assess_anemia {allMT}R Documentation

Assess hematological toxicities: Anemia


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


assess_anemia(input_files_path, hb_range, duration_hb = NA)



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


Hemoglobin (HB) value range of c(Anemic HB threshold, recovered HB threshold). NOTE: Ensure that units are the same as unit of HB in the input data.


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


Returns a list with (1) the anemia 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_hb" is included in provided arguments

  3. User may save the result as a list, if required, to analyze each patient seperatly please use 1st element of list

See Also

assess_neutropenia(), assess_thrombocytopenia()


pat_data = system.file("extdata/processed_data/", "UPN_915.csv", package = "allMT")
assess_anemia(input_files_path = pat_data,
                      hb_range = c(7, 8), duration_hb = 3)

cohort_path = paste0(system.file("extdata/processed_data/", package = "allMT"), "/")
assess_anemia(input_files_path = cohort_path,
                      hb_range = c(7, 8), duration_hb = 3)

result <- assess_anemia(input_files_path = pat_data,
                      hb_range = c(7, 8), duration_hb = 3)

[Package allMT version 0.1.0 Index]