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Tidying tlf-demographic.Rmd removing {pilot1wrappers} package dependency. #178

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merged 5 commits into from
Apr 18, 2024
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Tidying tlf-demographic.Rmd removing {pilot1wrappers} package dependency. #178

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524d38b
Tidying tlf-demographic.Rmd removing {pilot1wrappers} package depende…
Apr 12, 2024
0386a43
Tidying vignettes removing {pilot1wrappers} package dependency and up…
Apr 12, 2024
1b3251b
Merge branch 'main' into 177-refresh-report-tlfpdf
Apr 12, 2024
4c01bc0
Tidying vignettes removing {pilot1wrappers} package dependency and up…
Apr 12, 2024
8b018ad
updated outputs with todays timestamp and combined pdf now generated …
laxamanaj Apr 17, 2024
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10 changes: 5 additions & 5 deletions vignettes/tlf-demographic.Rmd
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Original file line number Diff line number Diff line change
@@ -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.
Expand All @@ -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)
```


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15 changes: 6 additions & 9 deletions vignettes/tlf-efficacy.Rmd
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Expand Up @@ -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}
Expand Down Expand Up @@ -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)

Expand All @@ -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)

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