calculate_score_animals: Calculate animal model scores for abstracts
In JulFriedrich/miRetrieve: miRNA Text Mining in Abstracts

Description Usage Arguments Details Value See Also

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

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

`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.

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().

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.

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()