Analyze physicians' compliance to dosing guidelines: REDUCE DOSE
Source:R/assess_reduced_doses.R
assess_reduced_doses.RdEvaluate number of times blood counts did not support physicians' REDUCE DOSE decision
Usage
assess_reduced_doses(
input_files_path,
anc_range = NA,
plt_range = NA,
hb_range = NA,
reduction_factor
)Arguments
- input_files_path
path to a file or a folder with MT csv files (in quotes).
- anc_range
Absolute neutrophil count (ANC) range between which doses should be reduce. NOTE: Ensure that values are represented with same unit as of the input ANC data.
- plt_range
Platelet (PLT) range between which doses should be reduce. NOTE: Ensure that values are represented with same unit as of the input PLT data.
- hb_range
Hemoglobin (HB) range between which doses should be stopped. NOTE: Ensure that values are represented with same unit as of the input Hb data.
- reduction_factor
Percentage of 6MP starting dose (first visit dose) dose that will be called as "reduced" dose. Default = 50% of starting dose.
Value
Returns a list with (1) the 'REDUCE 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 reduced dose (a)
Number of times blood counts did not support dose reduction (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_reduced_doses(input_files_path = pat_data,
anc_range = c(0.5,0.75), plt_range = c(50,75),
hb_range = c(7,8), reduction_factor = 50)
#> NOTE: Analyzing provided input file only
#> NOTE: Analysis will be carried out with provided parameters: anc_range, plt_range and hb_range
#> Quitting
#> Bye Bye: Did you know that sunset on Mars is blue :)?
#> [[1]]
#> ID No. of 'dose reduce' decisions
#> 1 UPN_915 1
#> No. of times the counts did not support dose decision Discordance (%)
#> 1 0 0%
#>
#> [[2]]
#>
#>
#> ===================================================== =======
#> Parameter Result
#> ===================================================== =======
#> ID UPN_915
#> No. of 'dose reduce' decisions 1
#> No. of times the counts did not support dose decision 0
#> Discordance (%) 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: 'REDUCED 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 reduce' decisions</td>
#> <td style='width: 200px; background-color: #e6e6e6; text-align: center;'>1</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;'>0</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;'>0%</td>
#> </tr>
#> </tbody>
#> </table>
# \donttest{
cohort_path = paste0(system.file("extdata/processed_data/", package = "allMT"), "/")
assess_reduced_doses(input_files_path = cohort_path,
anc_range = c(0.5,0.75), plt_range = c(50,75),
hb_range = c(7,8), reduction_factor = 50)
#> NOTE: Analyzing provided input file only
#> NOTE: Analysis will be carried out with provided parameters: anc_range, plt_range and hb_range
#> Quitting
#> Bye Bye: Did you know that sunset on Mars is blue :)?
#> [[1]]
#> ID No. of 'dose reduce' decisions
#> 1 UPN_1 1
#> 2 UPN_2 1
#> 3 UPN_914 0
#> 4 UPN_915 1
#> 5 UPN_916 0
#> 6 UPN_917 0
#> 7 UPN_918 1
#> No. of times the counts did not support dose decision Discordance (%)
#> 1 1 100%
#> 2 1 100%
#> 3 0 NaN%
#> 4 0 0%
#> 5 0 NaN%
#> 6 0 NaN%
#> 7 1 100%
#>
#> [[2]]
#>
#>
#> ====================================================== =======
#> Parameter Results
#> ====================================================== =======
#> No. of patients analyzed 7
#> Total no. of 'REDUCED DOSE' decisions 4
#> Total no. of time counts did not support dose decision 3
#> 'REDUCED DOSE' decisions: median [IQR] 1 [0-1]
#> Counts did not support dose decision: median [IQR] 0 [0-1]
#> ====================================================== =======
#>
#> [[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: 'REDUCED 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 'REDUCED DOSE' decisions</td>
#> <td style='width: 250px; background-color: #e6e6e6; text-align: center;'>4</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;'>3</td>
#> </tr>
#> <tr style='background-color: #e6e6e6;'>
#> <td style='width: 250px; background-color: #e6e6e6; text-align: left;'>'REDUCED DOSE' decisions: median [IQR]</td>
#> <td style='width: 250px; background-color: #e6e6e6; text-align: center;'>1 [0-1]</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;'>0 [0-1]</td>
#> </tr>
#> </tbody>
#> </table>
# }