Treatment Compliance Table
trt_compliance.Rmd
library(metalite)
library(metalite.sl)
#> Error in get(paste0(generic, ".", class), envir = get_method_env()) :
#> object 'type_sum.accel' not found
library(dplyr)Create Treatment Compliance Table
The objective of this tutorial is to generate a production-ready Treatment Compliance specification analyses.
This report produces a table that contains a summary of treatment compliance information. The report consists of a treatment compliance category section and a treatment compliance statistics section. To accomplish this using metalite.sl, three essential functions are required:
prepare_trt_compliance ():this function is a wrapper function ofprepare_sl_summary ()which prepares data for treatment compliance analysis.format_trt_compliance(): prepare analysis outdata with proper format.rtf_trt_compliance(): transfer output dataset to RTF table.
An example output:
Example data
Within metalite.sl, we utilized the ADSL datasets from the metalite package to create an illustrative dataset. The metadata structure remains consistent across all analysis examples within metalite.sl. To calculate treatment compliance percent and treatment compliance range, we utilized adex dataset. Additional information can be accessed on the metalite package website.
Build a metadata
adsl <- r2rtf::r2rtf_adsl
adex <- metalite.ae::metalite_ae_adex
adex1 <- adex |>
filter(EXNUMDOS > 0 & !(is.na(AENDY))) |>
group_by(USUBJID) |>
slice(n()) |>
select(USUBJID, AENDY) |>
rename(ADURN = AENDY)
adsl <- merge(adsl, adex1, by = "USUBJID")
adsl <- adsl |>
mutate(
TRTDUR = as.numeric(TRTDUR),
ADURN = as.numeric(ADURN),
CMPLPCT = round((ADURN / TRTDUR) * 100, 2)
)
adsl <- adsl |>
mutate(
CMPLRNG = case_when(
CMPLPCT >= 0 & CMPLPCT <= 20 ~ "0% to <=20%",
CMPLPCT > 20 & CMPLPCT <= 40 ~ ">20% to <=40%",
CMPLPCT > 40 & CMPLPCT <= 60 ~ ">40% to <=60%",
CMPLPCT > 60 & CMPLPCT <= 80 ~ ">60% to <=80%",
CMPLPCT > 80 ~ ">80%"
),
CMPLRNGN = case_when(
CMPLPCT >= 0 & CMPLPCT <= 20 ~ 1,
CMPLPCT > 20 & CMPLPCT <= 40 ~ 2,
CMPLPCT > 40 & CMPLPCT <= 60 ~ 3,
CMPLPCT > 60 & CMPLPCT <= 80 ~ 4,
CMPLPCT > 80 ~ 5
)
)
head(adsl)
#> USUBJID STUDYID SUBJID SITEID SITEGR1 ARM
#> 1 01-701-1015 CDISCPILOT01 1015 701 701 Placebo
#> 2 01-701-1023 CDISCPILOT01 1023 701 701 Placebo
#> 3 01-701-1028 CDISCPILOT01 1028 701 701 Xanomeline High Dose
#> 4 01-701-1033 CDISCPILOT01 1033 701 701 Xanomeline Low Dose
#> 5 01-701-1034 CDISCPILOT01 1034 701 701 Xanomeline High Dose
#> 6 01-701-1047 CDISCPILOT01 1047 701 701 Placebo
#> TRT01P TRT01PN TRT01A TRT01AN TRTSDT
#> 1 Placebo 0 Placebo 0 2014-01-02
#> 2 Placebo 0 Placebo 0 2012-08-05
#> 3 Xanomeline High Dose 81 Xanomeline High Dose 81 2013-07-19
#> 4 Xanomeline Low Dose 54 Xanomeline Low Dose 54 2014-03-18
#> 5 Xanomeline High Dose 81 Xanomeline High Dose 81 2014-07-01
#> 6 Placebo 0 Placebo 0 2013-02-12
#> TRTEDT TRTDUR AVGDD CUMDOSE AGE AGEGR1 AGEGR1N AGEU RACE RACEN SEX
#> 1 2014-07-02 182 0.0 0 63 <65 1 YEARS WHITE 1 F
#> 2 2012-09-01 28 0.0 0 64 <65 1 YEARS WHITE 1 M
#> 3 2014-01-14 180 77.7 13986 71 65-80 2 YEARS WHITE 1 M
#> 4 2014-03-31 14 54.0 756 74 65-80 2 YEARS WHITE 1 M
#> 5 2014-12-30 183 76.9 14067 77 65-80 2 YEARS WHITE 1 F
#> 6 2013-03-09 26 0.0 0 85 >80 3 YEARS WHITE 1 F
#> ETHNIC SAFFL ITTFL EFFFL COMP8FL COMP16FL COMP24FL DISCONFL
#> 1 HISPANIC OR LATINO Y Y Y Y Y Y
