The exposure duration analysis aims to provide table to summarize by each identified duration category. The development of exposure duration analysis involves functions:
meta_sl_exposure_example: build the metadata
(meta object) for analysis.prepare_exp_duration: prepare analysis raw
datasets.format_exp_duration: prepare analysis outdata with
proper format.rtf_exp_duration: transfer (mock) output dataset to RTF
table.There are two steps in meta_sl_exposure_example function
in order to build the metadata (meta object): processing
the ADaM dataset and save meta information for A&R reporting.
Step1: ADEXSUM, the ADaM dataset for Drug Exposrue Summary Data, is utilized to:
upcase(trim(left(paramcd))) = "TRTDUR".adexsum$AVAL for all
participants.adexsum$EXDURGR i.e.”>=1
day”, “>=7 days”,“>=28 days”, “>=12 weeks” and “>=24
weeks”.adsl <- r2rtf::r2rtf_adsl
adexsum <- data.frame(USUBJID = adsl$USUBJID)
adexsum$TRTA <- factor(adsl$TRT01A,
levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"),
labels = c("Placebo", "Low Dose", "High Dose")
)
adexsum$APERIODC <- "Base"
adexsum$APERIOD <- 1
set.seed(123) # Set a seed for reproducibility
adexsum$AVAL <- sample(x = 0:(24 * 7), size = length(adexsum$USUBJID), replace = TRUE)
adexsum$EXDURGR <- "not treated"
adexsum$EXDURGR[adexsum$AVAL >= 1] <- ">=1 day"
adexsum$EXDURGR[adexsum$AVAL >= 7] <- ">=7 days"
adexsum$EXDURGR[adexsum$AVAL >= 28] <- ">=28 days"
adexsum$EXDURGR[adexsum$AVAL >= 12 * 7] <- ">=12 weeks"
adexsum$EXDURGR[adexsum$AVAL >= 24 * 7] <- ">=24 weeks"
adexsum$EXDURGR <- factor(adexsum$EXDURGR,
levels = c("not treated", ">=1 day", ">=7 days", ">=28 days", ">=12 weeks", ">=24 weeks")
)
unique(adexsum$EXDURGR)## [1] >=12 weeks >=7 days >=28 days >=1 day >=24 weeks not treated
## Levels: not treated >=1 day >=7 days >=28 days >=12 weeks >=24 weeksStep2: Save analysis plan and metadata(parameter and analysis) information, then build meta object.
plan <- metalite::plan(
analysis = "exp_dur", population = "apat",
observation = "apat", parameter = "expdur"
)
meta <- metalite::meta_adam(
population = adexsum,
observation = adexsum
) |>
metalite::define_plan(plan) |>
metalite::define_population(
name = "apat",
group = "TRTA",
subset = quote(APERIOD == 1 & AVAL > 0)
) |>
metalite::define_parameter(
name = "expdur",
var = "AVAL",
label = "Exposure Duration (Days)",
vargroup = "EXDURGR"
) |>
metalite::define_analysis(
name = "exp_dur",
title = "Summary of Exposure Duration",
label = "exposure duration table"
) |>
metalite::meta_build()The input of the function prepare_exp_duration() is a
meta object created by the metalite package. The resulting
output comprises a collection of raw datasets for analysis and
reporting.
## List of 14
## $ meta :List of 7
## $ population : chr "apat"
## $ observation : chr "apat"
## $ parameter : chr "expdur"
## $ n :'data.frame': 1 obs. of 6 variables:
## $ order : NULL
## $ group : chr "TRTA"
## $ reference_group: NULL
## $ char_n :List of 1
## $ char_var : chr "AVAL"
## $ char_prop :List of 1
## $ var_type :List of 1
## $ group_label : Factor w/ 3 levels "Placebo","Low Dose",..: 1 3 2
## $ analysis : chr "exp_dur"Number of participants in population
## name n_1 n_2 n_3 n_9999
## 1 Participants in population 86 83 84 253Number of participants in each duration category
## name Placebo Low.Dose High.Dose Total
## 1 not treated 0 0 0 0
## 2 >=1 day 2 4 3 9
## 3 >=7 days 13 11 9 33
## 4 >=28 days 31 20 27 78
## 5 >=12 weeks 39 48 45 132
## 6 >=24 weeks 1 0 0 1Proportion of participants in each duration category
## name Placebo Low.Dose High.Dose Total
## 1 not treated 0.000000 0.000000 0.000000 0.0000000
## 2 >=1 day 2.325581 4.819277 3.571429 3.5573123
## 3 >=7 days 15.116279 13.253012 10.714286 13.0434783
## 4 >=28 days 36.046512 24.096386 32.142857 30.8300395
## 5 >=12 weeks 45.348837 57.831325 53.571429 52.1739130
## 6 >=24 weeks 1.162791 0.000000 0.000000 0.3952569Statistical summary of exposure duration for each treatment
## name Placebo Low.Dose High.Dose Total
## 8 Mean 81.5 90.8 87.6 86.6
## 9 SD 49.1 51.3 48.8 49.7
## 10 SE 5.3 5.6 5.3 3.1
## 11 Median 76.0 93.0 90.0 88.0
## 12 Min 3.0 1.0 4.0 1.0
## 13 Max 168.0 167.0 167.0 168.0
## 14 Q1 to Q3 41.25 to 123.25 48 to 137.5 44.75 to 129.25 44 to 133
## 15 Range 3 to 168 1 to 167 4 to 167 1 to 168format_exp_duration to prepare analysis dataset before
generate RTF output
## name n_1 p_1 n_2 p_2 n_3 p_3 n_9999 p_9999
## 1 Participants in population 86 <NA> 83 <NA> 84 <NA> 253 <NA>
## 2 not treated 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0)
## 3 >=1 day 2 (2.3) 4 (4.8) 3 (3.6) 9 (3.6)
## 4 >=7 days 13 (15.1) 11 (13.3) 9 (10.7) 33 (13.0)
## 5 >=28 days 31 (36.0) 20 (24.1) 27 (32.1) 78 (30.8)
## 6 >=12 weeks 39 (45.3) 48 (57.8) 45 (53.6) 132 (52.2)
## var_label
## 1 -----
## 2 Exposure Duration (Days)
## 3 Exposure Duration (Days)
## 4 Exposure Duration (Days)
## 5 Exposure Duration (Days)
## 6 Exposure Duration (Days)rtf_exp_duration to generate RTF output
outdata <- format_exp_duration(outdata, display_col = c("n", "prop", "total")) |>
rtf_exp_duration(
source = "Source: [CDISCpilot: adam-adexsum]",
path_outdata = tempfile(fileext = ".Rdata"),
path_outtable = "outtable/exp0duration.rtf"
)## The outdata is saved in/rtmp/RtmpkBEdeP/file3606c11b807918.Rdata## The output is saved in/rtmp/Rtmp7YMja5/Rbuild3605e43666ac3c/metalite.sl/vignettes/outtable/exp0duration.rtf