Evaluate number of neutropenia episodes and their duration for a given patient or cohort
Arguments
- input_files_path
path to a file or a folder with MT csv files (in quotes).
- anc_range
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.
- duration_anc
numeric duration (in weeks) that is used to categorize event as "long duration neutropenia" (optional)
Value
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.
Pat ID
Number of particular toxicity episodes
Duration of particular toxicity (in weeks)
Number of long duration toxicity episodes
Duration of long duration toxicity (in weeks)
Note
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
Long duration toxicity is only analyzed if "duration_anc" is included in provided arguments
User may save the result as a list, if required, to analyze each patient neutropenia analysis by analyzing 1st element of list
Examples
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)
#> NOTE: Analyzing provided input file only
#> Quitting
#> Bye Bye: Did you know that Earth is spherical in shape :)?
#> [[1]]
#> ID Number of episodes Duration (weeks)
#> 1 UPN_915 2 2
#> Number of long duration toxicity episodes Duration of long duration toxicity
#> 1 0 0
#>
#> [[2]]
#>
#>
#> ========================================= =======
#> Parameter Result
#> ========================================= =======
#> ID UPN_915
#> Number of episodes 2
#> Duration (weeks) 2
#> Number of long duration toxicity episodes 0
#> Duration of long duration toxicity 0
#> ========================================= =======
#>
#> [[3]]
#> <table class='gmisc_table' style='border-collapse: collapse; margin-top: 1em; margin-bottom: 1em;' >
#> <thead>
#> <tr><td colspan='2' style='text-align: left;'>
#> Table: Neutropenia analysis</td></tr>
#> <tr>
#> <th style='background-color: #e6e6e6; border-bottom: 1px solid grey; border-top: 2px solid grey; text-align: center;'>Parameter</th>
#> <th style='background-color: #e6e6e6; border-bottom: 1px solid grey; border-top: 2px solid grey; text-align: center;'>Result</th>
#> </tr>
#> </thead>
#> <tbody>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; text-align: left;'>ID</td>
#> <td style='width: 200px; background-color: #ffffff; text-align: center;'>UPN_915</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: left;'>Number of episodes</td>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: center;'>2</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; text-align: left;'>Duration (weeks)</td>
#> <td style='width: 200px; background-color: #ffffff; text-align: center;'>2</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: left;'>Number of long duration toxicity episodes</td>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: center;'>0</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; border-bottom: 2px solid grey; text-align: left;'>Duration of long duration toxicity</td>
#> <td style='width: 200px; background-color: #ffffff; border-bottom: 2px solid grey; text-align: center;'>0</td>
#> </tr>
#> </tbody>
#> </table>
# \donttest{
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)
#> NOTE: Including all files in input folder
#> Quitting
#> Bye Bye: Did you know that Earth is spherical in shape :)?
#> [[1]]
#> ID Number of episodes Duration (weeks)
#> 1 UPN_1 0 0
#> 2 UPN_2 0 0
#> 3 UPN_914 1 3
#> 4 UPN_915 2 2
#> 5 UPN_916 3 10
#> 6 UPN_917 3 8
#> 7 UPN_918 0 0
#> Number of long duration toxicity episodes Duration of long duration toxicity
#> 1 0 0
#> 2 0 0
#> 3 1 3
#> 4 0 0
#> 5 3 10
#> 6 1 4
#> 7 0 0
#>
#> [[2]]
#>
#>
#> ========================================= =======
#> Parameter Result
#> ========================================= =======
#> Number of patients analyzed 7
#> Number of episodes 1 [0-3]
#> Duration (weeks) 2 [0-6]
#> Number of long duration toxicity episodes 0 [0-1]
#> Duration of long duration toxicity 0 [0-4]
#> ========================================= =======
#>
#> [[3]]
#> <table class='gmisc_table' style='border-collapse: collapse; margin-top: 1em; margin-bottom: 1em;' >
#> <thead>
#> <tr><td colspan='2' style='text-align: left;'>
#> Table: Neutropenia analysis</td></tr>
#> <tr>
#> <th style='background-color: #e6e6e6; border-bottom: 1px solid grey; border-top: 2px solid grey; text-align: center;'>Parameter</th>
#> <th style='background-color: #e6e6e6; border-bottom: 1px solid grey; border-top: 2px solid grey; text-align: center;'>Result</th>
#> </tr>
#> </thead>
#> <tbody>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; text-align: left;'>Number of patients analyzed</td>
#> <td style='width: 200px; background-color: #ffffff; text-align: center;'>7</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: left;'>Number of episodes</td>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: center;'>1 [0-3]</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; text-align: left;'>Duration (weeks)</td>
#> <td style='width: 200px; background-color: #ffffff; text-align: center;'>2 [0-6]</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: left;'>Number of long duration toxicity episodes</td>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: center;'>0 [0-1]</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; border-bottom: 2px solid grey; text-align: left;'>Duration of long duration toxicity</td>
#> <td style='width: 200px; background-color: #ffffff; border-bottom: 2px solid grey; text-align: center;'>0 [0-4]</td>
#> </tr>
#> </tbody>
#> </table>
result <- assess_neutropenia(input_files_path = pat_data,
anc_range = c(0.5, 0.75), duration_anc = 3)
#> NOTE: Analyzing provided input file only
#> Quitting
#> Bye Bye: Did you know that Earth is spherical in shape :)?
print(result[[1]])
#> ID Number of episodes Duration (weeks)
#> 1 UPN_915 2 2
#> Number of long duration toxicity episodes Duration of long duration toxicity
#> 1 0 0
print(result[[2]])
#>
#>
#> ========================================= =======
#> Parameter Result
#> ========================================= =======
#> ID UPN_915
#> Number of episodes 2
#> Duration (weeks) 2
#> Number of long duration toxicity episodes 0
#> Duration of long duration toxicity 0
#> ========================================= =======
print(result[[3]])
#> <table class='gmisc_table' style='border-collapse: collapse; margin-top: 1em; margin-bottom: 1em;' >
#> <thead>
#> <tr><td colspan='2' style='text-align: left;'>
#> Table: Neutropenia analysis</td></tr>
#> <tr>
#> <th style='background-color: #e6e6e6; border-bottom: 1px solid grey; border-top: 2px solid grey; text-align: center;'>Parameter</th>
#> <th style='background-color: #e6e6e6; border-bottom: 1px solid grey; border-top: 2px solid grey; text-align: center;'>Result</th>
#> </tr>
#> </thead>
#> <tbody>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; text-align: left;'>ID</td>
#> <td style='width: 200px; background-color: #ffffff; text-align: center;'>UPN_915</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: left;'>Number of episodes</td>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: center;'>2</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; text-align: left;'>Duration (weeks)</td>
#> <td style='width: 200px; background-color: #ffffff; text-align: center;'>2</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: left;'>Number of long duration toxicity episodes</td>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: center;'>0</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; border-bottom: 2px solid grey; text-align: left;'>Duration of long duration toxicity</td>
#> <td style='width: 200px; background-color: #ffffff; border-bottom: 2px solid grey; text-align: center;'>0</td>
#> </tr>
#> </tbody>
#> </table>
# }