDFLAGS=-L/usr/local/lib
+SHLIB_OPENMP_CFLAGS= -fopenmp
+SHLIB_OPENMP_FCFLAGS= -fopenmp
+SHLIB_OPENMP_FFLAGS= -fopenmp
+SHLIB_OPENMP_CXXFLAGS= -fopenmp
+CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

Compile

-
R CMD INSTALL "rmetasim-master" # Terminal command
-sudo rm -R rmetasim* # to remove the folders no longer required
+
R CMD INSTALL "rmetasim-master" # Terminal command
+sudo rm -R rmetasim* # to remove the folders no longer required
@@ -807,10 +819,10 @@

Download the github version

-
# terminal
-cd Downloads
-git clone --recursive https://github.com/dmlc/xgboost
-cd xgboost
+
# terminal
+cd Downloads
+git clone --recursive https://github.com/dmlc/xgboost
+cd xgboost

Error? @@ -827,44 +839,44 @@

Modification
# Go to line 1676
-# change
-ac_pkg_openmp=no
-# to
-ac_pkg_openmp=yes
-#save the file under the same name

+
# Go to line 1676
+# change
+ac_pkg_openmp=no
+# to
+ac_pkg_openmp=yes
+#save the file under the same name

Makevars configuration

XGBoost requires these Makevars specifications. If you have other lines, comment (#) before compiling:

-
+
 usethis::edit_r_makevars()

-
CC=/usr/local/bin/gcc
-CXX=/usr/local/bin/g++
-CXX11=/usr/local/bin/g++
-CXX14=/usr/local/bin/g++
-CXX17=/usr/local/bin/g++
-SHLIB_OPENMP_CFLAGS= -fopenmp
-SHLIB_OPENMP_FCFLAGS= -fopenmp
-SHLIB_OPENMP_FFLAGS= -fopenmp
-SHLIB_OPENMP_CXXFLAGS= -fopenmp
-CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
-CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
-LDFLAGS=-L/usr/local/lib -Wl,-rpath,/usr/local/lib
-CPPFLAGS=-I/usr/local/include -I/usr/local/include

+
CC=/usr/local/bin/gcc
+CXX=/usr/local/bin/g++
+CXX11=/usr/local/bin/g++
+CXX14=/usr/local/bin/g++
+CXX17=/usr/local/bin/g++
+SHLIB_OPENMP_CFLAGS= -fopenmp
+SHLIB_OPENMP_FCFLAGS= -fopenmp
+SHLIB_OPENMP_FFLAGS= -fopenmp
+SHLIB_OPENMP_CXXFLAGS= -fopenmp
+CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
+CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
+LDFLAGS=-L/usr/local/lib -Wl,-rpath,/usr/local/lib
+CPPFLAGS=-I/usr/local/include -I/usr/local/include

Compile

-
sudo R CMD INSTALL R-package
+
sudo R CMD INSTALL R-package

Test R-package

You should see a time difference between both runs

-
+
 require(xgboost)
 x <-  matrix(rnorm(100*10000), 10000, 100)
 y <-  x %*% rnorm(100) + rnorm(1000)
@@ -884,28 +896,28 @@ 

 

 
Download and install CMake
 

-
#In browser or using curl in Terminal
-https://cmake.org/files/v3.12/cmake-3.12.2-Darwin-x86_64.dmg
-# double-click on the disk image and follow instructions

+
#In browser or using curl in Terminal
+https://cmake.org/files/v3.12/cmake-3.12.2-Darwin-x86_64.dmg
+# double-click on the disk image and follow instructions

 
To add CMake to the PATH:

-
PATH="/Applications/CMake.app/Contents/bin":"$PATH"
-# Or, to install symlinks to '/usr/local/bin', run:
-sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install
-# Or, to install symlinks to another directory, run:
-sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install=/path/to/bin
-#Then, run the following commands to install LightGBM:

+
PATH="/Applications/CMake.app/Contents/bin":"$PATH"
+# Or, to install symlinks to '/usr/local/bin', run:
+sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install
+# Or, to install symlinks to another directory, run:
+sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install=/path/to/bin
+#Then, run the following commands to install LightGBM:

 

 

 
Download and Install LightGBM
 

-
cd Downloads
-git clone --recursive https://github.com/Microsoft/LightGBM
-cd LightGBM
-Rscript build_r.R
-# previous version required running these lines instead
-#cd LightGBM/R-package
-#export CC=/usr/local/bin/gcc CXX=/usr/local/bin/g++
-#R CMD INSTALL --build . --no-multiarch

+
cd Downloads
+git clone --recursive https://github.com/Microsoft/LightGBM
+cd LightGBM
+Rscript build_r.R
+# previous version required running these lines instead
+#cd LightGBM/R-package
+#export CC=/usr/local/bin/gcc CXX=/usr/local/bin/g++
+#R CMD INSTALL --build . --no-multiarch

 

 

 

@@ -920,38 +932,38 @@ 
Makevars configuration
 
Check that the lines below are not commented in your
 ~/.R/Makevars file:

-
+
-
CC=/usr/local/bin/gcc
-CXX=/usr/local/bin/g++
-CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
-CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
-PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp
-PKG_CXXFLAGS=-fopenmp -std=c++11
-FC=/usr/local/bin/gfortran
-F77=/usr/local/bin/gfortran
-LDFLAGS=-L/usr/local/lib
-PKG_LIBS = "-liconv"

+
CC=/usr/local/bin/gcc
+CXX=/usr/local/bin/g++
+CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
+CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
+PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp
+PKG_CXXFLAGS=-fopenmp -std=c++11
+FC=/usr/local/bin/gfortran
+F77=/usr/local/bin/gfortran
+LDFLAGS=-L/usr/local/lib
+PKG_LIBS = "-liconv"

 

 

 
Download and install
 

 
From the Terminal run these steps to download and compile
 randomForestSRC:

-
cd ~/Downloads
-curl -L https://cran.r-project.org/src/contrib/randomForestSRC_2.9.3.tar.gz | tar xf -
-cd randomForestSRC

+
cd ~/Downloads
+curl -L https://cran.r-project.org/src/contrib/randomForestSRC_2.9.3.tar.gz | tar xf -
+cd randomForestSRC

 
Make sure you have autoconf installed:

-
# in Terminal
-cd ~/Downloads
-autoconf

+
# in Terminal
+cd ~/Downloads
+autoconf

 
Should output: autoconf: error: no input file, if not,
 install following the steps here.

-
# in Terminal
-cd ~/Downloads/randomForestSRC
-autoconf
-cd ~/Downloads
-R CMD INSTALL --preclean --clean randomForestSRC

+
# in Terminal
+cd ~/Downloads/randomForestSRC
+autoconf
+cd ~/Downloads
+R CMD INSTALL --preclean --clean randomForestSRC

 
You want to make sure that this line is printed during execution of
 the previous command:
 checking whether OpenMP will work in a package... yes or
@@ -964,7 +976,7 @@ 

 

 
ranger is easy to
 install.

-
+
 install.packages("ranger")

 

 

@@ -973,7 +985,7 @@ 

 

 
missRanger is
 also very easy to install.

-
+
 install.packages("missRanger")

 

 

@@ -982,7 +994,7 @@ 

 

 
miceRanger
 easy to install.

-
+
 install.packages("miceRanger")

 

 

@@ -991,7 +1003,7 @@ 

 

 
To install pcaMethods, from
 bioconductor:

-
+
 BiocManager::install("pcaMethods")

 

 

@@ -999,27 +1011,27 @@ 

 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
 

-
curl -O http://cmpg.unibe.ch/software/fastsimcoal2/downloads/fsc26_linux64.zip
-unzip fsc26_linux64.zip
-sudo mv fsc26_linux64/fsc26 /usr/local/bin/fsc26 # will ask for your computer password

+
curl -O http://cmpg.unibe.ch/software/fastsimcoal2/downloads/fsc26_linux64.zip
+unzip fsc26_linux64.zip
+sudo mv fsc26_linux64/fsc26 /usr/local/bin/fsc26 # will ask for your computer password

 

 

 
MacOS
 

-
cd ~/Downloads
-curl -O http://cmpg.unibe.ch/software/fastsimcoal2/downloads/fsc26_mac64.zip
-unzip fsc26_mac64.zip
-sudo mv fsc26_mac64/fsc26 /usr/local/bin/fsc26 # will ask for your computer password

+
cd ~/Downloads
+curl -O http://cmpg.unibe.ch/software/fastsimcoal2/downloads/fsc26_mac64.zip
+unzip fsc26_mac64.zip
+sudo mv fsc26_mac64/fsc26 /usr/local/bin/fsc26 # will ask for your computer password

 

 

 
Common to both OS:
 

-
sudo chmod 777 /usr/local/bin/fsc26
-fsc26

+
sudo chmod 777 /usr/local/bin/fsc26
+fsc26

 
Re-start R and the software fastsimcoal2 will automatically be in
 your PATH…

 

@@ -1028,13 +1040,13 @@ 
PATH
 

 
To see the path of the installation, in the
 Terminal:

-
which fsc26
-# in macOS:
-# /usr/local/bin/fsc26

+
which fsc26
+# in macOS:
+# /usr/local/bin/fsc26

 
If that doesn’t work, do:

-
source ~/.bash_profile

+
source ~/.bash_profile

 
Remove the files in the folder:

-
sudo rm -R ~/Downloads/fsc26_mac64*

+
sudo rm -R ~/Downloads/fsc26_mac64*

 

 

 

@@ -1047,14 +1059,14 @@ 

 
MacOS
 

 
The old openmpi version (openmpi-1.6.5) is required, saddly.

-
cd ~/Downloads
-curl -L https://download.open-mpi.org/release/open-mpi/v1.6/openmpi-1.6.5.tar.gz | tar xf -
-cd openmpi-1.6.5
-export TMPDIR=/tmp
-./configure F77=gfortran #--prefix=/usr/local -openmp # no longer work for some reason
-make -j 12
-sudo make install
-sudo rm -R ~/Downloads/openmpi*

+
cd ~/Downloads
+curl -L https://download.open-mpi.org/release/open-mpi/v1.6/openmpi-1.6.5.tar.gz | tar xf -
+cd openmpi-1.6.5
+export TMPDIR=/tmp
+./configure F77=gfortran #--prefix=/usr/local -openmp # no longer work for some reason
+make -j 12
+sudo make install
+sudo rm -R ~/Downloads/openmpi*

 
To download COLONY, follow instructions on Jinliang Wang ZSL website. The
 file you need to uncompress is named:
 colony2.mac_.20180730.zip.