#> 2 HISPANIC OR LATINO Y Y Y N N N Y
#> 3 NOT HISPANIC OR LATINO Y Y Y Y Y Y
#> 4 NOT HISPANIC OR LATINO Y Y Y N N N Y
#> 5 NOT HISPANIC OR LATINO Y Y Y Y Y Y
#> 6 NOT HISPANIC OR LATINO Y Y Y N N N Y
#> DSRAEFL DTHFL BMIBL BMIBLGR1 HEIGHTBL WEIGHTBL EDUCLVL DISONSDT DURDIS
#> 1 25.1 25-<30 147.3 54.4 16 2010-04-30 43.9
#> 2 Y 30.4 >=30 162.6 80.3 14 2006-03-11 76.4
#> 3 31.4 >=30 177.8 99.3 16 2009-12-16 42.8
#> 4 28.8 25-<30 175.3 88.5 12 2009-08-02 55.3
#> 5 26.1 25-<30 154.9 62.6 9 2011-09-29 32.9
#> 6 Y 30.4 >=30 148.6 67.1 8 2009-07-26 42.0
#> DURDSGR1 VISIT1DT RFSTDTC RFENDTC VISNUMEN RFENDT
#> 1 >=12 2013-12-26 2014-01-02 2014-07-02 12 2014-07-02
#> 2 >=12 2012-07-22 2012-08-05 2012-09-02 5 2012-09-02
#> 3 >=12 2013-07-11 2013-07-19 2014-01-14 12 2014-01-14
#> 4 >=12 2014-03-10 2014-03-18 2014-04-14 5 2014-04-14
#> 5 >=12 2014-06-24 2014-07-01 2014-12-30 12 2014-12-30
#> 6 >=12 2013-01-22 2013-02-12 2013-03-29 6 2013-03-29
#> DCDECOD DCREASCD MMSETOT ADURN CMPLPCT CMPLRNG
#> 1 COMPLETED Completed 23 182 100 >80%
#> 2 ADVERSE EVENT Adverse Event 23 28 100 >80%
#> 3 COMPLETED Completed 23 180 100 >80%
#> 4 STUDY TERMINATED BY SPONSOR Sponsor Decision 23 14 100 >80%
#> 5 COMPLETED Completed 21 183 100 >80%
#> 6 ADVERSE EVENT Adverse Event 23 26 100 >80%
#> CMPLRNGN
#> 1 5
#> 2 5
#> 3 5
#> 4 5
#> 5 5
#> 6 5
adsl$TRTA <- adsl$TRT01A
adsl$TRTA <- factor(adsl$TRTA,
levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"),
labels = c("Placebo", "Low Dose", "High Dose")
)
plan <- plan(
analysis = "trt_compliance", population = "apat",
observation = "apat", parameter = "CMPLRNG;CMPLPCT"
)
meta <- meta_adam(
population = adsl,
observation = adsl
) |>
define_plan(plan = plan) |>
define_population(
name = "apat",
group = "TRTA",
subset = quote(SAFFL == "Y"),
var = c("USUBJID", "TRTA", "SAFFL", "CMPLPCT", "CMPLRNG")
) |>
metalite::define_parameter(
name = "CMPLPCT",
var = "CMPLPCT",
label = "Treatment Compliance Percent",
) |>
metalite::define_parameter(
name = "CMPLRNG",
var = "CMPLRNG",
label = "Treatment Compliance Range",
) |>
define_analysis(
name = "trt_compliance",
title = "Summary of Treatment Compliance",
label = "treatment compliance table"
) |>
meta_build()Click to show the output
meta
#> ADaM metadata:
#> .$data_population Population data with 252 subjects
#> .$data_observation Observation data with 252 records
#> .$plan Analysis plan with 1 plans
#>
#>
#> Analysis population type:
#> name id group var subset
#> 1 'apat' 'USUBJID' 'TRTA' USUBJID, TRTA, SAFFL, CMPLPCT, CMPLRNG SAFFL == 'Y'
#> label
#> 1 'All Participants as Treated'
#>
#>
#> Analysis observation type:
#> name id group var subset label
#> 1 'apat' 'USUBJID' 'TRTA' 'All Participants as Treated'
#>
#>
#> Analysis parameter type:
#> name label subset
#> 1 'CMPLPCT' 'Treatment Compliance Percent'
#> 2 'CMPLRNG' 'Treatment Compliance Range'
#>
#>
#> Analysis function:
#> name label
#> 1 'trt_compliance' 'treatment compliance table'Analysis preparation
The function prepare_trt_compliance() is written to
prepare data for treatment compliance analysis.The function takes four
arguments:
meta is metadata object created by metalite and it contains data from ADSL. Analysis, Population, and Parameter arguments are used to subset and process the meta data. They have default values, which rely on the meta data object.
