calculate_score_animals {miRetrieve}

Calculate animal model scores for abstracts

Description

Calculate animal model score for each abstract to indicate possible use of animal models.

Usage

calculate_score_animals(
  df,
  keywords = animal_keywords,
  case = FALSE,
  threshold = NULL,
  indicate = FALSE,
  discard = FALSE,
  col.abstract = Abstract
)

Arguments

df

Data frame containing abstracts.

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.

case

Boolean. If case = TRUE, terms contained in keywords are case sensitive. If case = FALSE, terms contained in keywords are case insensitive.

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.

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.

discard

Boolean. If discard = TRUE, only abstracts are kept where animal models are present.

col.abstract

Symbol. Column containing abstracts.

Details

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().

Value

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.

See Also

plot_score_animals()

Other score functions: assign_topic(), calculate_score_biomarker(), calculate_score_patients(), calculate_score_topic(), plot_score_animals(), plot_score_biomarker(), plot_score_patients(), plot_score_topic()