@@ -1085,31 +1097,31 @@ 
Update 
 
 
-
cd ~/Downloads
-curl -L http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz | tar xf -
-cd autoconf-2.69
-./configure
-make
-sudo make install
-cd .. 
-sudo rm -R ~/Downloads/autoconf-*

+
cd ~/Downloads
+curl -L http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz | tar xf -
+cd autoconf-2.69
+./configure
+make
+sudo make install
+cd .. 
+sudo rm -R ~/Downloads/autoconf-*

 
    
 
  1. Install Github
    2. 
 

-
git --version                   # show current git version installed
-which git                       # returns where is git on your computer
-cd ~/Downloads
-git clone https://github.com/git/git # install the latest Git
-cd git
-make configure
-./configure
-make -j12
-sudo make install
-cd .. 
-sudo rm -R ~/Downloads/git/     # remove git folder
-source ~/.bash_profile          # reload startup script
-git --version                   # confirmed the version you just installed
-which git                       # returns /usr/local/bin

+
git --version                   # show current git version installed
+which git                       # returns where is git on your computer
+cd ~/Downloads
+git clone https://github.com/git/git # install the latest Git
+cd git
+make configure
+./configure
+make -j12
+sudo make install
+cd .. 
+sudo rm -R ~/Downloads/git/     # remove git folder
+source ~/.bash_profile          # reload startup script
+git --version                   # confirmed the version you just installed
+which git                       # returns /usr/local/bin

 

 

 
macOS Terminal from specific folder
@@ -1128,14 +1140,14 @@ 
Shortcut to folder path
 
With macOS, open the Automator
 application.

-
File -> New (cmd-N)
-Choose: Services
-Left panel, choose: Library -> Utilities
-Middle, choose: Copy to Clipboard and drag it to the right panel
-Now you want to have: Service receives selected FILES OR FOLDERS in FINDER>
-You should have something similar to the image below:

+
File -> New (cmd-N)
+Choose: Services
+Left panel, choose: Library -> Utilities
+Middle, choose: Copy to Clipboard and drag it to the right panel
+Now you want to have: Service receives selected FILES OR FOLDERS in FINDER>
+You should have something similar to the image below:

 

-
Save (cmd-S) or File -> Save service as: copy path to clipboard

+
Save (cmd-S) or File -> Save service as: copy path to clipboard

 
Go in the Finder, select a folder and right click on it you should
 see ‘copy path to clipboard’ at the bottom or in
 Services.

@@ -1160,7 +1172,7 @@ 
Shortcut to folder path
   

-
Site built with pkgdown 2.0.7.

+
Site built with pkgdown 2.0.9.

 

 
       
diff --git a/docs/authors.html b/docs/authors.html
index 2e704015..72d0627b 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
 
-Authors and Citation • radiatorAuthors and Citation • radiator
@@ -17,7 +17,7 @@
       
       
         radiator
-        1.3.1
+        1.3.3
       
     

 
@@ -63,7 +63,7 @@
   

     

       

-        
Authors

+        
Authors and Citation

       

 
       
@@ -108,7 +108,7 @@ 
Citation

 

 
 

-  
Site built with pkgdown 2.0.7.

+  
Site built with pkgdown 2.0.9.

 

 
       

diff --git a/docs/index.html b/docs/index.html
index 0b4f0649..510d9ab7 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,7 +6,7 @@
 
 
 RADseq Data Exploration, Manipulation and Visualization using R • radiator
-
+
 
 
 
@@ -33,7 +33,7 @@
       
       
         radiator
-        1.3.1
+        1.3.3
       
     

 
@@ -111,6 +111,7 @@ 
Installationdevtools::package_info(pkgs = "SeqArray") # to verify version
 
 # If manually installing SeqArray is necessary
+install.packages("BiocManager")
 BiocManager::install("SeqArray")

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

    @@ -176,8 +177,8 @@

    Dev status

    • lifecycle
    • Project Status: Active – The project has reached a stable, usable state and is being actively developed.
      • -
    • packageversion
      • -
    • Last-changedate
      • +
    • packageversion
      • +
    • Last-changedate
    • R-CMD-check
    • DOI
    @@ -194,7 +195,7 @@

    Dev status

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/news/index.html b/docs/news/index.html index db134455..3392e5c0 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,5 +1,5 @@ -Changelog • radiatorChangelog • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3
@@ -66,6 +66,16 @@

Changelog

Source: NEWS.md
+
+

radiator 1.3.3 2024-05-15

+
  • Fix issue #188 related to coverage in DArT 1row and 2rows format
    • +
+
+

radiator 1.3.2 2024-04-30

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

radiator 1.3.1 2024-04-24

  • works with R 4.3.3
    • @@ -339,7 +349,7 @@

    radia

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 20f8fba7..2c5230e6 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,9 +1,9 @@ -pandoc: 3.1.1 -pkgdown: 2.0.7 +pandoc: 3.1.11 +pkgdown: 2.0.9 pkgdown_sha: ~ articles: get_started: get_started.html life_cycle: life_cycle.html rad_genomics_computer_setup: rad_genomics_computer_setup.html -last_built: 2024-04-24T14:02Z +last_built: 2024-05-15T13:57Z diff --git a/docs/reference/Exposition_pipe_operator.html b/docs/reference/Exposition_pipe_operator.html index 7e585840..add8660c 100644 --- a/docs/reference/Exposition_pipe_operator.html +++ b/docs/reference/Exposition_pipe_operator.html @@ -1,5 +1,5 @@ -Exposition pipe-operator — %$% • radiatorExposition pipe-operator — %$% • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

Exposition pipe-operator

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/allele_count.html b/docs/reference/allele_count.html index 6bcd42ca..565376ec 100644 --- a/docs/reference/allele_count.html +++ b/docs/reference/allele_count.html @@ -1,5 +1,5 @@ -allele_count — allele_count • radiatorallele_count — allele_count • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

allele_count

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/allele_frequencies.html b/docs/reference/allele_frequencies.html index 3b863a1b..d58b50db 100644 --- a/docs/reference/allele_frequencies.html +++ b/docs/reference/allele_frequencies.html @@ -1,5 +1,5 @@ -Compute allele frequencies per markers and populations — allele_frequencies • radiatorCompute allele frequencies per markers and populations — allele_frequencies • radiatorassign_defaults — assign_defaults • radiatorassign_defaults — assign_defaults • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

assign_defaults

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/bayescan_one.html b/docs/reference/bayescan_one.html index a8adae0b..8a6f12a7 100644 --- a/docs/reference/bayescan_one.html +++ b/docs/reference/bayescan_one.html @@ -1,5 +1,5 @@ -bayescan one iteration — bayescan_one • radiatorbayescan one iteration — bayescan_one • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -103,7 +103,7 @@

bayescan one iteration

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/betas_estimator.html b/docs/reference/betas_estimator.html index c1fdc4a1..b4db4eeb 100644 --- a/docs/reference/betas_estimator.html +++ b/docs/reference/betas_estimator.html @@ -1,5 +1,5 @@ -Estimate \(\beta\)s per population — betas_estimator • radiatorEstimate \(\beta\)s per population — betas_estimator • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -172,7 +172,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/blacklist_hw.html b/docs/reference/blacklist_hw.html index 1c47c918..237ff851 100644 --- a/docs/reference/blacklist_hw.html +++ b/docs/reference/blacklist_hw.html @@ -1,5 +1,5 @@ -blacklist_hw — blacklist_hw • radiatorblacklist_hw — blacklist_hw • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -99,7 +99,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/boxplot_stats.html b/docs/reference/boxplot_stats.html index b5b179e9..c488e1c2 100644 --- a/docs/reference/boxplot_stats.html +++ b/docs/reference/boxplot_stats.html @@ -1,5 +1,5 @@ -boxplot_stats — boxplot_stats • radiatorboxplot_stats — boxplot_stats • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -101,7 +101,7 @@

boxplot_stats

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/calibrate_alleles.html b/docs/reference/calibrate_alleles.html index 0f867bc4..690ede22 100644 --- a/docs/reference/calibrate_alleles.html +++ b/docs/reference/calibrate_alleles.html @@ -1,5 +1,5 @@ -Calibrate REF and ALT alleles based on count — calibrate_alleles • radiatorCalibrate REF and ALT alleles based on count — calibrate_alleles • radiator radiator - 1.3.1 + 1.3.3 @@ -165,7 +165,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/change_pop_names.html b/docs/reference/change_pop_names.html index a09c11c8..47c61e5a 100644 --- a/docs/reference/change_pop_names.html +++ b/docs/reference/change_pop_names.html @@ -1,5 +1,5 @@ -Transform into a factor the STRATA column, change names and reorder the levels — change_pop_names • radiatorTransform into a factor the STRATA column, change names and reorder the levels — change_pop_names • radiatorcheck_args_class — check_args_class • radiatorcheck_args_class — check_args_class • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

check_args_class

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/check_dart.html b/docs/reference/check_dart.html index a93d4ee6..7a6b21a6 100644 --- a/docs/reference/check_dart.html +++ b/docs/reference/check_dart.html @@ -1,5 +1,5 @@ -check_dart — check_dart • radiatorcheck_dart — check_dart • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

check_dart

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/check_header_source_vcf.html b/docs/reference/check_header_source_vcf.html index 327b5485..bb585c73 100644 --- a/docs/reference/check_header_source_vcf.html +++ b/docs/reference/check_header_source_vcf.html @@ -1,5 +1,5 @@ -Check the vcf header and detect vcf source — check_header_source_vcf • radiatorCheck the vcf header and detect vcf source — check_header_source_vcf • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

Check the vcf header and detect vcf source

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/check_pop_levels.html b/docs/reference/check_pop_levels.html index eb4f0879..f50fc651 100644 --- a/docs/reference/check_pop_levels.html +++ b/docs/reference/check_pop_levels.html @@ -1,5 +1,5 @@ -Check the use of pop.levels, pop.labels and pop.select arguments. — check_pop_levels • radiatorCheck the use of pop.levels, pop.labels and pop.select arguments. — check_pop_levels • radiatorclean_dart_colnames — clean_dart_colnames • radiatorclean_dart_colnames — clean_dart_colnames • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -93,7 +93,7 @@

clean_dart_colnames

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/clean_dart_locus.html b/docs/reference/clean_dart_locus.html index d36c600d..bcf4cf4e 100644 --- a/docs/reference/clean_dart_locus.html +++ b/docs/reference/clean_dart_locus.html @@ -1,5 +1,5 @@ -clean_dart_locus — clean_dart_locus • radiatorclean_dart_locus — clean_dart_locus • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

