From ae839253d9253a2eca7c5630d5a0a2a642735cac Mon Sep 17 00:00:00 2001
From: jeffersonfparil <jeffersonparil@gmail.com>
Date: Thu, 4 Jul 2024 10:11:53 +1000
Subject: [PATCH] adding details to the main function listing all public-facing
 function for users to use

---
 R/main.R  | 38 ++++++++++++++++++++++++++++++++++++++
 man/gp.Rd | 41 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 79 insertions(+)

diff --git a/R/main.R b/R/main.R
index 0cd78f5..16c1f5d 100644
--- a/R/main.R
+++ b/R/main.R
@@ -204,6 +204,44 @@
 #'          - $model: best performing genomic prediction model based on within population cross-validation 
 #'              which yielded these effects.
 #'  _ Err: gpError
+#' @details
+#' Functions list per module:
+#'  1. io.R
+#'      1.1. fn_G_extract_names
+#'      1.2. fn_G_split_off_alternative_allele
+#'      1.3. fn_G_numeric_to_non_numeric
+#'      1.4. fn_G_non_numeric_to_numeric
+#'      1.5. fn_G_to_vcf
+#'      1.6. fn_vcf_to_G
+#'      1.7. fn_classify_allele_frequencies
+#'      1.8. fn_simulate_data
+#'      1.9. fn_load_genotype
+#'      1.10. fn_filter_genotype
+#'      1.11. fn_save_genotype
+#'      1.12. fn_load_phenotype
+#'      1.13. fn_filter_phenotype
+#'      1.14. fn_save_phenotype
+#'      1.15. fn_merge_genotype_and_phenotype
+#'      1.16. fn_subset_merged_genotype_and_phenotype
+#'      1.17. fn_estimate_memory_footprint
+#'  2. cross_validation.R
+#'      2.1. fn_cv_1
+#'      2.2. fn_cross_validation_preparation
+#'      2.3. fn_cross_validation_within_population
+#'      2.4. fn_cross_validation_across_populations_bulk
+#'      2.5. fn_cross_validation_across_populations_pairwise
+#'      2.6. fn_cross_validation_across_populations_lopo
+#'  3. models.R
+#'      3.1. fn_ols
+#'      3.2. fn_ridge
+#'      3.3. fn_lasso
+#'      3.4. fn_elastic_net
+#'      3.5. fn_Bayes_A
+#'      3.6. fn_Bayes_B
+#'      3.7. fn_Bayes_C
+#'      3.8. fn_gBLUP
+#'  4. metrics.R
+#'      4.1. fn_prediction_performance_metrics
 #' @examples
 #' list_sim = fn_simulate_data(n=300, n_pop=3, verbose=TRUE)
 #' df_pheno = read.delim(list_sim$fname_pheno_tsv, header=TRUE)
diff --git a/man/gp.Rd b/man/gp.Rd
index 95c2dfe..5247266 100644
--- a/man/gp.Rd
+++ b/man/gp.Rd
@@ -242,6 +242,47 @@ _ Err: gpError
 \description{
 Main genomic prediction cross-validation within and across populations
 }
+\details{
+Functions list per module:
+\enumerate{
+\item io.R
+1.1. fn_G_extract_names
+1.2. fn_G_split_off_alternative_allele
+1.3. fn_G_numeric_to_non_numeric
+1.4. fn_G_non_numeric_to_numeric
+1.5. fn_G_to_vcf
+1.6. fn_vcf_to_G
+1.7. fn_classify_allele_frequencies
+1.8. fn_simulate_data
+1.9. fn_load_genotype
+1.10. fn_filter_genotype
+1.11. fn_save_genotype
+1.12. fn_load_phenotype
+1.13. fn_filter_phenotype
+1.14. fn_save_phenotype
+1.15. fn_merge_genotype_and_phenotype
+1.16. fn_subset_merged_genotype_and_phenotype
+1.17. fn_estimate_memory_footprint
+\item cross_validation.R
+2.1. fn_cv_1
+2.2. fn_cross_validation_preparation
+2.3. fn_cross_validation_within_population
+2.4. fn_cross_validation_across_populations_bulk
+2.5. fn_cross_validation_across_populations_pairwise
+2.6. fn_cross_validation_across_populations_lopo
+\item models.R
+3.1. fn_ols
+3.2. fn_ridge
+3.3. fn_lasso
+3.4. fn_elastic_net
+3.5. fn_Bayes_A
+3.6. fn_Bayes_B
+3.7. fn_Bayes_C
+3.8. fn_gBLUP
+\item metrics.R
+4.1. fn_prediction_performance_metrics
+}
+}
 \examples{
 list_sim = fn_simulate_data(n=300, n_pop=3, verbose=TRUE)
 df_pheno = read.delim(list_sim$fname_pheno_tsv, header=TRUE)