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rerun at 2022/02/01
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‎output/tlf-demographic.out

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@@ -36,5 +36,5 @@ MMSE Total
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------------------------------------------------------------------------------------------------
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Program: tlf_demographic.Rmd
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2022-01-19 01:08:16
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2022-02-01 17:21:29
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‎output/tlf-kmplot.pdf

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‎output/tlf-primary.rtf

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\par\ql
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{\f1\fs20\i [3] Pairwise comparison with treatment as a categorical variable: p-values without adjustment for multiple comparisons.}
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\par\ql\tx7245\tqr\tx12960
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{\f1\fs20\i Source: <run interactively>}\pmartabqr
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{\f1\fs20\i 21:47 Monday, January 31, 2022}\par
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{\f1\fs20\i }\pmartabqr
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{\f1\fs20\i 17:21 Tuesday, February 01, 2022}\par
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}
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{
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\trowd

‎vignettes/ectd/r0pkg.txt

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@@ -101,7 +101,7 @@ Package: pilot1wrappers
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File: NEWS.md
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Format: text
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Content:
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# pilot1wrappers 0.1.0
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# pilot1wrappers 0.1.1
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* Address reviewer comments for `tlf-efficacy.Rmd` and `tlf-primary`.
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* Change running R version to R4.1.2
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## FDA Response
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- Response to initial submission
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+ response letter <
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- Initial submission
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+ version: [v0.1.0](https://github.com/RConsortium/submissions-pilot1/releases/tag/v0.1.0)
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+ [FDA statistical review and evaluation](https://github.com/RConsortium/submissions-pilot1/blob/main/vignettes/fda/fda-response-2021-11-22.pdf)
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## Running Environment
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The project is developed and tested in the environment below:
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- [Marwick, B., Boettiger, C., & Mullen, L. (2018). Packaging data analytical work reproducibly using R (and friends). The American Statistician, 72(1), 80-88.](https://peerj.com/preprints/3192/)
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- [Wu, P., Palukuru, U. P., Luo, Y., Nepal, S., & Zhang, Y. (2021) Analysis and reporting in regulated clinical trial environment using R. PharmaSUG 2021](https://www.pharmasug.org/proceedings/2021/AD/PharmaSUG-2021-AD-079.pdf)
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More details related to organize a clinical project and submission package can be found in Chapter 9-14
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of the [R for Clinical Study Reports and Submission](https://r4csr.org/index.html) book.
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### R function and Analysis Scripts
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In short, the project is organized as an R package.
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#' @export
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#'
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efficacy_models <- function(data, var=NULL, wk=NULL) {
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# Need to set contrasts to work for Type III SS. See analysis results metadata for
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# table 14-3.01. Reference for R here: https://www.r-bloggers.com/anova-%E2%80%93-type-iiiiii-ss-explained/
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op <- options(contrasts = c("contr.sum","contr.poly"))

‎vignettes/ectd/tlf-demographic.r

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@@ -4,9 +4,9 @@
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# The path variable needs to be defined by using example code below
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#
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# path = list(adam = "path/to/esub/analysis/adam/datasets") # Modify path to the actual location
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# path$outtable = path$outgraph = "." # Output saved in current folder
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# path$output = "." # Output saved in current folder
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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# Working directory requires write permission
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if(file.access(".", 2) != 0){
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warning(
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}
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## ----setup, message=FALSE------------------------------------------------------------------
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## ----setup, message=FALSE------------------------------------------------------------------------------------------------------
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# CRAN package, please using install.packages() to install
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library(haven)
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library(dplyr)
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library(pilot1wrappers)
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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adsl <- read_xpt(file.path(path$adam, "adsl.xpt"))
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adsl_labels <- var_labels(adsl)
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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adsl <- adsl %>%
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dplyr::filter(
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STUDYID == "CDISCPILOT01",
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)
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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# Table layout
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vars <- c("AGE", "AGEGR1", "RACE", "HEIGHTBL", "WEIGHTBL", "BMIBL", "MMSETOT")
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lyt <- basic_table(title = "Protocol: CDISCPILOT01",
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tbl
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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# Output .out file
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tbl %>%
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toString() %>%