The function assign default value Analysis to
trt_compliance, Population to the population value
associated with the trt_compliance analysis in meta plan,
and parameter to the parameter(s) associated with the
trt_compliance analysis in meta$plan.
However, the user can also manually specify the analysis, population, and parameter values when calling the function, if they want to override the default values.
In the body of the function, it calls another function
prepare_sl_summary with the same meta, analysis, population, and
parameter arguments. prepare_sl_summary takes the meta
data, subsets it based on the analysis, population, and parameter
values, and then calculates and returns a summary of the relevant
data.
The result of prepare_sl_summary is then returned as the result of prepare_trt_compliance.
The resulting output of the function
prepare_trt_compliance() comprises a collection of raw
datasets for analysis and reporting.
outdata <- prepare_trt_compliance(meta)Click to show the output
outdata
#> List of 14
#> $ meta :List of 7
#> $ population : chr "apat"
#> $ observation : chr "apat"
#> $ parameter : chr "CMPLRNG;CMPLPCT"
#> $ n :'data.frame': 1 obs. of 6 variables:
#> $ order : NULL
#> $ group : chr "TRTA"
#> $ reference_group: NULL
#> $ char_n :List of 2
#> $ char_var : chr [1:2] "CMPLRNG" "CMPLPCT"
#> $ char_prop :List of 2
#> $ var_type :List of 2
#> $ group_label : Factor w/ 3 levels "Placebo","Low Dose",..: 1 3 2
#> $ analysis : chr "trt_compliance"-
parameter: parameter name
outdata$parameter
#> [1] "CMPLRNG;CMPLPCT"-
n: number of participants in population
outdata$n
#> name n_1 n_2 n_3 n_9999 var_label
#> 1 Participants in population 85 84 83 252 -----The resulting dataset contains frequently used statistics, with
variables indexed according to the order specified in
outdata$group.
outdata$group
#> [1] "TRTA"-
char_n: number of participants completed vs not completed in each parameter
outdata$char_n
#> [[1]]
#> name Placebo Low Dose High Dose Total var_label
#> 1 >20% to <=40% 0 0 1 1 Treatment Compliance Range
#> 2 >80% 84 83 81 248 Treatment Compliance Range
#> 3 0% to <=20% 1 1 1 3 Treatment Compliance Range
#>
#> [[2]]
#> name Placebo Low Dose High Dose Total
#> 1 Mean 99.0 99.0 98.1 98.7
#> 2 SD 9.4 9.5 12.2 10.4
#> 3 SE 1.0 1.0 1.3 0.7
#> 4 Median 100.0 100.0 100.0 100.0
#> 5 Min 12.9 13.2 8.9 8.9
#> 6 Max 100.0 100.0 100.0 100.0
#> 7 Q1 to Q3 100 to 100 100 to 100 100 to 100 100 to 100
#> 8 Range 12.93 to 100 13.25 to 100 8.88 to 100 8.88 to 100
#> var_label
#> 1 Treatment Compliance Percent
#> 2 Treatment Compliance Percent
#> 3 Treatment Compliance Percent
#> 4 Treatment Compliance Percent
#> 5 Treatment Compliance Percent
#> 6 Treatment Compliance Percent
#> 7 Treatment Compliance Percent
#> 8 Treatment Compliance Percent-
char_var: name of parameter
outdata$char_var
#> [1] "CMPLRNG" "CMPLPCT"-
char_prop: proportion of subject with treatment compliance
outdata$char_prop
#> [[1]]
#> name Placebo Low Dose High Dose Total
#> 1 >20% to <=40% 0.000000 0.000000 1.204819 0.3968254
#> 2 >80% 98.823529 98.809524 97.590361 98.4126984
#> 3 0% to <=20% 1.176471 1.190476 1.204819 1.1904762
#> var_label
#> 1 Treatment Compliance Range
#> 2 Treatment Compliance Range
#> 3 Treatment Compliance Range
#>
#> [[2]]
#> name Placebo Low Dose High Dose Total var_label
#> 1 Mean NA NA NA NA Treatment Compliance Percent
#> 2 SD NA NA NA NA Treatment Compliance Percent
#> 3 SE NA NA NA NA Treatment Compliance Percent
#> 4 Median NA NA NA NA Treatment Compliance Percent
#> 5 Min NA NA NA NA Treatment Compliance Percent
#> 6 Max NA NA NA NA Treatment Compliance Percent
#> 7 Q1 to Q3 NA NA NA NA Treatment Compliance Percent
#> 8 Range NA NA NA NA Treatment Compliance PercentFormat output
Once the raw analysis results are obtained, the
format_trt_compliance() function can be employed to prepare
the outdata,ensuring its compatibility with production-ready RTF
tables.
