calculate_score_patients: Calculate patients scores for abstracts
In JulFriedrich/miRetrieve: miRNA Text Mining in Abstracts

Description Usage Arguments Details Value See Also

Calculate patients score for each abstract to indicate possible use of patient material.

calculate_score_patients(
  df,
  keywords = patients_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::patients_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 use of patient tissue is present in an abstract or not. If `indicate = TRUE` or `discard = TRUE` and `threshold` 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 patient tissue in abstracts.
`discard`	Boolean. If `discard = TRUE`, only abstracts are kept where use of patient tissue is present.
`col.abstract`	Symbol. Column containing abstracts.

Calculate patient score for each abstract to indicate possible use of patient material. This score is added to the data frame as an additional column Patient_score, containing the calculated patients score. To decide which abstracts are considered to contain patient material, a threshold can be set via the threshold argument. Furthermore, an additional column can be added, verbally indicating the general use of patient material. Choosing the right threshold can be facilitated using plot_score_patients().

Data frame with calculated patient scores. If discard = FALSE, adds extra columns to the original data frame with the calculated patient tissue scores. If discard = TRUE, only abstracts with use of patient tissue are kept.

plot_score_patients()

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