rerun at 2022/02/01

RConsortium · Feb 1, 2022 · 694a207 · 694a207
1 parent a46e694
commit 694a207
Show file tree

Hide file tree

Showing 10 changed files with 74 additions and 71 deletions.
diff --git a/output/tlf-demographic.out b/output/tlf-demographic.out
@@ -36,5 +36,5 @@ MMSE Total
 ------------------------------------------------------------------------------------------------
 
 Program: tlf_demographic.Rmd 
-2022-01-19 01:08:16
+2022-02-01 17:21:29
 
diff --git a/output/tlf-kmplot.pdf b/output/tlf-kmplot.pdf
diff --git a/output/tlf-primary.rtf b/output/tlf-primary.rtf
@@ -58,8 +58,8 @@
 \par\ql
 {\f1\fs20\i [3] Pairwise comparison with treatment as a categorical variable: p-values without adjustment for multiple comparisons.}
 \par\ql\tx7245\tqr\tx12960
-{\f1\fs20\i Source: <run interactively>}\pmartabqr 
-{\f1\fs20\i 21:47 Monday, January 31, 2022}\par
+{\f1\fs20\i }\pmartabqr 
+{\f1\fs20\i 17:21 Tuesday, February 01, 2022}\par
 }
 {
 \trowd

diff --git a/vignettes/ectd/r0pkg.txt b/vignettes/ectd/r0pkg.txt
@@ -101,7 +101,7 @@ Package: pilot1wrappers
 File: NEWS.md
 Format: text
 Content:
-  # pilot1wrappers 0.1.0
+  # pilot1wrappers 0.1.1
 
   * Address reviewer comments for `tlf-efficacy.Rmd` and `tlf-primary`.
   * Change running R version to R4.1.2
@@ -141,8 +141,10 @@ Content:
 
   ## FDA Response 
 
-  - Response to initial submission
-    + response letter <
+  - Initial submission
+    + version: [v0.1.0](https://github.com/RConsortium/submissions-pilot1/releases/tag/v0.1.0) 
+    + [FDA statistical review and evaluation](https://github.com/RConsortium/submissions-pilot1/blob/main/vignettes/fda/fda-response-2021-11-22.pdf)
+
   ## Running Environment 
 
   The project is developed and tested in the environment below:
@@ -159,6 +161,9 @@ Content:
   - [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/)
   - [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)
 
+  More details related to organize a clinical project and submission package can be found in Chapter 9-14
+  of the  [R for Clinical Study Reports and Submission](https://r4csr.org/index.html) book.
+
   ### R function and Analysis Scripts 
 
   In short, the project is organized as an R package. 
@@ -214,8 +219,7 @@ Content:
   #' @export
   #'
   efficacy_models <- function(data, var=NULL, wk=NULL) {
-
-
+
     # Need to set contrasts to work for Type III SS. See analysis results metadata for
     # table 14-3.01. Reference for R here: https://www.r-bloggers.com/anova-%E2%80%93-type-iiiiii-ss-explained/
     op <- options(contrasts = c("contr.sum","contr.poly"))

diff --git a/vignettes/ectd/tlf-demographic.r b/vignettes/ectd/tlf-demographic.r
@@ -4,9 +4,9 @@
 # The path variable needs to be defined by using example code below
 #
 # path = list(adam = "path/to/esub/analysis/adam/datasets")    	# Modify path to the actual location
-# path$outtable = path$outgraph = "."                           # Output saved in current folder
+# path$output = "."                                             # Output saved in current folder
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 # Working directory requires write permission
 if(file.access(".", 2) != 0){
   warning(
@@ -16,7 +16,7 @@ if(file.access(".", 2) != 0){
 }
 
 
-## ----setup, message=FALSE------------------------------------------------------------------
+## ----setup, message=FALSE------------------------------------------------------------------------------------------------------
 # CRAN package, please using install.packages() to install
 library(haven) 
 library(dplyr)
@@ -26,12 +26,12 @@ library(rtables)
 library(pilot1wrappers)
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 adsl  <- read_xpt(file.path(path$adam, "adsl.xpt")) 
 adsl_labels <- var_labels(adsl)
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 adsl <- adsl %>%
   dplyr::filter(
     STUDYID == "CDISCPILOT01",
@@ -44,7 +44,7 @@ adsl <- adsl %>%
   ) 
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 # Table layout
 vars <- c("AGE", "AGEGR1", "RACE", "HEIGHTBL", "WEIGHTBL", "BMIBL", "MMSETOT")
 lyt <- basic_table(title = "Protocol: CDISCPILOT01",
@@ -75,7 +75,7 @@ tbl <- build_table(lyt, adsl)
 tbl
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 # Output .out file 
 tbl %>%
   toString() %>%