clean_dart_locus

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/clean_ind_names.html b/docs/reference/clean_ind_names.html index f6566a96..71478aea 100644 --- a/docs/reference/clean_ind_names.html +++ b/docs/reference/clean_ind_names.html @@ -1,5 +1,5 @@ -Clean individual's names for radiator and other packages — clean_ind_names • radiatorClean individual's names for radiator and other packages — clean_ind_names • radiator radiator - 1.3.1 + 1.3.3 @@ -104,7 +104,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/clean_markers_names.html b/docs/reference/clean_markers_names.html index 1a6e9aed..397d0bdc 100644 --- a/docs/reference/clean_markers_names.html +++ b/docs/reference/clean_markers_names.html @@ -1,5 +1,5 @@ -Clean marker's names for radiator and other packages — clean_markers_names • radiatorClean marker's names for radiator and other packages — clean_markers_names • radiator radiator - 1.3.1 + 1.3.3 @@ -106,7 +106,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/clean_pop_names.html b/docs/reference/clean_pop_names.html index 296e6aba..94dd1e30 100644 --- a/docs/reference/clean_pop_names.html +++ b/docs/reference/clean_pop_names.html @@ -1,5 +1,5 @@ -Clean population's names for radiator and other packages — clean_pop_names • radiatorClean population's names for radiator and other packages — clean_pop_names • radiator radiator - 1.3.1 + 1.3.3 @@ -102,7 +102,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/compound_assignment_pipe_operator.html b/docs/reference/compound_assignment_pipe_operator.html index 5a529ad4..f640917c 100644 --- a/docs/reference/compound_assignment_pipe_operator.html +++ b/docs/reference/compound_assignment_pipe_operator.html @@ -1,5 +1,5 @@ -compound assignment pipe operator — %<>% • radiatorcompound assignment pipe operator — %<>% • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

compound assignment pipe operator

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/compute_maf.html b/docs/reference/compute_maf.html index 1c34155f..6b834ca0 100644 --- a/docs/reference/compute_maf.html +++ b/docs/reference/compute_maf.html @@ -1,5 +1,5 @@ -compute_maf — compute_maf • radiatorcompute_maf — compute_maf • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

compute_maf

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/count_monomorphic.html b/docs/reference/count_monomorphic.html index e55d510e..0c38d811 100644 --- a/docs/reference/count_monomorphic.html +++ b/docs/reference/count_monomorphic.html @@ -1,5 +1,5 @@ -count_monomorphic — count_monomorphic • radiatorcount_monomorphic — count_monomorphic • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

count_monomorphic

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/dart2gds.html b/docs/reference/dart2gds.html index 3dea5ec0..251edeea 100644 --- a/docs/reference/dart2gds.html +++ b/docs/reference/dart2gds.html @@ -1,5 +1,5 @@ -dart2gds — dart2gds • radiatordart2gds — dart2gds • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -99,7 +99,7 @@

dart2gds

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/data_info.html b/docs/reference/data_info.html index a97edb43..936c40f2 100644 --- a/docs/reference/data_info.html +++ b/docs/reference/data_info.html @@ -1,5 +1,5 @@ -data_info — data_info • radiatordata_info — data_info • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

data_info

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/detect_all_missing.html b/docs/reference/detect_all_missing.html index 690c591f..84cf31f5 100644 --- a/docs/reference/detect_all_missing.html +++ b/docs/reference/detect_all_missing.html @@ -1,5 +1,5 @@ -Detect markers with all missing genotypes — detect_all_missing • radiatorDetect markers with all missing genotypes — detect_all_missing • radiatorDetect alternate allele problems — detect_allele_problems • radiatorDetect alternate allele problems — detect_allele_problems • radiator radiator - 1.3.1 + 1.3.3 @@ -205,7 +205,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/detect_biallelic_markers.html b/docs/reference/detect_biallelic_markers.html index ac7683dc..5f2b50e3 100644 --- a/docs/reference/detect_biallelic_markers.html +++ b/docs/reference/detect_biallelic_markers.html @@ -1,5 +1,5 @@ -Detect biallelic data — detect_biallelic_markers • radiatorDetect biallelic data — detect_biallelic_markers • radiatorDetect biallelic problems — detect_biallelic_problems • radiatorDetect biallelic problems — detect_biallelic_problems • radiator radiator - 1.3.1 + 1.3.3 @@ -133,7 +133,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/detect_dart_format.html b/docs/reference/detect_dart_format.html index b6ba0b20..f52c93ab 100644 --- a/docs/reference/detect_dart_format.html +++ b/docs/reference/detect_dart_format.html @@ -1,5 +1,5 @@ -detect_dart_format — detect_dart_format • radiatordetect_dart_format — detect_dart_format • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

detect_dart_format

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/detect_duplicate_genomes.html b/docs/reference/detect_duplicate_genomes.html index 9e4f22d2..e6abab3e 100644 --- a/docs/reference/detect_duplicate_genomes.html +++ b/docs/reference/detect_duplicate_genomes.html @@ -1,7 +1,5 @@ -Compute pairwise genome similarity or distance between individuals -to highligh potential duplicate individuals — detect_duplicate_genomes • radiatorCompute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals — detect_duplicate_genomes • radiator radiator - 1.3.1 + 1.3.3 @@ -69,8 +67,7 @@
-

Compute pairwise genome similarity or distance between individuals -to highligh potential duplicate individuals

+

Compute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals

Source: R/detect_duplicate_genomes.R
@@ -297,7 +294,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/detect_genomic_format.html b/docs/reference/detect_genomic_format.html index 14d3d237..4b0d6ee4 100644 --- a/docs/reference/detect_genomic_format.html +++ b/docs/reference/detect_genomic_format.html @@ -1,5 +1,5 @@ -Used internally in radiator to detect the file format — detect_genomic_format • radiatorUsed internally in radiator to detect the file format — detect_genomic_format • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -130,7 +130,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/detect_het_outliers.html b/docs/reference/detect_het_outliers.html index 702bf5f5..ca7342c0 100644 --- a/docs/reference/detect_het_outliers.html +++ b/docs/reference/detect_het_outliers.html @@ -1,5 +1,5 @@ -Detect heterozygotes outliers and estimate miscall rate — detect_het_outliers • radiatorDetect heterozygotes outliers and estimate miscall rate — detect_het_outliers • radiator radiator - 1.3.1 + 1.3.3 @@ -225,7 +225,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/detect_microsatellites.html b/docs/reference/detect_microsatellites.html index f7e5e99a..b60d6b7b 100644 --- a/docs/reference/detect_microsatellites.html +++ b/docs/reference/detect_microsatellites.html @@ -1,5 +1,5 @@ -Detect microsatellites — detect_microsatellites • radiatorDetect microsatellites — detect_microsatellites • radiatorDetect mixed genomes — detect_mixed_genomes • radiatorDetect mixed genomes — detect_mixed_genomes • radiatorDetect paralogs — detect_paralogs • radiatorDetect paralogs — detect_paralogs • radiator radiator - 1.3.1 + 1.3.3 @@ -222,7 +222,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/detect_ref_genome.html b/docs/reference/detect_ref_genome.html index 05ee8f5e..4676fd68 100644 --- a/docs/reference/detect_ref_genome.html +++ b/docs/reference/detect_ref_genome.html @@ -1,5 +1,5 @@ -Detect reference genome — detect_ref_genome • radiatorDetect reference genome — detect_ref_genome • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -127,7 +127,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/diagnostic_maf.html b/docs/reference/diagnostic_maf.html index dcecdbf8..b6b327e7 100644 --- a/docs/reference/diagnostic_maf.html +++ b/docs/reference/diagnostic_maf.html @@ -1,5 +1,5 @@ -MA diagnostic — diagnostic_ma • radiatorMA diagnostic — diagnostic_ma • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -122,7 +122,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/distance2tibble.html b/docs/reference/distance2tibble.html index 36fdf555..157cfb52 100644 --- a/docs/reference/distance2tibble.html +++ b/docs/reference/distance2tibble.html @@ -1,5 +1,5 @@ -distance2tibble — distance2tibble • radiatordistance2tibble — distance2tibble • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -96,7 +96,7 @@

distance2tibble

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/distance_individuals.html b/docs/reference/distance_individuals.html index a423ff06..fe9f0c8d 100644 --- a/docs/reference/distance_individuals.html +++ b/docs/reference/distance_individuals.html @@ -1,5 +1,5 @@ -Distance individuals — distance_individuals • radiatorDistance individuals — distance_individuals • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -93,7 +93,7 @@

Distance individuals

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/erase_genotypes.html b/docs/reference/erase_genotypes.html index d0cc71f7..aeb4a710 100644 --- a/docs/reference/erase_genotypes.html +++ b/docs/reference/erase_genotypes.html @@ -1,5 +1,5 @@ -Erase genotypes — erase_genotypes • radiatorErase genotypes — erase_genotypes • radiatorheterozygotes miscall rate — estimate_m • radiatorheterozygotes miscall rate — estimate_m • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -126,7 +126,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/extract_coverage.html b/docs/reference/extract_coverage.html index e2f7194e..2ab35ee5 100644 --- a/docs/reference/extract_coverage.html +++ b/docs/reference/extract_coverage.html @@ -1,5 +1,5 @@ -check_coverage — check_coverage • radiatorcheck_coverage — check_coverage • radiatorExtract DArT target id — extract_dart_target_id • radiatorExtract DArT target id — extract_dart_target_id • radiatorextract_data_source — extract_data_source • radiatorextract_data_source — extract_data_source • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

extract_data_source

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/extract_dots.html b/docs/reference/extract_dots.html index 26b971f3..4bc3de01 100644 --- a/docs/reference/extract_dots.html +++ b/docs/reference/extract_dots.html @@ -1,5 +1,5 @@ -extract_dots — extract_dots • radiatorextract_dots — extract_dots • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

extract_dots

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/extract_genotypes_metadata.html b/docs/reference/extract_genotypes_metadata.html index 2c89293f..c04158be 100644 --- a/docs/reference/extract_genotypes_metadata.html +++ b/docs/reference/extract_genotypes_metadata.html @@ -1,5 +1,5 @@ -extract_genotypes_metadata — extract_genotypes_metadata • radiatorextract_genotypes_metadata — extract_genotypes_metadata • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -138,7 +138,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/extract_individuals_metadata.html b/docs/reference/extract_individuals_metadata.html index bb8154cf..8d096840 100644 --- a/docs/reference/extract_individuals_metadata.html +++ b/docs/reference/extract_individuals_metadata.html @@ -1,5 +1,5 @@ -extract_individuals_metadata — extract_individuals_metadata • radiatorextract_individuals_metadata — extract_individuals_metadata • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -123,7 +123,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/extract_individuals_vcf.html b/docs/reference/extract_individuals_vcf.html index 44dffcf8..af261215 100644 --- a/docs/reference/extract_individuals_vcf.html +++ b/docs/reference/extract_individuals_vcf.html @@ -1,5 +1,5 @@ -Extract individuals from vcf file — extract_individuals_vcf • radiatorExtract individuals from vcf file — extract_individuals_vcf • radiatorextract_info_vcf — extract_info_vcf • radiatorextract_info_vcf — extract_info_vcf • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