‎vignettes/ectd/tlf-efficacy.r

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# The path variable needs to be defined by using example code below
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#
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# path = list(adam = "path/to/esub/analysis/adam/datasets") # Modify path to the actual location
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# path$outtable = path$outgraph = "." # Output saved in current folder
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# path$output = "." # Output saved in current folder
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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# Working directory requires write permission
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if(file.access(".", 2) != 0){
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warning(
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}
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## ----setup, message=FALSE------------------------------------------------------------------
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## ----setup, message=FALSE------------------------------------------------------------------------------------------------------
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knitr::opts_chunk$set(echo = TRUE)
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# CRAN package, please using install.packages() to install
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library(pilot1wrappers)
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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adsl <- read_xpt(file.path(path$adam, "adsl.xpt"))
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adlb <- read_xpt(file.path(path$adam, "adlbc.xpt"))
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## ------------------------------------------------------------------------------------------
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adlb1 <- subset(adlb, TRTPN %in% c(0, 81) & PARAMCD == "GLUC" & !is.na(AVISITN)) %>%
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## ------------------------------------------------------------------------------------------------------------------------------
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itt <- adsl[adsl[["ITTFL"]] == "Y", c("STUDYID", "USUBJID")]
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adlb1 <- adlb %>%
42+
dplyr::right_join(itt, by = c("STUDYID", "USUBJID")) %>%
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subset(TRTPN %in% c(0, 81) & PARAMCD == "GLUC" & !is.na(AVISITN)) %>%
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mutate(TRTPN = ifelse(TRTPN == 0, 99, TRTPN)) # change treatment order for pairwise comparison
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## Fit data for linear model
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)
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t11 <- adlb1 %>%
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filter(AVISITN == 20) %>%
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filter(AVISITN == 20, !is.na(CHG), !is.na(BASE)) %>%
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group_by(TRTPN, TRTP) %>%
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summarise(
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N_20 = n(),
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merge(t12) %>%
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mutate(emmean_sd = SE * sqrt(df)) %>%
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mutate(
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Trt = c("Study Drug", "Placebo"),
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Trt = c("Xanomeline High Dose", "Placebo"),
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N1 = N,
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Mean1 = pilot1wrappers::fmt_est(mean_bl, sd_bl),
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N2 = N_20,
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apr0ancova1
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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t2 <- data.frame(pairs(t12))
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## Treatment Comparison
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upper = estimate + 1.96 * SE
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) %>%
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mutate(
99-
comp = "Study Drug vs. Placebo",
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comp = "Xanomeline High Dose vs. Placebo",
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mean = pilot1wrappers::fmt_ci(estimate, lower, upper),
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p = pilot1wrappers::fmt_pval(p.value)
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) %>%
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apr0ancova2
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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### Calculate root mean square and save data in output folder
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apr0ancova3 <- data.frame(rmse = paste0(
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"Root Mean Squared Error of Change = ",
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formatC(sd(gluc_lmfit$residuals), digits = 2, format = "f", flag = "0")
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formatC(sqrt(mean((gluc_lmfit$residuals)^2)), digits = 2, format = "f", flag = "0")
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))
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apr0ancova3
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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tbl_1 <- apr0ancova1 %>%
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rtf_title(
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title = "ANCOVA of Change from Baseline at Week 20"
122127
) %>%
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rtf_colheader(
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colheader = " | Baseline{^a} | Week 20 | Change from Baseline",
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col_rel_width = c(3, 4, 4, 9)
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col_rel_width = c(4, 3.5, 3.5, 7.5)
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) %>%
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rtf_colheader(
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colheader = "Treatment | N | Mean (SD) | N | Mean (SD) | N | Mean (SD) | LS Mean (95% CI){^b}",
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col_rel_width = c(3, 1, 3, 1, 3, 1, 3, 5)
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col_rel_width = c(4, 1, 2.5, 1, 2.5, 1, 2.5, 4)
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) %>%
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rtf_body(
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col_rel_width = c(3, 1, 3, 1, 3, 1, 3, 5),
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col_rel_width = c(4, 1, 2.5, 1, 2.5, 1, 2.5, 4),
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text_justification = c("l", rep("c", 7)),
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last_row = FALSE
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) %>%
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)
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) %>%
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rtf_source(
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source = "Source: [pilot1wrappers: adam-adlbc]",
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source = "Source: [pilot1wrappers: adam-adsl; adlbc]",
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text_justification = "c"
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)
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149-
## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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tbl_2 <- apr0ancova2 %>%
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rtf_colheader(
152157
colheader = "Pairwise Comparison | Difference in LS Mean (95% CI){^b} | p-Value",
153158
text_justification = c("l", "c", "c"),
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col_rel_width = c(8, 7, 5)
159+
col_rel_width = c(7.5, 7, 4)
155160
) %>%
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rtf_body(
157-
col_rel_width = c(8, 7, 5),
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col_rel_width = c(7.5, 7, 4),
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text_justification = c("l", "c", "c"),
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last_row = FALSE
160165
)
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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tbl_3 <- apr0ancova3 %>%
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rtf_body(
166171
as_colheader = FALSE,
167172
text_justification = "l"
168173
)
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171-
## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
172177
tbl <- list(tbl_1, tbl_2, tbl_3)
173178
tbl %>%
174179
rtf_encode() %>%
175180
write_rtf(file.path(path$output, "tlf-efficacy.rtf"))
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## ---- out.width = "100%", out.height = "400px", echo = FALSE, fig.align = "center"---------
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knitr::include_graphics("pdf/tlf-efficacy.pdf")
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‎vignettes/ectd/tlf-kmplot.r

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# The path variable needs to be defined by using example code below
55
#
66
# path = list(adam = "path/to/esub/analysis/adam/datasets") # Modify path to the actual location
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# path$outtable = path$outgraph = "." # Output saved in current folder
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# path$output = "." # Output saved in current folder
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## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
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# Working directory requires write permission
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if(file.access(".", 2) != 0){
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warning(
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## ----setup, message=FALSE------------------------------------------------------------------
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## ----setup, message=FALSE------------------------------------------------------------------------------------------------------
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knitr::opts_chunk$set(echo = TRUE)
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3130
library(pilot1wrappers)
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3332

34-
## ------------------------------------------------------------------------------------------
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## ------------------------------------------------------------------------------------------------------------------------------
3534
adsl <- read_xpt(file.path(path$adam, "adsl.xpt"))
3635
adtte <- read_xpt(file.path(path$adam, "adtte.xpt"))
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39-
## ------------------------------------------------------------------------------------------
38+
## ------------------------------------------------------------------------------------------------------------------------------
4039
anl <- adsl %>%
4140
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4241
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5655

57-
## ------------------------------------------------------------------------------------------
56+
## ------------------------------------------------------------------------------------------------------------------------------
5857
# estimate survival
5958
surv_mod <- visR::estimate_KM(data = anl, strata = "TRT01A")
6059

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101100

102101
print(KM)
103102
dev.off()
104-
105-
106-
## ---- out.width = "100%", out.height = "400px", echo = FALSE, fig.align = "center"---------
107-
knitr::include_graphics("pdf/tlf-kmplot.pdf")
108-

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