Merge pull request #178 from RConsortium/177-refresh-report-tlfpdf

Tidying tlf-demographic.Rmd removing {pilot1wrappers} package dependency. Close #177 . Thanks for the check @robertdevine . As for the sig digits. We did have it this way in our initial Pilot 3 submission and I don't believe they commented on this in our feedback. So I'm ok to leave as-is.
RConsortium · Apr 18, 2024 · 6ce6012 · 6ce6012
2 parents 605ace5 + 8b018ad
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diff --git a/submission/output/tlf-demographic-pilot3.out b/submission/output/tlf-demographic-pilot3.out
@@ -36,5 +36,5 @@ MMSE Total
 —————————————————————————————————————————————————————————————————————————————————————————————————
 
 Program: tlf-demographic.r 
-2024-04-12 18:40:11
+2024-04-17 20:01:23
 
diff --git a/submission/output/tlf-efficacy-pilot3.rtf b/submission/output/tlf-efficacy-pilot3.rtf
@@ -127,7 +127,7 @@
 \clbrdrl\brdrs\brdrw15\clbrdrt\brdrs\brdrw15\clbrdrr\brdrs\brdrw15\clbrdrb\brdrdb\brdrw15\clvertalt\cellx9000
 \pard\hyphpar0\sb15\sa15\fi0\li0\ri0\ql\fs18{\f0 Root Mean Squared Error of Change = 1.30}\cell
 \intbl\row\pard
-{\pard\hyphpar\sb15\sa15\fi0\li0\ri0\qc\fs18{\f0 Table generated on: 2024-04-12 18:40:28}\par}
+{\pard\hyphpar\sb15\sa15\fi0\li0\ri0\qc\fs18{\f0 Table generated on: 2024-04-17 20:01:10}\par}
 {\pard\hyphpar\sb15\sa15\fi0\li0\ri0\qc\fs18{\f0 Source: [pilot3: adam-adsl; adlbc]}\par}
 
 

diff --git a/submission/output/tlf-efficacy-pilot3.rtf.pdf b/submission/output/tlf-efficacy-pilot3.rtf.pdf
diff --git a/submission/output/tlf-kmplot-pilot3.pdf b/submission/output/tlf-kmplot-pilot3.pdf
diff --git a/submission/output/tlf-primary-pilot3.rtf b/submission/output/tlf-primary-pilot3.rtf
@@ -59,7 +59,7 @@
 {\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 18:40 Friday, April 12, 2024}\par
+{\f1\fs20\i 20:01 Wednesday, April 17, 2024}\par
 }
 {
 \trowd

diff --git a/submission/output/tlf-primary-pilot3.rtf.pdf b/submission/output/tlf-primary-pilot3.rtf.pdf
diff --git a/submission/programs/report-tlf-pilot3.Rmd b/submission/programs/report-tlf-pilot3.Rmd
@@ -30,10 +30,11 @@ source("/cloud/project/submission/programs/tlf-demographic.r")
 print(tbl)
 ```
 
+\newpage
+
 #### Figure 14-1
 #### Time to Dermatologic Event by Treatment Group
-\
-\
+
 ```{r plot, echo=FALSE, message=FALSE, comment=NA, fig.align="center",out.width="100%"}
 setwd("/cloud/project")
 source("/cloud/project/submission/programs/tlf-kmplot.r")

diff --git a/submission/programs/report-tlf-pilot3.pdf b/submission/programs/report-tlf-pilot3.pdf
diff --git a/vignettes/tlf-demographic.Rmd b/vignettes/tlf-demographic.Rmd
@@ -1,11 +1,14 @@
 ---
-title: "CDISC Pilot: Summary of Demographic and Baseline Characteristics"
+title: 'CDISC Pilot: Summary of Demographic and Baseline Characteristics'
 output:
+  pdf_document:
+    toc: yes
+    toc_depth: '2'
   html_document:
     df_print: paged
     toc: yes
     toc_depth: '2'
-    toc_float: true
+    toc_float: yes
 ---
 