extract_info_vcf

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/extract_markers_metadata.html b/docs/reference/extract_markers_metadata.html index 8d87be81..a7dd8bab 100644 --- a/docs/reference/extract_markers_metadata.html +++ b/docs/reference/extract_markers_metadata.html @@ -1,5 +1,5 @@ -extract_markers_metadata — extract_markers_metadata • radiatorextract_markers_metadata — extract_markers_metadata • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -123,7 +123,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_blacklist_genotypes.html b/docs/reference/filter_blacklist_genotypes.html index 161e4acc..288991d3 100644 --- a/docs/reference/filter_blacklist_genotypes.html +++ b/docs/reference/filter_blacklist_genotypes.html @@ -1,5 +1,5 @@ -Filter dataset with blacklist of genotypes — filter_blacklist_genotypes • radiatorFilter dataset with blacklist of genotypes — filter_blacklist_genotypes • radiatorFilter common markers between strata — filter_common_markers • radiatorFilter common markers between strata — filter_common_markers • radiator radiator - 1.3.1 + 1.3.3 @@ -167,7 +167,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_coverage.html b/docs/reference/filter_coverage.html index 3c226460..8ea5b2cc 100644 --- a/docs/reference/filter_coverage.html +++ b/docs/reference/filter_coverage.html @@ -1,5 +1,5 @@ -Filter markers mean coverage — filter_coverage • radiatorFilter markers mean coverage — filter_coverage • radiator radiator - 1.3.1 + 1.3.3 @@ -207,7 +207,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_dart_reproducibility.html b/docs/reference/filter_dart_reproducibility.html index 4e2442e7..e5af3849 100644 --- a/docs/reference/filter_dart_reproducibility.html +++ b/docs/reference/filter_dart_reproducibility.html @@ -1,5 +1,5 @@ -Filter data based on DArT reproducibility statistics — filter_dart_reproducibility • radiatorFilter data based on DArT reproducibility statistics — filter_dart_reproducibility • radiatorFis filter — filter_fis • radiatorFis filter — filter_fis • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -162,7 +162,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_genotyping.html b/docs/reference/filter_genotyping.html index 0da88aad..6e5d2357 100644 --- a/docs/reference/filter_genotyping.html +++ b/docs/reference/filter_genotyping.html @@ -1,5 +1,5 @@ -Filter markers based on genotyping/missing rate — filter_genotyping • radiatorFilter markers based on genotyping/missing rate — filter_genotyping • radiatorHeterozygosity filter — filter_het • radiatorHeterozygosity filter — filter_het • radiator radiator - 1.3.1 + 1.3.3 @@ -345,7 +345,7 @@

See also

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_hwe.html b/docs/reference/filter_hwe.html index 4cc14942..c0e1080d 100644 --- a/docs/reference/filter_hwe.html +++ b/docs/reference/filter_hwe.html @@ -1,5 +1,5 @@ -Filter markers based on Hardy-Weinberg Equilibrium — filter_hwe • radiatorFilter markers based on Hardy-Weinberg Equilibrium — filter_hwe • radiator radiator - 1.3.1 + 1.3.3 @@ -360,7 +360,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_individuals.html b/docs/reference/filter_individuals.html index 8fefca43..e803b995 100644 --- a/docs/reference/filter_individuals.html +++ b/docs/reference/filter_individuals.html @@ -1,7 +1,5 @@ -Filter individuals based on genotyping/missingness rate, -heterozygosity and total coverage — filter_individuals • radiatorFilter individuals based on genotyping/missingness rate, heterozygosity and total coverage — filter_individuals • radiator radiator - 1.3.1 + 1.3.3 @@ -73,8 +71,7 @@
-

Filter individuals based on genotyping/missingness rate, -heterozygosity and total coverage

+

Filter individuals based on genotyping/missingness rate, heterozygosity and total coverage

Source: R/filter_individuals.R
@@ -225,7 +222,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_ld.html b/docs/reference/filter_ld.html index 20912083..952131bf 100644 --- a/docs/reference/filter_ld.html +++ b/docs/reference/filter_ld.html @@ -1,5 +1,5 @@ -GBS/RADseq short and long distance linkage disequilibrium pruning — filter_ld • radiatorGBS/RADseq short and long distance linkage disequilibrium pruning — filter_ld • radiator radiator - 1.3.1 + 1.3.3 @@ -291,7 +291,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_monomorphic.html b/docs/reference/filter_monomorphic.html index 93257372..83349936 100644 --- a/docs/reference/filter_monomorphic.html +++ b/docs/reference/filter_monomorphic.html @@ -1,5 +1,5 @@ -Filter monomorphic markers — filter_monomorphic • radiatorFilter monomorphic markers — filter_monomorphic • radiator radiator - 1.3.1 + 1.3.3 @@ -173,7 +173,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_rad.html b/docs/reference/filter_rad.html index e5362d09..9a213313 100644 --- a/docs/reference/filter_rad.html +++ b/docs/reference/filter_rad.html @@ -1,5 +1,5 @@ -ONE FUNCTION TO RULE THEM ALL — filter_rad • radiatorONE FUNCTION TO RULE THEM ALL — filter_rad • radiatorFilter SNP number per locus/read — filter_snp_number • radiator radiator - 1.3.1 + 1.3.3 @@ -207,7 +207,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_snp_position_read.html b/docs/reference/filter_snp_position_read.html index bca08dbe..bdee4aca 100644 --- a/docs/reference/filter_snp_position_read.html +++ b/docs/reference/filter_snp_position_read.html @@ -1,5 +1,5 @@ -Filter markers/SNP based on their position on the read — filter_snp_position_read • radiatorFilter markers/SNP based on their position on the read — filter_snp_position_read • radiator radiator - 1.3.1 + 1.3.3 @@ -200,7 +200,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/filter_whitelist.html b/docs/reference/filter_whitelist.html index a7729b2f..41bcfaf2 100644 --- a/docs/reference/filter_whitelist.html +++ b/docs/reference/filter_whitelist.html @@ -1,5 +1,5 @@ -Filter dataset with whitelist of markers — filter_whitelist • radiatorFilter dataset with whitelist of markers — filter_whitelist • radiatorfolder_prefix — folder_prefix • radiatorfolder_prefix — folder_prefix • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

folder_prefix

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/folder_short.html b/docs/reference/folder_short.html index a8cff0a1..54236246 100644 --- a/docs/reference/folder_short.html +++ b/docs/reference/folder_short.html @@ -1,5 +1,5 @@ -folder_short — folder_short • radiatorfolder_short — folder_short • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -98,7 +98,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/gds2tidy.html b/docs/reference/gds2tidy.html index 3b80f9c8..e0cfeea9 100644 --- a/docs/reference/gds2tidy.html +++ b/docs/reference/gds2tidy.html @@ -1,5 +1,5 @@ -gds2tidy — gds2tidy • radiatorgds2tidy — gds2tidy • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -100,7 +100,7 @@

gds2tidy

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/generate_filename.html b/docs/reference/generate_filename.html index 664cfa6c..c3c42a0a 100644 --- a/docs/reference/generate_filename.html +++ b/docs/reference/generate_filename.html @@ -1,5 +1,5 @@ -Filename radiator — generate_filename • radiatorFilename radiator — generate_filename • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -95,7 +95,7 @@

Filename radiator

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/generate_folder.html b/docs/reference/generate_folder.html index 201ae808..807918d8 100644 --- a/docs/reference/generate_folder.html +++ b/docs/reference/generate_folder.html @@ -1,5 +1,5 @@ -generate_folder — generate_folder • radiatorgenerate_folder — generate_folder • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -135,7 +135,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/generate_geno_freq_boundaries.html b/docs/reference/generate_geno_freq_boundaries.html index e30b3d3b..c67920ed 100644 --- a/docs/reference/generate_geno_freq_boundaries.html +++ b/docs/reference/generate_geno_freq_boundaries.html @@ -1,5 +1,5 @@ -generate_geno_freq_boundaries — generate_geno_freq_boundaries • radiatorgenerate_geno_freq_boundaries — generate_geno_freq_boundaries • radiatorgenerate_hzar — generate_hzar • radiatorgenerate_hzar — generate_hzar • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

generate_hzar

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/generate_markers_metadata.html b/docs/reference/generate_markers_metadata.html index eee683c3..17b90f9a 100644 --- a/docs/reference/generate_markers_metadata.html +++ b/docs/reference/generate_markers_metadata.html @@ -1,5 +1,5 @@ -Generate markers metadata — generate_markers_metadata • radiatorGenerate markers metadata — generate_markers_metadata • radiatorgenerate_squeleton_folders — generate_squeleton_folders • radiatorgenerate_squeleton_folders — generate_squeleton_folders • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -93,7 +93,7 @@

generate_squeleton_folders

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/generate_strata.html b/docs/reference/generate_strata.html index b6274262..5d5aff18 100644 --- a/docs/reference/generate_strata.html +++ b/docs/reference/generate_strata.html @@ -1,5 +1,5 @@ -Generate strata object from the data — generate_strata • radiatorGenerate strata object from the data — generate_strata • radiatorgenerate_whitelist — generate_whitelist • radiatorgenerate_whitelist — generate_whitelist • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -92,7 +92,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/genome_similarity.html b/docs/reference/genome_similarity.html index c6ef4036..5ac856a7 100644 --- a/docs/reference/genome_similarity.html +++ b/docs/reference/genome_similarity.html @@ -1,5 +1,5 @@ -genome_similarity — genome_similarity • radiatorgenome_similarity — genome_similarity • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -95,7 +95,7 @@

genome_similarity

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/genomic_converter.html b/docs/reference/genomic_converter.html index fa82c724..dce77f29 100644 --- a/docs/reference/genomic_converter.html +++ b/docs/reference/genomic_converter.html @@ -1,5 +1,5 @@ -Conversion tool among several genomic formats — genomic_converter • radiatorConversion tool among several genomic formats — genomic_converter • radiator radiator - 1.3.1 + 1.3.3 @@ -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")) @@ -380,7 +380,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/gt2array.html b/docs/reference/gt2array.html index f68e906e..c79214dd 100644 --- a/docs/reference/gt2array.html +++ b/docs/reference/gt2array.html @@ -1,5 +1,5 @@ -gt2array — gt2array • radiatorgt2array — gt2array • radiatorhaplotype_reconstruction — haplotype_reconstruction • radiatorhaplotype_reconstruction — haplotype_reconstruction • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -105,7 +105,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/hwe_analysis.html b/docs/reference/hwe_analysis.html index e6a87236..6165b475 100644 --- a/docs/reference/hwe_analysis.html +++ b/docs/reference/hwe_analysis.html @@ -1,5 +1,5 @@ -hwe_analysis — hwe_analysis • radiatorhwe_analysis — hwe_analysis • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -92,7 +92,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/ibdg_fh.html b/docs/reference/ibdg_fh.html index 41f86bfe..84dead9c 100644 --- a/docs/reference/ibdg_fh.html +++ b/docs/reference/ibdg_fh.html @@ -1,5 +1,5 @@ -FH measure of IBDg — ibdg_fh • radiatorFH measure of IBDg — ibdg_fh • radiator radiator - 1.3.1 + 1.3.3 @@ -245,7 +245,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/import_dart.html b/docs/reference/import_dart.html index 045b26b5..a4f02264 100644 --- a/docs/reference/import_dart.html +++ b/docs/reference/import_dart.html @@ -1,5 +1,5 @@ -import_dart — import_dart • radiatorimport_dart — import_dart • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -95,7 +95,7 @@

import_dart

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/ind_total_reads.html b/docs/reference/ind_total_reads.html index 219b763a..605e8e8e 100644 --- a/docs/reference/ind_total_reads.html +++ b/docs/reference/ind_total_reads.html @@ -1,5 +1,5 @@ -ind_total_reads — ind_total_reads • radiatorind_total_reads — ind_total_reads • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

ind_total_reads

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/index.html b/docs/reference/index.html index bd9be9f0..46de0e9f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,5 +1,5 @@ -Function reference • radiatorFunction reference • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -236,8 +236,7 @@

Filter <

filter_individuals()

-

Filter individuals based on genotyping/missingness rate, -heterozygosity and total coverage

+

Filter individuals based on genotyping/missingness rate, heterozygosity and total coverage

filter_ld()

@@ -301,8 +300,7 @@

Detect <

detect_duplicate_genomes()

-

Compute pairwise genome similarity or distance between individuals -to highligh potential duplicate individuals

+

Compute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals

detect_genomic_format()

@@ -390,8 +388,7 @@

Write

write_bayescan()

-

Write a BayeScan -file from a tidy data frame

+

Write a BayeScan file from a tidy data frame

write_betadiv()

@@ -439,8 +436,7 @@

Write

write_gtypes()

-

Write a strataG object from -radiator GDS and tidy data file or object.

