Analyze physicians' compliance to dosing guidelines: STOP DOSE
Source:R/assess_stop_doses.R
assess_stop_doses.RdEvaluate number of times blood counts did not support physicians' STOP DOSE decision
Usage
assess_stop_doses(
input_files_path,
anc_threshold = NA,
plt_threshold = NA,
hb_threshold = NA
)Arguments
- input_files_path
path to a file or a folder with MT csv files (in quotes).
- anc_threshold
Absolute neutrophil count (ANC) value threshold below which doses should be stopped. NOTE: Ensure that the threshold value is represented with same unit as of the input ANC data.
- plt_threshold
Platelet (PLT) value threshold below which doses should be stopped. NOTE: Ensure that the threshold value is represented with same unit as of the input PLT data.
- hb_threshold
Hemoglobin (HB) value threshold below which doses should be stopped. NOTE: Ensure that the threshold value is represented with same unit as of the input Hb data.
Value
Returns a list with (1) the 'STOP DOSE' analysis for each patient as listed below, (2) analysis summary as dataframe (3) analysis summary as HTML table in viewer.
Pat ID
Number of decisions where the physician stopped dose (a)
Number of times blood counts did not support dose suspension (b)
Discordance (%) = (\((b/a)*100)\)
Note
Atleast one of the threshold parameters (anc_threshold, plt_threshold, hb_threshold) must be provided to carry out analysis. Missing threshold parameter will not be considered.
If the function is used for cohort analysis then a and b will be 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
User may save the result as a list, if required, to analyze each patient separately - use 1st element of list. Please refer to examples from assess_anemia
Examples
pat_data <- system.file("extdata/processed_data/", "UPN_915.csv", package = "allMT")
assess_stop_doses(input_files_path = pat_data,
anc_threshold = 0.5, plt_threshold = 50, hb_threshold = 7)
#> NOTE: Analyzing provided input file only
#> NOTE: Analysis will be carried out with provided parameters: anc_threshold, plt_threshold and hb_threshold
#> Quitting
#> Bye Bye: Did you know that Earth is 3rd planet from sun :)?
#> [[1]]
#> ID No. of 'dose stop' decisions
#> 1 UPN_915 7
#> No. of times the counts did not support dose decision Discordance (%)
#> 1 3 42.86%
#>
#> [[2]]
#>
#>
#> ===================================================== =======
#> Parameter Result
#> ===================================================== =======
#> ID UPN_915
#> No. of 'dose stop' decisions 7
#> No. of times the counts did not support dose decision 3
#> Discordance (%) 42.86%
#> ===================================================== =======
#>
#> [[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: 'STOP DOSE' 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;'>No. of 'dose stop' decisions</td>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: center;'>7</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; text-align: left;'>No. of times the counts did not support dose decision</td>
#> <td style='width: 200px; background-color: #ffffff; text-align: center;'>3</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 200px; background-color: #e6e6e6; border-bottom: 2px solid grey; text-align: left;'>Discordance (%)</td>
#> <td style='width: 200px; background-color: #e6e6e6; border-bottom: 2px solid grey; text-align: center;'>42.86%</td>
#> </tr>
#> </tbody>
#> </table>
# \donttest{
assess_stop_doses(input_files_path = pat_data,
anc_threshold = 0.5)
#> NOTE: Analyzing provided input file only
#> NOTE: Analysis will be carried out with provided parameter: anc_threshold
#> Quitting
#> Bye Bye: Did you know that Earth is 3rd planet from sun :)?
#> [[1]]
#> ID No. of 'dose stop' decisions
#> 1 UPN_915 7
#> No. of times the counts did not support dose decision Discordance (%)
#> 1 5 71.43%
#>
#> [[2]]
#>
#>
#> ===================================================== =======
#> Parameter Result
#> ===================================================== =======
#> ID UPN_915
#> No. of 'dose stop' decisions 7
#> No. of times the counts did not support dose decision 5
#> Discordance (%) 71.43%
#> ===================================================== =======
#>
#> [[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: 'STOP DOSE' 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;'>No. of 'dose stop' decisions</td>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: center;'>7</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 200px; background-color: #ffffff; text-align: left;'>No. of times the counts did not support dose decision</td>
#> <td style='width: 200px; background-color: #ffffff; text-align: center;'>5</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 200px; background-color: #e6e6e6; border-bottom: 2px solid grey; text-align: left;'>Discordance (%)</td>
#> <td style='width: 200px; background-color: #e6e6e6; border-bottom: 2px solid grey; text-align: center;'>71.43%</td>
#> </tr>
#> </tbody>
#> </table>
cohort_path = paste0(system.file("extdata/processed_data/", package = "allMT"), "/")
assess_stop_doses(input_files_path = cohort_path,
anc_threshold = 0.5,plt_threshold = 50, hb_threshold = 7)
#> NOTE: Including all files in input folder
#> NOTE: Analysis will be carried out with provided parameters: anc_threshold, plt_threshold and hb_threshold
#> Quitting
#> Bye Bye: Did you know that Earth is 3rd planet from sun :)?
#> [[1]]
#> ID No. of 'dose stop' decisions
#> 1 UPN_1 4
#> 2 UPN_2 4
#> 3 UPN_914 3
#> 4 UPN_915 7
#> 5 UPN_916 6
#> 6 UPN_917 6
#> 7 UPN_918 4
#> No. of times the counts did not support dose decision Discordance (%)
#> 1 4 100%
#> 2 4 100%
#> 3 1 33.33%
#> 4 3 42.86%
#> 5 2 33.33%
#> 6 2 33.33%
#> 7 4 100%
#>
#> [[2]]
#>
#>
#> ====================================================== =======
#> Parameter Results
#> ====================================================== =======
#> No. of patients analyzed 7
#> Total no. of 'STOP DOSE' decisions 34
#> Total no. of time counts did not support dose decision 20
#> 'STOP DOSE' decisions: median [IQR] 4 [4-6]
#> Counts did not support dose decision: median [IQR] 3 [2-4]
#> ====================================================== =======
#>
#> [[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: 'STOP DOSE' 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;'>Results</th>
#> </tr>
#> </thead>
#> <tbody>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 250px; background-color: #ffffff; text-align: left;'>No. of patients analyzed</td>
#> <td style='width: 250px; background-color: #ffffff; text-align: center;'>7</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 250px; background-color: #e6e6e6; text-align: left;'>Total no. of 'STOP DOSE' decisions</td>
#> <td style='width: 250px; background-color: #e6e6e6; text-align: center;'>34</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 250px; background-color: #ffffff; text-align: left;'>Total no. of time counts did not support dose decision</td>
#> <td style='width: 250px; background-color: #ffffff; text-align: center;'>20</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 250px; background-color: #e6e6e6; text-align: left;'>'STOP DOSE' decisions: median [IQR]</td>
#> <td style='width: 250px; background-color: #e6e6e6; text-align: center;'>4 [4-6]</td>
#> </tr>
#> <tr style='background-color: #ffffff;'>
#> <td style='width: 250px; background-color: #ffffff; border-bottom: 2px solid grey; text-align: left;'>Counts did not support dose decision: median [IQR]</td>
#> <td style='width: 250px; background-color: #ffffff; border-bottom: 2px solid grey; text-align: center;'>3 [2-4]</td>
#> </tr>
#> </tbody>
#> </table>
# }