diff --git a/vignettes/ectd/tlf-efficacy.r b/vignettes/ectd/tlf-efficacy.r
@@ -4,10 +4,9 @@
 # The path variable needs to be defined by using example code below
 #
 # path = list(adam = "path/to/esub/analysis/adam/datasets")    	# Modify path to the actual location
-# path$outtable = path$outgraph = "."                           # Output saved in current folder
+# path$output = "."                                             # Output saved in current folder
 
-
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 # Working directory requires write permission
 if(file.access(".", 2) != 0){
   warning(
@@ -17,7 +16,7 @@ if(file.access(".", 2) != 0){
 }
 
 
-## ----setup, message=FALSE------------------------------------------------------------------
+## ----setup, message=FALSE------------------------------------------------------------------------------------------------------
 knitr::opts_chunk$set(echo = TRUE)
 
 # CRAN package, please using install.packages() to install
@@ -30,12 +29,18 @@ library(emmeans)
 library(pilot1wrappers)
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
+adsl <- read_xpt(file.path(path$adam, "adsl.xpt"))
 adlb <- read_xpt(file.path(path$adam, "adlbc.xpt"))
 
 
-## ------------------------------------------------------------------------------------------
-adlb1 <- subset(adlb, TRTPN %in% c(0, 81) & PARAMCD == "GLUC" & !is.na(AVISITN)) %>%
+## ------------------------------------------------------------------------------------------------------------------------------
+
+itt <- adsl[adsl[["ITTFL"]] == "Y", c("STUDYID", "USUBJID")]
+
+adlb1 <- adlb %>%
+  dplyr::right_join(itt, by = c("STUDYID", "USUBJID")) %>%
+  subset(TRTPN %in% c(0, 81) & PARAMCD == "GLUC" & !is.na(AVISITN)) %>%
   mutate(TRTPN = ifelse(TRTPN == 0, 99, TRTPN)) # change treatment order for pairwise comparison
 
 ## Fit data for linear model
@@ -54,7 +59,7 @@ t10 <- adlb1 %>%
   )
 
 t11 <- adlb1 %>%
-  filter(AVISITN == 20) %>%
+  filter(AVISITN == 20, !is.na(CHG), !is.na(BASE)) %>%
   group_by(TRTPN, TRTP) %>%
   summarise(
     N_20 = n(),
@@ -72,7 +77,7 @@ apr0ancova1 <- merge(t10, t11)  %>%
   merge(t12) %>% 
   mutate(emmean_sd = SE * sqrt(df)) %>%
   mutate(
-    Trt = c("Study Drug", "Placebo"),
+    Trt = c("Xanomeline High Dose", "Placebo"),
     N1 = N,
     Mean1 = pilot1wrappers::fmt_est(mean_bl, sd_bl),
     N2 = N_20,
@@ -86,7 +91,7 @@ apr0ancova1 <- merge(t10, t11)  %>%
 apr0ancova1
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 t2 <- data.frame(pairs(t12))
 
 ## Treatment Comparison
@@ -96,7 +101,7 @@ apr0ancova2 <- t2 %>%
     upper = estimate + 1.96 * SE
   ) %>%
   mutate(
-    comp = "Study Drug vs. Placebo",
+    comp = "Xanomeline High Dose vs. Placebo",
     mean = pilot1wrappers::fmt_ci(estimate, lower, upper),
     p = pilot1wrappers::fmt_pval(p.value)
   ) %>%
@@ -105,31 +110,31 @@ apr0ancova2 <- t2 %>%
 apr0ancova2
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 ### Calculate root mean square and save data in output folder
 apr0ancova3 <- data.frame(rmse = paste0(
   "Root Mean Squared Error of Change = ",
-  formatC(sd(gluc_lmfit$residuals), digits = 2, format = "f", flag = "0")
+  formatC(sqrt(mean((gluc_lmfit$residuals)^2)), digits = 2, format = "f", flag = "0")
 ))
 
