Merge pull request #110 from RConsortium/59_report-tlf

59 report tlf. closes #59

submission/output/tlf-demographic-pilot3.out

@@ -36,5 +36,5 @@ MMSE Total
 —————————————————————————————————————————————————————————————————————————————————————————————————
 
 Program: tlf_demographic.R 
-2023-08-11 17:14:16
+2023-08-17 18:25:20
 

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: 2023-08-11 17:24:01}\par}
+{\pard\hyphpar\sb15\sa15\fi0\li0\ri0\qc\fs18{\f0 Table generated on: 2023-08-17 18:22:20}\par}
 {\pard\hyphpar\sb15\sa15\fi0\li0\ri0\qc\fs18{\f0 Source: [pilot3: adam-adsl; adlbc]}\par}
 
 

submission/output/tlf-primary-pilot3.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 17:15 Friday, August 11, 2023}\par
+{\f1\fs20\i }\pmartabqr 
+{\f1\fs20\i 15:34 Thursday, August 17, 2023}\par
 }
 {
 \trowd

submission/programs/report-tlf-pilot3.Rmd

@@ -0,0 +1,73 @@
+---
+title: "R Consortium R Submission Pilot 3 - Summary Tables and Figures"
+author: "Pilot 3 Team"
+date: "`r Sys.Date()`"
+output: 
+  pdf_document:
+    latex_engine: pdflatex
+header-includes:
+- \usepackage{pdfpages}
+---
+
+Note : In Pilot 3, following the same approach as Pilot1, different open-source packages were used when generating each of the 4 analysis outputs to test wider use case scenarios. The outputs were formatted differently intentionally to cover different company specific formatting choices.
+
+\newpage
+
+```{r path, echo=FALSE}
+path <- list(
+  sdtm = "./submission/sdtm",   # Modify path to the sdtm location
+  adam = "./submission/adam",    # Modify path to the adam location
+  output = "./submission/output"    # Modify path to the output location
+)
+```
+
+#### Table 14-2.01
+#### Summary of Demographic and Baseline Characteristics
+
+```{r demog, out.width = "40%", out.height = "400px", echo=FALSE, message=FALSE, comment=NA}
+setwd("/cloud/project") 
+source("/cloud/project/submission/programs/tlf-demographic.r")
+print(tbl)
+```
+
+\newpage
+
+#### Table 14-3.01
+#### Primary Endpoint Analysis: ADAS Cog (11) - Change from Baseline to Week 24 - LOCF
+
+```{r primary, echo=FALSE, message=FALSE, comment=NA}
+# setwd("/cloud/project")
+# source("/cloud/project/submission/programs/tlf-primary.r")
+```
+
+\hfill\break\hfill\break\hfill\break\includegraphics[page=1]{/cloud/project/submission/output/tlf-primary-pilot3.rtf.pdf}
+\
+\
+\hfill\break\hfill\break\hfill\break\includegraphics[page=2]{/cloud/project/submission/output/tlf-primary-pilot3.rtf.pdf}
+
+\newpage
+
+#### Table 14-3.02
+#### Primary Endpoint Analysis: Glucose (mmol/L) - Summary at Week 20 - LOCF
+
+```{r efficacy, echo=FALSE, message=FALSE, comment=NA}
+# setwd("/cloud/project")
+# source("/cloud/project/submission/programs/tlf-efficacy.r")
+# print(tbl)
+```
+
+\includegraphics[page=1]{/cloud/project/submission/output/tlf-efficacy-pilot3.rtf.pdf}
+
+\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")
+print(km)
+```
+
+

submission/programs/tlf-demographic.r

@@ -52,7 +52,7 @@ vars <- c("AGE", "AGEGR1", "RACE", "HEIGHTBL", "WEIGHTBL", "BMIBL", "MMSETOT")
 lyt <- basic_table(
   title = "Protocol: CDISCPILOT01",
   subtitles = "Population: Intent-to-Treat",
-  main_footer = paste0("Program: tlf_demographic.R \n", Sys.time())
+  main_footer = paste0("Program: tlf-demographic.r \n", Sys.time())
 ) %>%
   split_cols_by("TRT01P") %>%
   add_colcounts() %>%

submission/programs/tlf-kmplot.r

@@ -78,7 +78,7 @@ km <- km +
   ggplot2::geom_hline(yintercept = 0.5, linetype = "dashed")
 
 km <- km %>%
-  visR::add_risktable(group = "statlist")
+  visR::add_risktable(group = "statlist", rowgutter = 0.25)
 
 title <- cowplot::ggdraw() +
   cowplot::draw_label(
@@ -90,7 +90,7 @@ title <- cowplot::ggdraw() +
 
 caption <- cowplot::ggdraw() +
   cowplot::draw_label(
-    paste0("\nProgram: tlf_kmplot.R [", Sys.time(), "]"),
+    paste0("\nProgram: tlf-kmplot.r [", Sys.time(), "]"),
     fontfamily = "sans",
     size = 10
   )

vignettes/adrg.Rmd

@@ -9,4 +9,4 @@ output:
 ---
 
 
-![Cover Letter](pdf/adrg.pdf){width=700px height=1100px}
+![Cover Letter](pdf/adrg.pdf){width=700px height=1100px}

vignettes/cover-letter.Rmd

@@ -9,4 +9,4 @@ output:
 ---
 
 
-![Cover Letter](pdf/cover-letter.pdf){width=700px height=1100px}
+![Cover Letter](pdf/cover-letter.pdf){width=700px height=1100px}

vignettes/tlf-efficacy.Rmd

@@ -183,9 +183,6 @@ tbl_3 <- apr0ancova3 %>%
 
 ```{r, message = FALSE, echo = FALSE}
 tbl <- list(tbl_1, tbl_2, tbl_3)
-# tbl %>%
-#  rtf_encode() %>%
-#  write_rtf(file.path(path$output, "tlf-efficacy.rtf"))
 ```
 
 ```{r, out.width = "100%", out.height = "400px", echo = FALSE, fig.align = "center"}

vignettes/tlf-kmplot.Rmd

@@ -73,8 +73,6 @@ ggplot2::theme_set(theme_bw())
 
 pdf.options(reset = TRUE, onefile = FALSE)
 
-# pdf(file.path(path$output, "tlf-kmplot.pdf"))
-
 km <- visR::visr(surv_mod,
   y_label = "Probability of event\n",
   x_label = "Time to First Dermatologic Event (Days)",

vignettes/tlf-primary.Rmd

@@ -167,7 +167,6 @@ doc <- rtf_doc(ht) %>%
   )
 
 # Write out the RTF
-# write_rtf(doc, file = file.path(path$output, "tlf-primary.rtf"))
 ```
 
 ```{r, out.width = "100%", out.height = "400px", echo = FALSE, fig.align = "center"}