outdata <- outdata |> format_trt_compliance()Click to show the output
outdata$tbl
#> name n_1 p_1 n_2 p_2
#> 1 Participants in population 85 <NA> 84 <NA>
#> 2 >20% to <=40% 0 (0.0) 0 (0.0)
#> 3 >80% 84 (98.8) 83 (98.8)
#> 4 0% to <=20% 1 (1.2) 1 (1.2)
#> 5 Mean 99.0 <NA> 99.0 <NA>
#> 6 SD 9.4 <NA> 9.5 <NA>
#> 7 SE 1.0 <NA> 1.0 <NA>
#> 8 Median 100.0 <NA> 100.0 <NA>
#> 9 Q1 to Q3 100 to 100 <NA> 100 to 100 <NA>
#> 10 Range 12.93 to 100 <NA> 13.25 to 100 <NA>
#> n_3 p_3 n_9999 p_9999 var_label
#> 1 83 <NA> 252 <NA> -----
#> 2 1 (1.2) 1 (0.4) Treatment Compliance Range
#> 3 81 (97.6) 248 (98.4) Treatment Compliance Range
#> 4 1 (1.2) 3 (1.2) Treatment Compliance Range
#> 5 98.1 <NA> 98.7 <NA> Treatment Compliance Percent
#> 6 12.2 <NA> 10.4 <NA> Treatment Compliance Percent
#> 7 1.3 <NA> 0.7 <NA> Treatment Compliance Percent
#> 8 100.0 <NA> 100.0 <NA> Treatment Compliance Percent
#> 9 100 to 100 <NA> 100 to 100 <NA> Treatment Compliance Percent
#> 10 8.88 to 100 <NA> 8.88 to 100 <NA> Treatment Compliance PercentAdditional statistics
By using the display argument, we can choose specific
statistics to include.
tbl <- outdata |> format_trt_compliance(display_stat = c("mean", "sd", "median", "range"), display_col = c("n", "prop", "total"))Click to show the output
tbl$tbl
#> name n_1 p_1 n_2 p_2
#> 1 Participants in population 85 <NA> 84 <NA>
#> 2 >20% to <=40% 0 (0.0) 0 (0.0)
#> 3 >80% 84 (98.8) 83 (98.8)
#> 4 0% to <=20% 1 (1.2) 1 (1.2)
#> 5 Mean 99.0 <NA> 99.0 <NA>
#> 6 SD 9.4 <NA> 9.5 <NA>
#> 7 Median 100.0 <NA> 100.0 <NA>
#> 8 Range 12.93 to 100 <NA> 13.25 to 100 <NA>
#> n_3 p_3 n_9999 p_9999 var_label
#> 1 83 <NA> 252 <NA> -----
#> 2 1 (1.2) 1 (0.4) Treatment Compliance Range
#> 3 81 (97.6) 248 (98.4) Treatment Compliance Range
#> 4 1 (1.2) 3 (1.2) Treatment Compliance Range
#> 5 98.1 <NA> 98.7 <NA> Treatment Compliance Percent
#> 6 12.2 <NA> 10.4 <NA> Treatment Compliance Percent
#> 7 100.0 <NA> 100.0 <NA> Treatment Compliance Percent
#> 8 8.88 to 100 <NA> 8.88 to 100 <NA> Treatment Compliance PercentRTF tables
The last step is to prepare the RTF table using
rtf_trt_compliance.
outdata |>
format_trt_compliance() |>
rtf_trt_compliance(
"Source: [CDISCpilot: adam-adsl]",
path_outtable = "outtable/treatment0compliance.rtf"
)
#> The output is saved in/home/runner/work/metalite.sl/metalite.sl/vignettes/outtable/treatment0compliance.rtf