From 4a49f4b2fea96ad89c39a0db59d3ce006a267c04 Mon Sep 17 00:00:00 2001
From: egouldo <egouldo@users.noreply.github.com>
Date: Sun, 11 Aug 2024 12:44:08 +1000
Subject: [PATCH] #102 update roxygen examples and doc /document

---
 R/utils.R | 41 +++++++++++++++++++++++++++--------------
 1 file changed, 27 insertions(+), 14 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index a1611c2..6cbdf22 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,8 +1,9 @@
 #' Negative Value Matching
 #'
-#' See \code{base::[](`%in%`)} for details. %nin% is a binary operator, returning a logical vector indicating if there is a negative match or not.
+#' See \code{base::[](`%in%`)} for details. `%nin%` is a binary operator, 
+#' returning a logical vector indicating if there is a negative match or not.
 #'
-#' @name %in%
+#' @name %nin%
 #' @rdname NotIn
 #' @keywords internal
 #' @export
@@ -10,13 +11,14 @@
 #' @param lhs vector or NULL: the values to be matched. [Long vectors](http://127.0.0.1:59782/help/library/base/help/Long%20vectors) are supported.
 #' @param rhs vector or NULL: the values to be matched. [Long vectors](http://127.0.0.1:59782/help/library/base/help/Long%20vectors) are supported.
 #' @return A logical vector indicating which value of `lhs` are *not* matched in `rhs`
+#' @examples
+#' "A" %nin% LETTERS[1:10]
+#' "A" %in% LETTERS[1:10]
 `%nin%` <- Negate(`%in%`)
 
-
-
-#' Subsetting Functions for Zr analysis
+#' Subsetting Functions for effect-size meta-analysis
 #'
-#' @description Generates a list of functions that are used to subset the processed ManyEcoEvo dataset
+#' @description Generates a list of functions that are used to subset the processed [ManyEcoEvo::] dataset
 #'
 #' @return A named list of `lambda` functions
 #' @export
@@ -38,9 +40,15 @@ subset_fns_Zr <- function() { # TODO update calling of this fn (switch to fn rat
   return(out)
 }
 
-#' Subsetting Functions for yi analysis
+#' Subsetting Functions for out-of-sample predictions meta-analysis
 #'
-#' @description Generates a list of functions that are used to subset the processed ManyEcoEvo dataset containing out-of-sample predictions \(\code{y\_i}\)
+#' @description Generates a list of functions that are used to subset the 
+#' processed ManyEcoEvo dataset (e.g.`data(ManyEcoEvo_results`) containing 
+#' out-of-sample predictions $y_i$. 
+#' 
+#' @details 
+#' The subset functions are used to filter out predictions that are not 
+#' to be included in the meta-analysis.
 #'
 #' @return A named list of `lambda` functions
 #' @export
@@ -77,16 +85,19 @@ capwords <- function(s, strict = FALSE) {
   sapply(strsplit(s, split = " "), cap, USE.NAMES = !is.null(names(s)))
 }
 
-
-
 #' Removes infinite and NA values from a dataframe of standardised effects
 #'
-#' @param Z_colname unquoted or bare column name with the Z or Zr estimates
-#' @param VZ_colname unquoted or bare column name containing the VZ or VZr estimates
 #' @param effects_analysis A dataframe containing the standardised effects
+#' @param Z_colname unquoted or bare column name with the $Z$ or $Z_r$ estimates
+#' @param VZ_colname unquoted or bare column name containing the $VZ$ or $\text{VZ}_r$ estimates
 #'
 #' @return a dataframe without
 #' @export
+#' @examples
+#' data(ManyEcoEvo_results)
+#' ManyEcoEvo_results %>% 
+#' pluck("effects_analysis", 1) %>% 
+#' rm_inf_na(beta_estimate, beta_SE)
 rm_inf_na <- function(effects_analysis, Z_colname, VZ_colname) {
   effects_analysis %>%
     filter(
@@ -108,8 +119,10 @@ rm_inf_na <- function(effects_analysis, Z_colname, VZ_colname) {
 #' @export
 #' @importFrom dplyr group_split
 #' @examples
-#' named_group_split(ManyEcoEvo::euc_data, Property)
-#' named_group_split(ManyEcoEvo::blue_tit_data, hatch_Area)
+#' data(euc_data)
+#' data(blue_tit_data)
+#' named_group_split(euc_data, Property)
+#' named_group_split(blue_tit_data, hatch_Area)
 named_group_split <- function(.data, grouping_variable) {
   .data %>%
     group_by({{ grouping_variable }}) %>%