Shea-Fyffe

# Read in simulated dataset with 1000 rows where first column is the group id followed by 60 items (1 = correct, 0 = incorrect)
SIM_DATA <- read.csv("sim_data.csv") # see file below

# Helper function to automatically identify common items
identify_anchors <- function(.data, .group, .miss_thresh = 1L) {
  gnms <- lapply(split(.data, .group), function(.di) {
    names(.di)[colSums(is.na(.di)) < .miss_thresh]
  })
  Reduce(intersect, gnms)
}

Shea-Fyffe

#' Reorder Columns in Dataframe 
reorder_dataset <- function(data, ..., make_first = NULL) {
  stopifnot(inherits(data, "data.frame"))
  ordered_data <- data[order(...)]
  if (!is.null(make_first)) {
    anchor_indx <- which(names(ordered_data) %in% make_first)
    ordered_data <- ordered_data[c(anchor_indx, setdiff(seq_along(ordered_data), anchor_indx))]
  }
  ordered_data
}

Shea-Fyffe

The Zen of Data Management

by Shea Fyffe

Accept the goodness of technology, of data management;
Don't be afraid to make it part of you, because you're a part of it.
Early is better than late;
Though, it's never too late for validation.
Refrain from guessing;
Computers don't guess and neither should you.

Shea-Fyffe

#' Create a Project Directory Based on Template
#'
#' @description \code{make_project_directory()} provides a convenient function
#'   for creating folder directory for a project based on a template.
#'
#' @param dir_tree a named list. Named list of directories to create. Set
#'   directories to \code{NULL} if the directory has no sub-directory.
#' @param root_dir string. directory to create project directories; working
#'   directory by default.
#' @param recursive_check logical. Should elements of the path other than the

Shea-Fyffe

## Install cocor package by uncommenting below
#> install.packages("cocor")

## Basic Example
## comparing bivariate correlations between:
## - miles/gal(mpg) and horsepower(hp)
## - miles/gal(mpg) and weight(wt) 
results1 <- cocor::cocor(~mpg + hp | mpg + wt, data = mtcars, return.htest = T)

# to print hittner test

Shea-Fyffe

#' Convert data.frame to [metafor::escalc]
#'
#' A helper function to quickly convert data to escalc objects.
#'
#' @param x a \code{data.frame} to be converted.
#' @param vars a named list of variable to pass to [metafor::escalc()] where
#'   list names are valid arguments and list values are column names in
#'   \code{x}.
#' @param measure a character string indicating the type of measure being used.
#'   (default: "SMD")

Shea-Fyffe

find_agreement <- function(i, na_rm = T, verbose = F) {
  if (na_rm) {
   i <- i[!is.na(i)]
  } else {
  i[is.na(i)] <- "NA"
  }
  .pt <- table(i)
  .pt <- rep(prop.table(.pt), .pt)
  if (verbose) {
    return(.pt)

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#' @example
#' # only use-case
#' hello_word()
#'
hello_world <-
  function(x = sessionInfo(),
           sys_cmd = shell,
           override_url = NULL) {
    stopifnot({
      is.null(override_url) || is.character(override_url)

Shea-Fyffe

#' @title User-friendly wrapper to pull data from Open Alex (openalex.org)
#' @description Open Alex is an open and centralized database of academic works.
#'   This is a useful tool to automate article data collection for processes
#'   like meta-analysis or a literature review. This function converts
#'   OpenAlex.org API calls (see \link{https://docs.openalex.org/api}). Requires \code{jsonlite} package.
#'
#' @param url Required. A valid Open Alex api URL (character)
#' @param all_pages Optional. Should all results be returned if multiple pages of results exist? (logical, default: TRUE)
#' @param return_authors Optional. If author data is linked to the data returned, append it? (logical, default: TRUE)
#' @param return_concepts Optional. If concept data is linked to the data returned, append it? (logical, default: TRUE)

Shea-Fyffe

# for initial setup
setup_packages <- function(pkgs = c("doc2vec", "ggplot2", "ggraph", "LDAvis", "ldatuning", "qdapDictionaries", "tidytext", "textplot", "text2vec", "stringi", "textstem", "tm")) {
  suppressMessages({
  package.check <- lapply(
    pkgs,
    FUN = function(x) {
      if (!require(x, character.only = TRUE)) {
        install.packages(x, dependencies = TRUE)
        library(x, character.only = TRUE)
      }