 apr0ancova3
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 tbl_1 <- apr0ancova1 %>%
   rtf_title(
     title = "ANCOVA of Change from Baseline at Week 20"
   ) %>%
   rtf_colheader(
     colheader = " | Baseline{^a} | Week 20 | Change from Baseline",
-    col_rel_width = c(3, 4, 4, 9)
+    col_rel_width = c(4, 3.5, 3.5, 7.5)
   ) %>%
   rtf_colheader(
     colheader = "Treatment | N | Mean (SD) | N | Mean (SD) | N | Mean (SD) | LS Mean (95% CI){^b}",
-    col_rel_width = c(3, 1, 3, 1, 3, 1, 3, 5)
+    col_rel_width = c(4, 1, 2.5, 1, 2.5, 1, 2.5, 4)
   ) %>%
   rtf_body(
-    col_rel_width = c(3, 1, 3, 1, 3, 1, 3, 5),
+    col_rel_width = c(4, 1, 2.5, 1, 2.5, 1, 2.5, 4),
     text_justification = c("l", rep("c", 7)),
     last_row = FALSE
   ) %>%
@@ -141,40 +146,37 @@ tbl_1 <- apr0ancova1 %>%
     )
   ) %>%
   rtf_source(
-    source = "Source: [pilot1wrappers: adam-adlbc]",
+    source = "Source: [pilot1wrappers: adam-adsl; adlbc]",
     text_justification = "c"
   )
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 tbl_2 <- apr0ancova2 %>%
   rtf_colheader(
     colheader = "Pairwise Comparison | Difference in LS Mean (95% CI){^b} | p-Value",
     text_justification = c("l", "c", "c"),
-    col_rel_width = c(8, 7, 5)
+    col_rel_width = c(7.5, 7, 4)
   ) %>%
   rtf_body(
-    col_rel_width = c(8, 7, 5),
+    col_rel_width = c(7.5, 7, 4),
     text_justification = c("l", "c", "c"),
     last_row = FALSE
   )
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 tbl_3 <- apr0ancova3 %>%
   rtf_body(
     as_colheader = FALSE,
     text_justification = "l"
   )
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 tbl <- list(tbl_1, tbl_2, tbl_3)
 tbl %>%
   rtf_encode() %>%
   write_rtf(file.path(path$output, "tlf-efficacy.rtf"))
 
 
-## ---- out.width = "100%", out.height = "400px", echo = FALSE, fig.align = "center"---------
-knitr::include_graphics("pdf/tlf-efficacy.pdf")
-
diff --git a/vignettes/ectd/tlf-kmplot.r b/vignettes/ectd/tlf-kmplot.r
@@ -4,10 +4,9 @@
 # The path variable needs to be defined by using example code below
 #
 # path = list(adam = "path/to/esub/analysis/adam/datasets")    	# Modify path to the actual location
-# path$outtable = path$outgraph = "."                           # Output saved in current folder
+# path$output = "."                                             # Output saved in current folder
 
-
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 # Working directory requires write permission
 if(file.access(".", 2) != 0){
   warning(
@@ -17,7 +16,7 @@ if(file.access(".", 2) != 0){
 }
 
 
-## ----setup, message=FALSE------------------------------------------------------------------
+## ----setup, message=FALSE------------------------------------------------------------------------------------------------------
 knitr::opts_chunk$set(echo = TRUE)
 
 # CRAN package, please using install.packages() to install
@@ -31,12 +30,12 @@ library(visR)
 library(pilot1wrappers)
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 adsl <- read_xpt(file.path(path$adam, "adsl.xpt"))
 adtte <- read_xpt(file.path(path$adam, "adtte.xpt")) 
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 anl <- adsl %>% 
   dplyr::filter(
     SAFFL == "Y",
@@ -54,7 +53,7 @@ anl <- adsl %>%
   )
 
 
-## ------------------------------------------------------------------------------------------
+## ------------------------------------------------------------------------------------------------------------------------------
 # estimate survival
 surv_mod <- visR::estimate_KM(data = anl, strata = "TRT01A")
 
@@ -101,8 +100,3 @@ KM <- cowplot::plot_grid(
 
 print(KM)
 dev.off()
-
-
-## ---- out.width = "100%", out.height = "400px", echo = FALSE, fig.align = "center"---------
-knitr::include_graphics("pdf/tlf-kmplot.pdf")
-