+

Write a strataG object from radiator GDS and tidy data file or object.

write_hapmap()

@@ -464,8 +460,7 @@

Write

write_pcadapt()

-

Write a pcadapt -file from a tidy data frame

+

Write a pcadapt file from a tidy data frame

write_plink()

@@ -575,7 +570,7 @@

Run software
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/individuals2strata.html b/docs/reference/individuals2strata.html index f65e5c44..208a8235 100644 --- a/docs/reference/individuals2strata.html +++ b/docs/reference/individuals2strata.html @@ -1,5 +1,5 @@ -Create a strata file from a list of individuals — individuals2strata • radiatorCreate a strata file from a list of individuals — individuals2strata • radiator radiator - 1.3.1 + 1.3.3 @@ -168,7 +168,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/join_strata.html b/docs/reference/join_strata.html index 25aacfa1..f1dc86a2 100644 --- a/docs/reference/join_strata.html +++ b/docs/reference/join_strata.html @@ -1,5 +1,5 @@ -Join the strata with the data — join_strata • radiatorJoin the strata with the data — join_strata • radiatorld2df — ld2df • radiatorld2df — ld2df • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

ld2df

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/ld_boxplot.html b/docs/reference/ld_boxplot.html index 4367f28a..30ce41f2 100644 --- a/docs/reference/ld_boxplot.html +++ b/docs/reference/ld_boxplot.html @@ -1,5 +1,5 @@ -ld_boxplot — ld_boxplot • radiatorld_boxplot — ld_boxplot • radiatorPrune dataset based on LD and missingness. — ld_missing • radiatorPrune dataset based on LD and missingness. — ld_missing • radiatorPrune dataset based on LD. — ld_pruning • radiatorPrune dataset based on LD. — ld_pruning • radiatorList current active filters (individuals and markers) in radiator GDS object. — list_filters • radiatorList current active filters (individuals and markers) in radiator GDS object. — list_filters • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -114,7 +114,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/markers_genotyped_helper.html b/docs/reference/markers_genotyped_helper.html index 3c9df84c..aede1ab0 100644 --- a/docs/reference/markers_genotyped_helper.html +++ b/docs/reference/markers_genotyped_helper.html @@ -1,5 +1,5 @@ -markers_genotyped_helper — markers_genotyped_helper • radiatormarkers_genotyped_helper — markers_genotyped_helper • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

markers_genotyped_helper

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/merge_dart.html b/docs/reference/merge_dart.html index cb9c47dd..51313a01 100644 --- a/docs/reference/merge_dart.html +++ b/docs/reference/merge_dart.html @@ -1,5 +1,5 @@ -Merge DArT files — merge_dart • radiatorMerge DArT files — merge_dart • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -192,7 +192,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/message_func_call.html b/docs/reference/message_func_call.html index 71e6fd17..b0a90bd4 100644 --- a/docs/reference/message_func_call.html +++ b/docs/reference/message_func_call.html @@ -1,5 +1,5 @@ -message_func_call — message_func_call • radiatormessage_func_call — message_func_call • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

message_func_call

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/missing_per_pop.html b/docs/reference/missing_per_pop.html index 7f6547ff..f734e751 100644 --- a/docs/reference/missing_per_pop.html +++ b/docs/reference/missing_per_pop.html @@ -1,5 +1,5 @@ -missing_per_pop — missing_per_pop • radiatormissing_per_pop — missing_per_pop • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

missing_per_pop

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/n.html b/docs/reference/n.html index 241b72f8..650b55af 100644 --- a/docs/reference/n.html +++ b/docs/reference/n.html @@ -1,5 +1,5 @@ -The number of observations in the current group. — n • radiatorThe number of observations in the current group. — n • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

The number of observations in the current group.

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/not_common_markers.html b/docs/reference/not_common_markers.html index 38474933..52702221 100644 --- a/docs/reference/not_common_markers.html +++ b/docs/reference/not_common_markers.html @@ -1,5 +1,5 @@ -not_common_markers — not_common_markers • radiatornot_common_markers — not_common_markers • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

not_common_markers

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/parallel_core_opt.html b/docs/reference/parallel_core_opt.html index c90d8951..5988fc0e 100644 --- a/docs/reference/parallel_core_opt.html +++ b/docs/reference/parallel_core_opt.html @@ -1,5 +1,5 @@ -parallel_core_opt — parallel_core_opt • radiatorparallel_core_opt — parallel_core_opt • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

parallel_core_opt

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/parse_gds_metadata.html b/docs/reference/parse_gds_metadata.html index 0d7ab646..ad2f807e 100644 --- a/docs/reference/parse_gds_metadata.html +++ b/docs/reference/parse_gds_metadata.html @@ -1,5 +1,5 @@ -parse_gds_metadata — parse_gds_metadata • radiatorparse_gds_metadata — parse_gds_metadata • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

parse_gds_metadata

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/pi.html b/docs/reference/pi.html index 85ae2ceb..ac69dca4 100644 --- a/docs/reference/pi.html +++ b/docs/reference/pi.html @@ -1,5 +1,5 @@ -Nucleotide diversity — pi • radiatorNucleotide diversity — pi • radiator radiator - 1.3.1 + 1.3.3 @@ -181,7 +181,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/pi_pop.html b/docs/reference/pi_pop.html index 94dd9b17..60944089 100644 --- a/docs/reference/pi_pop.html +++ b/docs/reference/pi_pop.html @@ -1,5 +1,5 @@ -pi_pop — pi_pop • radiatorpi_pop — pi_pop • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -92,7 +92,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/pi_rad.html b/docs/reference/pi_rad.html index 7f101caa..aacecefd 100644 --- a/docs/reference/pi_rad.html +++ b/docs/reference/pi_rad.html @@ -1,5 +1,5 @@ -pi_rad — pi_rad • radiatorpi_rad — pi_rad • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -92,7 +92,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html index 57a5bcc1..0585be18 100644 --- a/docs/reference/pipe.html +++ b/docs/reference/pipe.html @@ -1,5 +1,5 @@ -Forward-pipe operator — %>% • radiatorForward-pipe operator — %>% • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

Forward-pipe operator

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/plot_bayescan.html b/docs/reference/plot_bayescan.html index 89023923..492e4e8e 100644 --- a/docs/reference/plot_bayescan.html +++ b/docs/reference/plot_bayescan.html @@ -1,5 +1,5 @@ -plot_bayescan — plot_bayescan • radiatorplot_bayescan — plot_bayescan • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

plot_bayescan

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/plot_boxplot_coverage.html b/docs/reference/plot_boxplot_coverage.html index 84b023bf..17fbd811 100644 --- a/docs/reference/plot_boxplot_coverage.html +++ b/docs/reference/plot_boxplot_coverage.html @@ -1,5 +1,5 @@ -Figure box plot of coverage summary statistics — plot_boxplot_coverage • radiatorFigure box plot of coverage summary statistics — plot_boxplot_coverage • radiatorBox plot of the diversity (Gene and Haplotypes) — plot_boxplot_diversity • radiatorBox plot of the diversity (Gene and Haplotypes) — plot_boxplot_diversity • radiatorVisual diagnostic of coverage imbalance — plot_coverage_imbalance_diagnostic • radiatorVisual diagnostic of coverage imbalance — plot_coverage_imbalance_diagnostic • radiator radiator - 1.3.1 + 1.3.3 @@ -149,7 +149,7 @@

Details

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/plot_density_distribution_coverage.html b/docs/reference/plot_density_distribution_coverage.html index 1146cb10..0937fe36 100644 --- a/docs/reference/plot_density_distribution_coverage.html +++ b/docs/reference/plot_density_distribution_coverage.html @@ -1,5 +1,5 @@ -Figure of distribution (histogram) — plot_histogram • radiatorFigure of distribution (histogram) — plot_histogram • radiatorFigure density distribution of the observed heterozygosity -summary statistics. — plot_density_distribution_het • radiatorFigure density distribution of the observed heterozygosity summary statistics. — plot_density_distribution_het • radiatorFigure density distribution of minor allele frequency (MAF) -summary statistics. — plot_density_distribution_maf • radiatorFigure density distribution of minor allele frequency (MAF) summary statistics. — plot_density_distribution_maf • radiator @@ -19,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -64,8 +62,7 @@
-

Figure density distribution of minor allele frequency (MAF) -summary statistics.

+

Figure density distribution of minor allele frequency (MAF) summary statistics.

