still working on load functions

jeffersonfparil · May 27, 2024 · 2aefb76 · 2aefb76
1 parent 4384f35
commit 2aefb76
Show file tree

Hide file tree

Showing 18 changed files with 1,333 additions and 684 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1 @@
+.github/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -14,6 +14,10 @@ Suggests:
 Remotes:
     jeffersonfparil/simquantgen
 Imports:
+    parallel,
+    cluster,
+    mgcv,
+    nlme,
     glmnet,
     BGLR,
     sommer,

diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,12 @@
+# Generated by roxygen2: do not edit by hand
+
+export(fn_G_extract_names)
+export(fn_G_non_numeric_to_numeric)
+export(fn_G_numeric_to_non_numeric)
+export(fn_G_split_off_alternative_allele)
+export(fn_G_to_vcf)
+export(fn_classify_allele_frequencies)
+export(fn_filter_loci)
+export(fn_load_genotype)
+export(fn_simulate_data)
+export(fn_vcf_to_G)
diff --git a/R/cross_validation.R b/R/cross_validation.R
@@ -1,7 +1,7 @@
-dirname_functions = dirname(sys.frame(1)$ofile)
-# dirname_functions = "/group/pasture/Jeff/genomic_selection/src"
-library(testthat)
-source(paste0(dirname_functions, "/models.R"))
+# dirname_functions = dirname(sys.frame(1)$ofile)
+# # dirname_functions = "/group/pasture/Jeff/genomic_selection/src"
+# library(testthat)
+# source(paste0(dirname_functions, "/models.R"))
 
 fn_kfold_cross_validation = function(i, vec_set_partition_groupings, mat_idx_shuffle, mat_params, G, y, COVAR=NULL, prefix_tmp="gsTmp", mem_mb=1000){
     # i = 34

diff --git a/R/load.R b/R/load.R
diff --git a/R/main.R b/R/main.R
diff --git a/R/models.R b/R/models.R
@@ -5,9 +5,9 @@ suppressWarnings(suppressPackageStartupMessages(library(BGLR)))
 suppressWarnings(suppressPackageStartupMessages(library(sommer)))
 # suppressWarnings(suppressPackageStartupMessages(library(epistasisfeatures)))
 
-dirname_functions = dirname(sys.frame(1)$ofile)
-# dirname_functions = "/group/pasture/Jeff/genomic_selection/src"
-source(paste0(dirname_functions, "/metrics.R"))
+# dirname_functions = dirname(sys.frame(1)$ofile)
+# # dirname_functions = "/group/pasture/Jeff/genomic_selection/src"
+# source(paste0(dirname_functions, "/metrics.R"))
 
 ### New models can be added by having the same input structure, i.e.:
 ###     1.) nxp matrix of numeric genotype data without missing values

diff --git a/man/fn_G_extract_names.Rd b/man/fn_G_extract_names.Rd
diff --git a/man/fn_G_non_numeric_to_numeric.Rd b/man/fn_G_non_numeric_to_numeric.Rd
diff --git a/man/fn_G_numeric_to_non_numeric.Rd b/man/fn_G_numeric_to_non_numeric.Rd
diff --git a/man/fn_G_split_off_alternative_allele.Rd b/man/fn_G_split_off_alternative_allele.Rd
diff --git a/man/fn_G_to_vcf.Rd b/man/fn_G_to_vcf.Rd
diff --git a/man/fn_classify_allele_frequencies.Rd b/man/fn_classify_allele_frequencies.Rd
diff --git a/man/fn_filter_loci.Rd b/man/fn_filter_loci.Rd
diff --git a/man/fn_load_genotype.Rd b/man/fn_load_genotype.Rd