14 Appendix: Tips, Profiles, .libPaths

14.1 Useful Profiles

Create ~/.Rprofile to set options (be careful on shared systems):

options(
  repos = c(CRAN = "https://cloud.r-project.org"),
  scipen = 999
)

14.2 Custom Library Paths

# In .Rprofile or project-level .Rprofile
.libPaths(c("/path/to/Rlibs", .libPaths()))

14.3 Format vs formatC (quick recap)

x <- c(123.456, 0.00123456)
format(x, digits = 4)

[1] "1.235e+02" "1.235e-03"

format(x, nsmall = 2)

[1] "1.23456e+02" "1.23456e-03"

formatC(x, digits = 3, format = "f")

[1] "123.456" "0.001"

14.4 POSIXct vs POSIXlt

POSIXct: seconds since epoch (numeric), compact, fast.
POSIXlt: list-like with components (year, mon, mday…), easier to extract parts.

14.5 Recommended Packages

tidyverse, lubridate, janitor, gt, gtsummary, survival, broom, here.
Pharma/CDISC: admiral, tlf/tern, pharmaverse meta-packages (explore as you grow).

14.6 Short Glossary

SDTM: Study Data Tabulation Model (FDA submission standard for raw domains).
ADaM: Analysis Data Model (derived analysis-ready datasets).
TLF: Tables, Listings, Figures for reporting.

---
title: "Appendix: Tips, Profiles, .libPaths"
---

## Useful Profiles
Create `~/.Rprofile` to set options (be careful on shared systems):
```r
options(
  repos = c(CRAN = "https://cloud.r-project.org"),
  scipen = 999
)
```

## Custom Library Paths
```r
# In .Rprofile or project-level .Rprofile
.libPaths(c("/path/to/Rlibs", .libPaths()))
```

## Format vs formatC (quick recap)
```{r}
x <- c(123.456, 0.00123456)
format(x, digits = 4)
format(x, nsmall = 2)
formatC(x, digits = 3, format = "f")
```

## POSIXct vs POSIXlt
- **POSIXct**: seconds since epoch (numeric), compact, fast.
- **POSIXlt**: list-like with components (year, mon, mday...), easier to extract parts.

## Recommended Packages
- `tidyverse`, `lubridate`, `janitor`, `gt`, `gtsummary`, `survival`, `broom`, `here`.
- Pharma/CDISC: `admiral`, `tlf`/`tern`, `pharmaverse` meta-packages (explore as you grow).

## Short Glossary
- **SDTM**: Study Data Tabulation Model (FDA submission standard for raw domains).
- **ADaM**: Analysis Data Model (derived analysis-ready datasets).
- **TLF**: Tables, Listings, Figures for reporting.