Source: R/visualization.R
@@ -134,7 +131,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/plot_distribution_diversity.html b/docs/reference/plot_distribution_diversity.html index 2d82b11a..410c85b0 100644 --- a/docs/reference/plot_distribution_diversity.html +++ b/docs/reference/plot_distribution_diversity.html @@ -1,5 +1,5 @@ -Density distribution of diversity (Gene and Haplotypes) — plot_distribution_diversity • radiatorDensity distribution of diversity (Gene and Haplotypes) — plot_distribution_diversity • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -112,7 +112,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/plot_het_outliers.html b/docs/reference/plot_het_outliers.html index e233c5f8..ae00754d 100644 --- a/docs/reference/plot_het_outliers.html +++ b/docs/reference/plot_het_outliers.html @@ -1,5 +1,5 @@ -plot_het_outliers — plot_het_outliers • radiatorplot_het_outliers — plot_het_outliers • radiatorFigure of the distribution of SNP per locus before and after filters — plot_snp_number_loci • radiatorFigure of the distribution of SNP per locus before and after filters — plot_snp_number_loci • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -98,7 +98,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/plot_snp_position_read.html b/docs/reference/plot_snp_position_read.html index 60991367..3d03575c 100644 --- a/docs/reference/plot_snp_position_read.html +++ b/docs/reference/plot_snp_position_read.html @@ -1,5 +1,5 @@ -Figure of the distribution of SNP nucleotide position alond the read — plot_snp_position_read • radiatorFigure of the distribution of SNP nucleotide position alond the read — plot_snp_position_read • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -102,7 +102,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/plot_upset.html b/docs/reference/plot_upset.html index 87e84ff1..aa1218d7 100644 --- a/docs/reference/plot_upset.html +++ b/docs/reference/plot_upset.html @@ -1,5 +1,5 @@ -plot_upset — plot_upset • radiatorplot_upset — plot_upset • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -94,7 +94,7 @@

plot_upset

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/private_alleles.html b/docs/reference/private_alleles.html index 1ac8a329..7ac1d578 100644 --- a/docs/reference/private_alleles.html +++ b/docs/reference/private_alleles.html @@ -1,5 +1,5 @@ -Find private alleles — private_alleles • radiatorFind private alleles — private_alleles • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -130,7 +130,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/private_haplotypes.html b/docs/reference/private_haplotypes.html index 70872333..1af437f0 100644 --- a/docs/reference/private_haplotypes.html +++ b/docs/reference/private_haplotypes.html @@ -1,5 +1,5 @@ -private haplotypes — private_haplotypes • radiatorprivate haplotypes — private_haplotypes • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -123,7 +123,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_common_arguments.html b/docs/reference/radiator_common_arguments.html index d9f1b8fc..3e9357f3 100644 --- a/docs/reference/radiator_common_arguments.html +++ b/docs/reference/radiator_common_arguments.html @@ -1,5 +1,5 @@ -radiator common arguments — radiator_common_arguments • radiatorradiator common arguments — radiator_common_arguments • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -73,6 +73,7 @@

radiator common arguments

radiator_common_arguments(
+  interactive.filter = TRUE,
   gds,
   data,
   parallel.core = parallel::detectCores() - 1,
@@ -84,7 +85,14 @@ 
radiator common arguments

 
     

     
Arguments

-    
gds

+    
interactive.filter

+
(optional, logical) Do you want the filtering session to
+be interactive. Figures of distribution are shown before asking for filtering
+thresholds.
+Default: interactive.filter = TRUE.

+
+
+
gds

 
(2 options) A Genomic Data Structure (GDS) file or object

 
How to get GDS ?
 Look into tidy_genomic_data,
@@ -125,13 +133,6 @@ 
Arguments

 for fine-tuning the function. Also used for legacy arguments (see details or
 special section)

 
-
-
interactive.filter

-
(optional, logical) Do you want the filtering session to
-be interactive. Figures of distribution are shown before asking for filtering
-thresholds.
-Default: interactive.filter = TRUE.

-
@@ -146,7 +147,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_dots.html b/docs/reference/radiator_dots.html index 9c01f70b..4a63653c 100644 --- a/docs/reference/radiator_dots.html +++ b/docs/reference/radiator_dots.html @@ -1,5 +1,5 @@ -radiator_dots — radiator_dots • radiatorradiator_dots — radiator_dots • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -93,7 +93,11 @@

radiator_dots

"keep.allele.names", "keep.gds", "calibrate.alleles", "vcf.metadata", "vcf.stats", "wide", "whitelist.markers", "write.tidy", "missing.memory", "dart.sequence", - "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart"), + "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart", "species", + "population", "tau", "threshold.y.markers", "threshold.y.silico.markers", + "sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD", + "threshold.x.markers.RD.silico", "mis.threshold.data", "mis.threshold.silicodata", + "zoom.data", "zoom.silicodata", "sex.id.input", "het.qr.input"), deprecated = c("maf.thresholds", "common.markers", "max.marker", "monomorphic.out", "snp.ld", "filter.call.rate", "filter.markers.coverage", "filter.markers.missing", "number.snp.reads", "mixed.genomes.analysis", "duplicate.genomes.analysis", @@ -144,7 +148,11 @@

Arguments

"write.tidy", "dart.sequence", "missing.memory", -"internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart").

+"internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart", +"species", "population", "tau", "threshold.y.markers", "threshold.y.silico.markers", +"sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD", "threshold.x.markers.RD.silico", +"mis.threshold.data", "mis.threshold.silicodata", "zoom.data", "zoom.silicodata", +"sex.id.input", "het.qr.input").

deprecated
@@ -174,7 +182,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_folder.html b/docs/reference/radiator_folder.html index fd38cd2d..f956f508 100644 --- a/docs/reference/radiator_folder.html +++ b/docs/reference/radiator_folder.html @@ -1,5 +1,5 @@ -radiator_folder — radiator_folder • radiatorradiator_folder — radiator_folder • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -107,7 +107,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_function_header.html b/docs/reference/radiator_function_header.html index 35429f6d..c34ad494 100644 --- a/docs/reference/radiator_function_header.html +++ b/docs/reference/radiator_function_header.html @@ -1,5 +1,5 @@ -radiator_function_header — radiator_function_header • radiatorradiator_function_header — radiator_function_header • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

radiator_function_header

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_gds.html b/docs/reference/radiator_gds.html index 578aa681..28716746 100644 --- a/docs/reference/radiator_gds.html +++ b/docs/reference/radiator_gds.html @@ -1,5 +1,5 @@ -radiator gds constructor — radiator_gds • radiatorradiator gds constructor — radiator_gds • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -102,7 +102,7 @@

radiator gds constructor

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_gds_skeleton.html b/docs/reference/radiator_gds_skeleton.html index a78cfc55..793c3f81 100644 --- a/docs/reference/radiator_gds_skeleton.html +++ b/docs/reference/radiator_gds_skeleton.html @@ -1,5 +1,5 @@ -radiator_gds_skeleton — radiator_gds_skeleton • radiatorradiator_gds_skeleton — radiator_gds_skeleton • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

radiator_gds_skeleton

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_packages_dep.html b/docs/reference/radiator_packages_dep.html index 46f362aa..8204a250 100644 --- a/docs/reference/radiator_packages_dep.html +++ b/docs/reference/radiator_packages_dep.html @@ -1,5 +1,5 @@ -radiator_packages_dep — radiator_packages_dep • radiatorradiator_packages_dep — radiator_packages_dep • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

radiator_packages_dep

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_parameters.html b/docs/reference/radiator_parameters.html index b06bdaac..c22bcb3b 100644 --- a/docs/reference/radiator_parameters.html +++ b/docs/reference/radiator_parameters.html @@ -1,5 +1,5 @@ -radiator_parameters — radiator_parameters • radiatorradiator_parameters — radiator_parameters • radiatorradiator packages install helper — radiator_pkg_install • radiatorradiator packages install helper — radiator_pkg_install • radiatorradiator_question — radiator_question • radiatorradiator_question — radiator_question • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

radiator_question

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_results_message.html b/docs/reference/radiator_results_message.html index 641a55df..3d806023 100644 --- a/docs/reference/radiator_results_message.html +++ b/docs/reference/radiator_results_message.html @@ -1,5 +1,5 @@ -radiator_results_message — radiator_results_message • radiatorradiator_results_message — radiator_results_message • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -93,7 +93,7 @@

radiator_results_message

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_snakecase.html b/docs/reference/radiator_snakecase.html index 4fc158a6..bf64d00a 100644 --- a/docs/reference/radiator_snakecase.html +++ b/docs/reference/radiator_snakecase.html @@ -1,5 +1,5 @@ -radiator_snakecase — radiator_snakecase • radiatorradiator_snakecase — radiator_snakecase • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

radiator_snakecase

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_split_tibble.html b/docs/reference/radiator_split_tibble.html index 962743d9..3b099191 100644 --- a/docs/reference/radiator_split_tibble.html +++ b/docs/reference/radiator_split_tibble.html @@ -1,5 +1,5 @@ -radiator_split_tibble — radiator_split_tibble • radiatorradiator_split_tibble — radiator_split_tibble • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

radiator_split_tibble

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_tic.html b/docs/reference/radiator_tic.html index 99347514..c249da60 100644 --- a/docs/reference/radiator_tic.html +++ b/docs/reference/radiator_tic.html @@ -1,5 +1,5 @@ -radiator_tic — radiator_tic • radiatorradiator_tic — radiator_tic • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

radiator_tic

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/radiator_toc.html b/docs/reference/radiator_toc.html index bc6b2b2f..76510cd7 100644 --- a/docs/reference/radiator_toc.html +++ b/docs/reference/radiator_toc.html @@ -1,5 +1,5 @@ -radiator_toc — radiator_toc • radiatorradiator_toc — radiator_toc • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -92,7 +92,7 @@

radiator_toc

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/read_blacklist_genotypes.html b/docs/reference/read_blacklist_genotypes.html index 4901fe12..cd49840b 100644 --- a/docs/reference/read_blacklist_genotypes.html +++ b/docs/reference/read_blacklist_genotypes.html @@ -1,5 +1,5 @@ -read blacklist of genotypes — read_blacklist_genotypes • radiatorread blacklist of genotypes — read_blacklist_genotypes • radiatorread_blacklist_id — read_blacklist_id • radiatorread_blacklist_id — read_blacklist_id • radiatorRead and tidy DArT output files. — read_dart • radiatorRead and tidy DArT output files. — read_dart • radiatorReads PLINK tped and bed files — read_plink • radiatorReads PLINK tped and bed files — read_plink • radiator radiator - 1.3.1 + 1.3.3 @@ -185,7 +185,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/read_rad.html b/docs/reference/read_rad.html index 40dab71c..5f85d666 100644 --- a/docs/reference/read_rad.html +++ b/docs/reference/read_rad.html @@ -1,5 +1,5 @@ -Read radiator file ending .gds, .rad, .gds.rad. — read_rad • radiatorRead radiator file ending .gds, .rad, .gds.rad. — read_rad • radiator radiator - 1.3.1 + 1.3.3 @@ -198,7 +198,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/read_strata.html b/docs/reference/read_strata.html index 147738eb..59858576 100644 --- a/docs/reference/read_strata.html +++ b/docs/reference/read_strata.html @@ -1,5 +1,5 @@ -read strata — read_strata • radiatorread strata — read_strata • radiator radiator - 1.3.1 + 1.3.3 @@ -269,7 +269,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/read_vcf.html b/docs/reference/read_vcf.html index fa3b6d0d..75b355f0 100644 --- a/docs/reference/read_vcf.html +++ b/docs/reference/read_vcf.html @@ -1,5 +1,5 @@ -Read VCF files and write a GDS file — read_vcf • radiatorRead VCF files and write a GDS file — read_vcf • radiator radiator - 1.3.1 + 1.3.3 @@ -376,7 +376,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/read_whitelist.html b/docs/reference/read_whitelist.html index a4d664c2..b9942883 100644 --- a/docs/reference/read_whitelist.html +++ b/docs/reference/read_whitelist.html @@ -1,5 +1,5 @@ -read whitelist of markers — read_whitelist • radiatorread whitelist of markers — read_whitelist • radiatorRead tidy genomic data file ending .rad — remove_duplicates • radiatorRead tidy genomic data file ending .rad — remove_duplicates • radiatorreplace_by_na — replace_by_na • radiatorreplace_by_na — replace_by_na • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

