diff --git a/submission/output/tlf-demographic-pilot3.out b/submission/output/tlf-demographic-pilot3.out index ed20472..5085975 100644 --- 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 index 6762efd..6e2fd09 100644 --- 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 index 2f01e99..b5ba59c 100644 Binary files a/submission/output/tlf-efficacy-pilot3.rtf.pdf and b/submission/output/tlf-efficacy-pilot3.rtf.pdf differ diff --git a/submission/output/tlf-kmplot-pilot3.pdf b/submission/output/tlf-kmplot-pilot3.pdf index 3ad60ac..a97a5ae 100644 Binary files a/submission/output/tlf-kmplot-pilot3.pdf and b/submission/output/tlf-kmplot-pilot3.pdf differ diff --git a/submission/output/tlf-primary-pilot3.rtf b/submission/output/tlf-primary-pilot3.rtf index 32e5552..6ffd715 100644 --- 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: }\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 index 832f0c3..995dcb3 100644 Binary files a/submission/output/tlf-primary-pilot3.rtf.pdf and b/submission/output/tlf-primary-pilot3.rtf.pdf differ diff --git a/submission/programs/report-tlf-pilot3.Rmd b/submission/programs/report-tlf-pilot3.Rmd index 0dc0849..de52c35 100644 --- 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 index a446c8b..6fc2d1c 100644 Binary files a/submission/programs/report-tlf-pilot3.pdf and b/submission/programs/report-tlf-pilot3.pdf differ diff --git a/vignettes/tlf-demographic.Rmd b/vignettes/tlf-demographic.Rmd index aad7d47..ba4baf9 100644 --- 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 index 5e80934..bc02335 100644 --- 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 index 3860c07..7b81c31 100644 --- 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 index cb6b2f2..5eb1234 100644 --- 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,