assess_neutropenia {allMT}R Documentation

Assess hematological toxicities: Neutropenia


Evaluate number of neutropenia episodes and their duration for a given patient or cohort


assess_neutropenia(input_files_path, anc_range, duration_anc = NA)



path to a file or a folder with MT csv files (in quotes).


Absolute neutrophil count (ANC) value range of c(Neutropenic ANC threshold, recovered ANC threshold). NOTE: Ensure that units are the same as unit of ANC in the input data.


numeric duration (in weeks) that is used to categorize event as "long duration neutropenia" (optional)


Returns a list with (1) the neutropenia information for each patient as listed below, (2) analysis summary as dataframe (3) analysis summary as HTML table.

  1. Pat ID

  2. Number of particular toxicity episodes

  3. Duration of particular toxicity (in weeks)

  4. Number of long duration toxicity episodes

  5. Duration of long duration toxicity (in weeks)


  1. If the function is used for cohort analysis then values are represented as median and interquartile range (IQR) (25%-75%). The median and IQR is rounded off to upper integer value if decimal value is greater or equal to 0.5, else to lower integer value. Example 1.4->1 and 3.75->4

  2. Long duration toxicity is only analyzed if "duration_anc" is included in provided arguments

  3. User may save the result as a list, if required, to analyze each patient neutropenia analysis by analyzing 1st element of list

See Also

assess_anemia(), assess_thrombocytopenia()


pat_data = system.file("extdata/processed_data/", "UPN_915.csv", package = "allMT")
assess_neutropenia(input_files_path = pat_data,
                      anc_range = c(0.5, 0.75), duration_anc = 3)

cohort_path = paste0(system.file("extdata/processed_data/", package = "allMT"), "/")
assess_neutropenia(input_files_path = cohort_path,
                      anc_range = c(0.5, 0.75), duration_anc = 3)

result <- assess_neutropenia(input_files_path = pat_data,
                      anc_range = c(0.5, 0.75), duration_anc = 3)

[Package allMT version 0.1.0 Index]