replace_by_na

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/reset_filters.html b/docs/reference/reset_filters.html index dbb492d7..458020b2 100644 --- a/docs/reference/reset_filters.html +++ b/docs/reference/reset_filters.html @@ -1,5 +1,5 @@ -Reset filters (individuals and markers) in radiator GDS object. — reset_filters • radiatorReset filters (individuals and markers) in radiator GDS object. — reset_filters • radiatorRun BayeScan — run_bayescan • radiatorRun BayeScan — run_bayescan • radiator radiator - 1.3.1 + 1.3.3 @@ -326,7 +326,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/separate_gt.html b/docs/reference/separate_gt.html index df80123a..9eaebe4f 100644 --- a/docs/reference/separate_gt.html +++ b/docs/reference/separate_gt.html @@ -1,5 +1,5 @@ -separate_gt — separate_gt • radiatorseparate_gt — separate_gt • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -99,7 +99,7 @@

separate_gt

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/separate_markers.html b/docs/reference/separate_markers.html index b209bfd0..cbd8734d 100644 --- a/docs/reference/separate_markers.html +++ b/docs/reference/separate_markers.html @@ -1,5 +1,5 @@ -Separate markers column into chrom, locus and pos — separate_markers • radiatorSeparate markers column into chrom, locus and pos — separate_markers • radiator radiator - 1.3.1 + 1.3.3 @@ -207,7 +207,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/sex_markers_plot.html b/docs/reference/sex_markers_plot.html index 4f8e71c0..a50121b0 100644 --- a/docs/reference/sex_markers_plot.html +++ b/docs/reference/sex_markers_plot.html @@ -1,5 +1,5 @@ -sex_markers_plot — sex_markers_plot • radiatorsex_markers_plot — sex_markers_plot • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -87,7 +87,8 @@

sex_markers_plot

qreg = FALSE, hist = FALSE, RD = FALSE, - plot.filename = NULL + plot.filename = NULL, + path = NULL ) @@ -104,7 +105,7 @@

sex_markers_plot

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/sexy_markers.html b/docs/reference/sexy_markers.html index 80804e96..666545ed 100644 --- a/docs/reference/sexy_markers.html +++ b/docs/reference/sexy_markers.html @@ -1,5 +1,5 @@ -sexy_markers finds sex-linked markers and re-assigns sex — sexy_markers • radiatorsexy_markers finds sex-linked markers and re-assigns sex — sexy_markers • radiator radiator - 1.3.1 + 1.3.3 @@ -85,8 +85,8 @@

sexy_markers finds sex-linked markers and re-assigns sex

sexy_markers(
   data,
   silicodata = NULL,
-  boost.analysis = FALSE,
   strata = NULL,
+  boost.analysis = FALSE,
   coverage.thresholds = 1,
   filters = TRUE,
   interactive.filter = TRUE,
@@ -111,13 +111,6 @@ 
Arguments

 Default: silicodata = NULL.

 
 
-
boost.analysis

-
(optional, logical) This method uses machine learning
-approaches to find sex markers and re-assign samples in sex group.

-The approach is currently been tested and will be available for uses soon.
-Default: boost.analysis = FALSE.

-
-
 
strata

 
(file) A tab delimited file with a minimum of
 2 columns (INDIVIDUALS, STRATA) for VCF files and 3 columns for DArT files
@@ -132,6 +125,13 @@ 
Arguments

 functions: extract_dart_target_id and extract_individuals_vcf

 
 
+
boost.analysis

+
(optional, logical) This method uses machine learning
+approaches to find sex markers and re-assign samples in sex group.

+The approach is currently under construction.
+Default: boost.analysis = FALSE.

+
+
 
coverage.thresholds

 
(optional, integer) The minimum coverage required
 to call a marker absent. For silico genotype data this must be < 1.

@@ -155,7 +155,7 @@ 
Arguments

 
 
folder.name

 
(optional,character) Name of the folder to store the results.
-Default: folder.name = "sexy_marker_date/time".

+Default: folder.name = NULL. The name sexy_markers_datetime will be generated.

 
 
 
parallel.core

@@ -250,7 +250,11 @@ 
Advance mode

     
 
 
-
dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
  • tau: The quantile used in regression to distinguish homogametic markers
+
    dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
    • species: To give your figures some meanings.
+Default species = NULL.
      • 
+
    • population: To give your figures some meanings.
+Default species = NULL.
      • 
+
    • tau: The quantile used in regression to distinguish homogametic markers
 with the heterozygosity method. See rq.
      
 Default tau = 0.03.
      • 
 
    • mis.threshold.data: Threshold to filter the SNP data on missingness.
@@ -325,7 +329,7 @@ 
      Examples
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/simulate_genos_from_posterior.html b/docs/reference/simulate_genos_from_posterior.html index 499054d1..8b9ec6f9 100644 --- a/docs/reference/simulate_genos_from_posterior.html +++ b/docs/reference/simulate_genos_from_posterior.html @@ -1,5 +1,5 @@ -simulate_genos_from_posterior — simulate_genos_from_posterior • radiatorsimulate_genos_from_posterior — simulate_genos_from_posterior • radiatorsplit_tibble_rows — split_tibble_rows • radiatorsplit_tibble_rows — split_tibble_rows • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -93,7 +93,7 @@

split_tibble_rows

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/split_vcf.html b/docs/reference/split_vcf.html index a43e07de..66b27d42 100644 --- a/docs/reference/split_vcf.html +++ b/docs/reference/split_vcf.html @@ -1,5 +1,5 @@ -Split a VCF file — split_vcf • radiatorSplit a VCF file — split_vcf • radiatorstrata_haplo — strata_haplo • radiatorstrata_haplo — strata_haplo • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

strata_haplo

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/subsampling_data.html b/docs/reference/subsampling_data.html index 60a1a87c..ae009819 100644 --- a/docs/reference/subsampling_data.html +++ b/docs/reference/subsampling_data.html @@ -1,5 +1,5 @@ -subsampling data — subsampling_data • radiatorsubsampling data — subsampling_data • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -93,7 +93,7 @@

subsampling data

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/summarise_genotypes.html b/docs/reference/summarise_genotypes.html index b9959c59..109c2e28 100644 --- a/docs/reference/summarise_genotypes.html +++ b/docs/reference/summarise_genotypes.html @@ -1,5 +1,5 @@ -summarise genotypes — summarise_genotypes • radiatorsummarise genotypes — summarise_genotypes • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -92,7 +92,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/summarize_sex.html b/docs/reference/summarize_sex.html index 14b66900..ff53f89d 100644 --- a/docs/reference/summarize_sex.html +++ b/docs/reference/summarize_sex.html @@ -1,5 +1,5 @@ -summarize_sex — summarize_sex • radiatorsummarize_sex — summarize_sex • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -94,7 +94,7 @@

summarize_sex

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/summary_gds.html b/docs/reference/summary_gds.html index 3abfb279..13a224e6 100644 --- a/docs/reference/summary_gds.html +++ b/docs/reference/summary_gds.html @@ -1,5 +1,5 @@ -summary_gds — summary_gds • radiatorsummary_gds — summary_gds • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -109,7 +109,7 @@

Arguments

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/summary_rad.html b/docs/reference/summary_rad.html index 5cc5e1b1..7972e1e3 100644 --- a/docs/reference/summary_rad.html +++ b/docs/reference/summary_rad.html @@ -1,5 +1,5 @@ -Summary statistics for RADseq data — summary_rad • radiatorSummary statistics for RADseq data — summary_rad • radiatorSummary of strata — summary_strata • radiatorSummary of strata — summary_strata • radiatorswitch_allele_count — switch_allele_count • radiatorswitch_allele_count — switch_allele_count • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

switch_allele_count

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/switch_genotypes.html b/docs/reference/switch_genotypes.html index c13b7296..8d2d3cc4 100644 --- a/docs/reference/switch_genotypes.html +++ b/docs/reference/switch_genotypes.html @@ -1,5 +1,5 @@ -switch_genotypes — switch_genotypes • radiatorswitch_genotypes — switch_genotypes • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

switch_genotypes

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/sync_gds.html b/docs/reference/sync_gds.html index c604aa3f..7e349b48 100644 --- a/docs/reference/sync_gds.html +++ b/docs/reference/sync_gds.html @@ -1,5 +1,5 @@ -sync_gds — sync_gds • radiatorsync_gds — sync_gds • radiatortibble_stats — tibble_stats • radiatortibble_stats — tibble_stats • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

tibble_stats

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/tidy2gds.html b/docs/reference/tidy2gds.html index 4cac68bc..a9d5a8e3 100644 --- a/docs/reference/tidy2gds.html +++ b/docs/reference/tidy2gds.html @@ -1,5 +1,5 @@ -tidy2gds — tidy2gds • radiatortidy2gds — tidy2gds • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

tidy2gds

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/tidy2wide.html b/docs/reference/tidy2wide.html index 57a23746..3a97c801 100644 --- a/docs/reference/tidy2wide.html +++ b/docs/reference/tidy2wide.html @@ -1,5 +1,5 @@ -tidy2wide — tidy2wide • radiatortidy2wide — tidy2wide • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -96,7 +96,7 @@