 The Pilot 1 Team generated the below output using R and it was delivered to the FDA. You can find the source code that generated this output [here](https://github.com/RConsortium/submissions-pilot1/blob/main/vignettes/tlf-demographic.Rmd) and a deeper dive of the process [here](https://rconsortium.github.io/submissions-pilot1/articles/tlf-demographic.html).  We delivered the identical output with the R generated ADaM.
@@ -30,9 +33,6 @@ if (file.access(".", 2) != 0) {
 library(haven)
 library(dplyr)
 library(rtables)
-
-# Propitiatory Package, please refer appendix of ADRG to install
-library(pilot1wrappers)
 ```
 
 

diff --git a/vignettes/tlf-efficacy.Rmd b/vignettes/tlf-efficacy.Rmd
@@ -33,9 +33,6 @@ library(dplyr)
 library(haven)
 library(r2rtf)
 library(emmeans)
-
-# Propitiatory Package, please refer appendix of ADRG to install
-library(pilot1wrappers)
 ```
 
 ```{r, message = FALSE, echo = FALSE}
@@ -87,12 +84,12 @@ apr0ancova1 <- merge(t10, t11) %>%
   mutate(
     Trt = c("Xanomeline High Dose", "Placebo"),
     N1 = N,
-    Mean1 = pilot1wrappers::fmt_est(mean_bl, sd_bl),
+    Mean1 = pilot3utils::fmt_est(mean_bl, sd_bl),
     N2 = N_20,
-    Mean2 = pilot1wrappers::fmt_est(mean, sd),
+    Mean2 = pilot3utils::fmt_est(mean, sd),
     N3 = N_20,
-    Mean3 = pilot1wrappers::fmt_est(mean_chg, sd_chg),
-    CI = pilot1wrappers::fmt_ci(emmean, lower.CL, upper.CL)
+    Mean3 = pilot3utils::fmt_est(mean_chg, sd_chg),
+    CI = pilot3utils::fmt_ci(emmean, lower.CL, upper.CL)
   ) %>%
   select(Trt:CI)
 
@@ -110,8 +107,8 @@ apr0ancova2 <- t2 %>%
   ) %>%
   mutate(
     comp = "Xanomeline High Dose vs. Placebo",
-    mean = pilot1wrappers::fmt_ci(estimate, lower, upper),
-    p = pilot1wrappers::fmt_pval(p.value)
+    mean = pilot3utils::fmt_ci(estimate, lower, upper),
+    p = pilot3utils::fmt_pval(p.value)
   ) %>%
   select(comp:p)
 

diff --git a/vignettes/tlf-kmplot.Rmd b/vignettes/tlf-kmplot.Rmd
@@ -35,9 +35,6 @@ library(dplyr)
 library(ggplot2)
 library(cowplot)
 library(visR)
-
-# Propitiatory Package, please refer appendix of ADRG to install
-library(pilot1wrappers)
 ```
 
 

diff --git a/vignettes/tlf-primary.Rmd b/vignettes/tlf-primary.Rmd
@@ -30,9 +30,6 @@ library(tidyr)
 library(dplyr)
 library(Tplyr)
 library(pharmaRTF)
-
-# Propitiatory Package, please refer appendix of ADRG to install
-library(pilot1wrappers)
 ```
 
 ```{r, echo = FALSE, message = FALSE}
@@ -86,7 +83,7 @@ hdr_fin <- stringr::str_replace_all(hdr_fin, "\\|Xanomeline ", "|Xanomeline\\\\l
 
 sum_data <- t %>%
   build() %>%
-  nest_rowlabels() %>%
+  pilot3utils::nest_rowlabels() %>%
   select(row_label, var1_Placebo, `var1_Xanomeline Low Dose`, `var1_Xanomeline High Dose`) %>%
   add_column_headers(
     hdr_fin,