calculate_score_patients {miRetrieve}

Calculate patients scores for abstracts

Description

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

Usage

calculate_score_patients(
  df,
  keywords = patients_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::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.

Details

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().

Value

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.

See Also

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()