#' Keywords - animals.
#'
#' Keywords to identify abstracts using animal models.
#' @export
animal_keywords <- c('mice', 'mouse', ' rats ',
'. rats ', ' rat ', 'elegans',
'zebrafish', 'horse', 'rabbit',
'porcine', 'piglet', 'monkey')
#' Calculate animal model scores for abstracts
#'
#' Calculate animal model score for each abstract to indicate possible
#' use of animal models.
#'
#' Calculate animal model score for each abstract to indicate possible
#' use of animal models. This score is added to the data frame as an additional
#' column `Animal_score`, containing the calculated animal model score.
#' To decide which abstracts are considered to contain animal models, a threshold
#' can be set via the `threshold` argument. Furthermore, an additional
#' column can be added, verbally indicating the use of animal models in
#' an abstract.
#' Choosing the right threshold can be facilitated using `plot_score_animals()`.
#'
#' @param df Data frame containing abstracts.
#' @param keywords Character vector. Vector containing keywords. The score is
#' calculated based on these keywords. How much weight a keyword in `keywords`
#' carries is determined by how often it is present in `keywords`, e.g. if
#' a keyword is mentioned twice in `keywords` and it is mentioned only once in
#' an abstract, it adds 2 points to the score.
#' The predefined keywords can be accessed via `miRetrieve::animal_keywords`.
#' @param case Boolean. If `case = TRUE`, terms contained in `keywords` are case
#' sensitive. If `case = FALSE`, terms contained in `keywords` are case insensitive.
#' @param threshold Integer. Optional. Threshold to decide if an abstract is
#' considered to use animal models or not. If `indicate = TRUE` or `discard = TRUE`
#' and `threshold` is not specified, `threshold` is automatically set to `1`.
#' @param indicate Boolean. If `indicate = TRUE`, an extra column is added. This
#' extra column contains "Yes" or "No", indicating the use of animal models
#' in abstracts.
#' @param discard Boolean. If `discard = TRUE`, only abstracts are kept where
#' animal models are present.
#' @param col.abstract Symbol. Column containing abstracts.
#'
#' @return Data frame with calculated animal model scores.
#' If `discard = FALSE`, adds extra columns
#' to the original data frame with the calculated animal model scores.
#' If `discard = TRUE`, only abstracts with animal models are kept.
#'
#' @seealso [plot_score_animals()]
#'
#' @family score functions
#'
#' @export
calculate_score_animals <- function(df,
keywords = animal_keywords,
case = FALSE,
threshold = NULL,
indicate = FALSE,
discard = FALSE,
col.abstract = Abstract) {
if(!is.null(threshold) & !is.numeric(threshold)) {
stop("'threshold' must be an integer >= 0")
}
if(indicate == TRUE & is.null(threshold)) {
threshold <- 1
}
if(discard == TRUE & is.null(threshold)) {
threshold <- 1
}
df_animals <- df %>%
dplyr::mutate(Animal_score = purrr::map_int({{col.abstract}},
~ calculate_score(string = .x,
keywords = keywords,
case = case)))
if (indicate == TRUE) {
df_animals <- df_animals %>%
dplyr::mutate(Animal_p = ifelse(Animal_score >= threshold, "Yes", "No"))
}
if (discard == TRUE) {
df_animals <- df_animals %>%
dplyr::filter(Animal_score >= threshold)
return(df_animals)
} else {
return(df_animals)
}
}
#' Plot frequency of animal model scores in abstracts
#'
#' Plot frequency of animal model scores in abstracts.
#'
#' Plots a frequency distribution of animal model scores in abstracts of a
#' data frame. The animal model score is influenced by the choice of
#' terms in `keywords`.
#' Plotting the distribution can help deciding if the
#' terms are well-chosen, or in choosing the right threshold to decide
#' which abstracts are considered to contain animal models.
#'
#' @param df Data frame containing abstracts.
#' @param keywords Character vector. Vector containing keywords. The animal
#' model score is calculated based on these keywords. How much weight a keyword
#' in `keywords` carries is determined how often it is present in `keywords`,
#' e.g. if a keyword is mentioned twice in `keywords` and it is mentioned only once in
#' an abstract, it adds 2 points to the score.
#' @param case Boolean. If `case = TRUE`, terms contained in `keywords` are case
#' sensitive. If `case = FALSE`, terms contained in `keywords` are case insensitive.
#' @param bins Integer. Specifies how many bins are used to plot
#' the distribution. If `bins = NULL`, bins are calculated over the whole
#' range of scores, with one bin per score.
#' @param colour String. Colour of histogram.
#' @param col.abstract Symbol. Column containing abstracts.
#' @param col.pmid Symbol. Column containing PubMed-IDs.
#' @param title String. Plot title.
#'
#' @return Histogram displaying the distribution of animal scores in abstracts.
#'
#' @seealso [calculate_score_animals()]
#'
#' @family score functions
#'
#' @export
plot_score_animals <- function(df,
keywords = animal_keywords,
case = FALSE,
bins = NULL,
colour = "steelblue3",
col.abstract = Abstract,
col.pmid = PMID,
title = NULL) {
if(is.null(title)) {
title <- "Animal models score distribution"
}
df_animals <- df %>%
dplyr::mutate(Animal_score = purrr::map_int({{col.abstract}}, ~ calculate_score(string = .x,
keywords = keywords,
case = case)))
if (is.null(bins)) {
bins <- max(df_animals$Animal_score) - min(df_animals$Animal_score)
}
df_animals <- df_animals %>%
dplyr::select({{col.pmid}}, Animal_score) %>%
dplyr::distinct()
plot <- ggplot(df_animals, aes(x = Animal_score)) +
geom_histogram(bins = bins,
fill = colour,
center = 0,
binwidth = 1) +
theme_classic() +
xlab("Animal model score") +
ylab("# of abstracts")+
ggtitle(title) +
scale_x_continuous(expand = c(0,0)) +
scale_y_continuous(expand = c(0,0))
return(plot)
}
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