tidy2wide

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/tidy_dart_metadata.html b/docs/reference/tidy_dart_metadata.html index aa4a9d7d..1d0dbbc1 100644 --- a/docs/reference/tidy_dart_metadata.html +++ b/docs/reference/tidy_dart_metadata.html @@ -1,5 +1,5 @@ -Import and tidy DArT metadata. — tidy_dart_metadata • radiatorImport and tidy DArT metadata. — tidy_dart_metadata • radiator radiator - 1.3.1 + 1.3.3 @@ -160,7 +160,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/tidy_fstat.html b/docs/reference/tidy_fstat.html index 108e395e..7ed7c4b4 100644 --- a/docs/reference/tidy_fstat.html +++ b/docs/reference/tidy_fstat.html @@ -1,5 +1,5 @@ -fstat file to tidy dataframe — tidy_fstat • radiatorfstat file to tidy dataframe — tidy_fstat • radiator radiator - 1.3.1 + 1.3.3 @@ -180,7 +180,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/tidy_genepop.html b/docs/reference/tidy_genepop.html index 93bf51fd..03b6fcb7 100644 --- a/docs/reference/tidy_genepop.html +++ b/docs/reference/tidy_genepop.html @@ -1,5 +1,5 @@ -Import genepop file and convert to a tidy dataframe — tidy_genepop • radiatorImport genepop file and convert to a tidy dataframe — tidy_genepop • radiator radiator - 1.3.1 + 1.3.3 @@ -253,7 +253,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/tidy_genind.html b/docs/reference/tidy_genind.html index 1acf7666..82e77677 100644 --- a/docs/reference/tidy_genind.html +++ b/docs/reference/tidy_genind.html @@ -1,5 +1,5 @@ -Tidy a genind object to a tidy dataframe — tidy_genind • radiatorTidy a genind object to a tidy dataframe — tidy_genind • radiatorTidy a genlight object to a tidy dataframe and/or GDS object/file — tidy_genlight • radiatorTidy a genlight object to a tidy dataframe and/or GDS object/file — tidy_genlight • radiatorTransform common genomic dataset format in a tidy data frame — tidy_genomic_data • radiatorTransform common genomic dataset format in a tidy data frame — tidy_genomic_data • radiator radiator - 1.3.1 + 1.3.3 @@ -247,7 +247,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/tidy_gtypes.html b/docs/reference/tidy_gtypes.html index cf8901d8..80a269d0 100644 --- a/docs/reference/tidy_gtypes.html +++ b/docs/reference/tidy_gtypes.html @@ -1,5 +1,5 @@ -Tidy a gtypes object to a tidy dataframe — tidy_gtypes • radiatorTidy a gtypes object to a tidy dataframe — tidy_gtypes • radiatorTidy PLINK tped and bed files — tidy_plink • radiatorTidy PLINK tped and bed files — tidy_plink • radiator radiator - 1.3.1 + 1.3.3 @@ -176,7 +176,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/tidy_vcf.html b/docs/reference/tidy_vcf.html index 2a5543b1..c62f87b1 100644 --- a/docs/reference/tidy_vcf.html +++ b/docs/reference/tidy_vcf.html @@ -1,5 +1,5 @@ -Tidy vcf file — tidy_vcf • radiatorTidy vcf file — tidy_vcf • radiator radiator - 1.3.1 + 1.3.3 @@ -326,7 +326,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/tidy_wide.html b/docs/reference/tidy_wide.html index 66a44b5b..b06ad6c8 100644 --- a/docs/reference/tidy_wide.html +++ b/docs/reference/tidy_wide.html @@ -1,5 +1,5 @@ -Read/Import a tidy genomic data frames. — tidy_wide • radiatorRead/Import a tidy genomic data frames. — tidy_wide • radiator radiator - 1.3.1 + 1.3.3 @@ -160,7 +160,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/update_bl_individuals.html b/docs/reference/update_bl_individuals.html index a1d79150..25b42f8f 100644 --- a/docs/reference/update_bl_individuals.html +++ b/docs/reference/update_bl_individuals.html @@ -1,5 +1,5 @@ -update_bl_individuals — update_bl_individuals • radiatorupdate_bl_individuals — update_bl_individuals • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -94,7 +94,7 @@

update_bl_individuals

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/update_bl_markers.html b/docs/reference/update_bl_markers.html index cf55b6ba..73bf184c 100644 --- a/docs/reference/update_bl_markers.html +++ b/docs/reference/update_bl_markers.html @@ -1,5 +1,5 @@ -update_bl_markers — update_bl_markers • radiatorupdate_bl_markers — update_bl_markers • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -94,7 +94,7 @@

update_bl_markers

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/update_filter_parameter.html b/docs/reference/update_filter_parameter.html index 5f2e7de4..46256cac 100644 --- a/docs/reference/update_filter_parameter.html +++ b/docs/reference/update_filter_parameter.html @@ -1,5 +1,5 @@ -update filter parameter file — update_filter_parameter • radiatorupdate filter parameter file — update_filter_parameter • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -99,7 +99,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/update_radiator_gds.html b/docs/reference/update_radiator_gds.html index a372c4dd..e8afd052 100644 --- a/docs/reference/update_radiator_gds.html +++ b/docs/reference/update_radiator_gds.html @@ -1,5 +1,5 @@ -update_radiator_gds — update_radiator_gds • radiatorupdate_radiator_gds — update_radiator_gds • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -97,7 +97,7 @@

update_radiator_gds

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/vcf_strata.html b/docs/reference/vcf_strata.html index a9630309..94c0861f 100644 --- a/docs/reference/vcf_strata.html +++ b/docs/reference/vcf_strata.html @@ -1,5 +1,5 @@ -Join stratification metadata to a VCF (population-aware VCF) — vcf_strata • radiatorJoin stratification metadata to a VCF (population-aware VCF) — vcf_strata • radiatorWrite an arlequin file from a tidy data frame — write_arlequin • radiatorWrite an arlequin file from a tidy data frame — write_arlequin • radiatorWrite a BayeScan -file from a tidy data frame — write_bayescan • radiatorWrite a BayeScan file from a tidy data frame — write_bayescan • radiatorWrite a betadiv file from a tidy data frame — write_betadiv • radiatorWrite a betadiv file from a tidy data frame — write_betadiv • radiatorWrite a COLONY input file — write_colony • radiatorWrite a COLONY input file — write_colony • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -272,7 +272,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_dadi.html b/docs/reference/write_dadi.html index 0436c0be..373976e1 100644 --- a/docs/reference/write_dadi.html +++ b/docs/reference/write_dadi.html @@ -1,5 +1,5 @@ -Write a dadi SNP input file from a tidy data frame. — write_dadi • radiatorWrite a dadi SNP input file from a tidy data frame. — write_dadi • radiator radiator - 1.3.1 + 1.3.3 @@ -192,7 +192,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_fasta.html b/docs/reference/write_fasta.html index 9f17ee5f..eb180aff 100644 --- a/docs/reference/write_fasta.html +++ b/docs/reference/write_fasta.html @@ -1,5 +1,5 @@ -Export FASTA — write_fasta • radiatorExport FASTA — write_fasta • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -88,7 +88,7 @@

Export FASTA

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_faststructure.html b/docs/reference/write_faststructure.html index 02db9643..9bce50dc 100644 --- a/docs/reference/write_faststructure.html +++ b/docs/reference/write_faststructure.html @@ -1,5 +1,5 @@ -Write a faststructure file from a tidy data frame — write_faststructure • radiatorWrite a faststructure file from a tidy data frame — write_faststructure • radiator radiator - 1.3.1 + 1.3.3 @@ -156,7 +156,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_fineradstructure.html b/docs/reference/write_fineradstructure.html index c7e40ff5..a5103558 100644 --- a/docs/reference/write_fineradstructure.html +++ b/docs/reference/write_fineradstructure.html @@ -1,5 +1,5 @@ -Write a fineRADstructure file from a tidy data frame — write_fineradstructure • radiatorWrite a fineRADstructure file from a tidy data frame — write_fineradstructure • radiatorWrite a GDS object from a tidy data frame — write_gds • radiatorWrite a GDS object from a tidy data frame — write_gds • radiator radiator - 1.3.1 + 1.3.3 @@ -165,7 +165,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_genepop.html b/docs/reference/write_genepop.html index 78f37767..0395c0bf 100644 --- a/docs/reference/write_genepop.html +++ b/docs/reference/write_genepop.html @@ -1,5 +1,5 @@ -Write a genepop file — write_genepop • radiatorWrite a genepop file — write_genepop • radiatorWrite a genepopedit flatten object — write_genepopedit • radiatorWrite a genepopedit flatten object — write_genepopedit • radiator radiator - 1.3.1 + 1.3.3 @@ -145,7 +145,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_genind.html b/docs/reference/write_genind.html index a064abd3..6810055d 100644 --- a/docs/reference/write_genind.html +++ b/docs/reference/write_genind.html @@ -1,5 +1,5 @@ -Write a genind object from a tidy data frame or GDS file or object. — write_genind • radiatorWrite a genind object from a tidy data frame or GDS file or object. — write_genind • radiatorWrite a genlight object from a tidy data frame or GDS file or object. — write_genlight • radiatorWrite a genlight object from a tidy data frame or GDS file or object. — write_genlight • radiatorWrite a gsi_sim file from a data frame (wide or long/tidy). — write_gsi_sim • radiatorWrite a gsi_sim file from a data frame (wide or long/tidy). — write_gsi_sim • radiatorWrite a strataG object from -radiator GDS and tidy data file or object. — write_gtypes • radiatorWrite a strataG object from radiator GDS and tidy data file or object. — write_gtypes • radiatorWrite a HapMap file from a tidy data frame — write_hapmap • radiatorWrite a HapMap file from a tidy data frame — write_hapmap • radiatorWrite a hierfstat file from a tidy data frame — write_hierfstat • radiatorWrite a hierfstat file from a tidy data frame — write_hierfstat • radiatorWrite a HZAR file from a tidy data frame. — write_hzar • radiatorWrite a HZAR file from a tidy data frame. — write_hzar • radiatorWrite a LDna object from a tidy data frame — write_ldna • radiatorWrite a LDna object from a tidy data frame — write_ldna • radiatorWrite a maverick file from a tidy data frame — write_maverick • radiatorWrite a maverick file from a tidy data frame — write_maverick • radiatorWrite a pcadapt -file from a tidy data frame — write_pcadapt • radiatorWrite a pcadapt file from a tidy data frame — write_pcadapt • radiator radiator - 1.3.1 + 1.3.3 @@ -69,8 +67,7 @@
-

Write a pcadapt -file from a tidy data frame

+

Write a pcadapt file from a tidy data frame

Source: R/write_pcadapt.R
@@ -187,7 +184,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_plink.html b/docs/reference/write_plink.html index 38314609..d5c324f3 100644 --- a/docs/reference/write_plink.html +++ b/docs/reference/write_plink.html @@ -1,5 +1,5 @@ -Write a plink tped/tfam file from a tidy data frame — write_plink • radiatorWrite a plink tped/tfam file from a tidy data frame — write_plink • radiatorWrite tidy genomic data file or close GDS file — write_rad • radiatorWrite tidy genomic data file or close GDS file — write_rad • radiator radiator - 1.3.1 + 1.3.3 @@ -199,7 +199,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_related.html b/docs/reference/write_related.html index f8b61592..2a39deb6 100644 --- a/docs/reference/write_related.html +++ b/docs/reference/write_related.html @@ -1,5 +1,5 @@ -Write a related file from a tidy data frame — write_related • radiatorWrite a related file from a tidy data frame — write_related • radiator radiator - 1.3.1 + 1.3.3 @@ -153,7 +153,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_rubias.html b/docs/reference/write_rubias.html index 388f7faa..7865aeb9 100644 --- a/docs/reference/write_rubias.html +++ b/docs/reference/write_rubias.html @@ -1,5 +1,5 @@ -Write a rubias object — write_rubias • radiatorWrite a rubias object — write_rubias • radiator @@ -17,7 +17,7 @@ radiator - 1.3.1 + 1.3.3 @@ -155,7 +155,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/reference/write_snprelate.html b/docs/reference/write_snprelate.html index 7a243f3e..3e474925 100644 --- a/docs/reference/write_snprelate.html +++ b/docs/reference/write_snprelate.html @@ -1,5 +1,5 @@ -Write a SNPRelate object from a tidy data frame — write_snprelate • radiatorWrite a SNPRelate object from a tidy data frame — write_snprelate • radiatorWrite a stockR dataset from a tidy data frame or GDS file or object. — write_stockr • radiatorWrite a stockR dataset from a tidy data frame or GDS file or object. — write_stockr • radiatorWrite a structure file from a tidy data frame — write_structure • radiatorWrite a structure file from a tidy data frame — write_structure • radiatorWrite a vcf file from a tidy data frame — write_vcf • radiatorWrite a vcf file from a tidy data frame — write_vcf • radiator