---
title: "Clinical Workflows"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Clinical Workflows}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

This vignette shows practical combinations of `kstools` functions for common clinical programming tasks.

```{r}
library(kstools)
```

## 1. Incidence Rate and Proportion Comparisons

```{r}
ks_eairdiff_mn(n1 = 10, n2 = 5, T1 = 100, T2 = 100)

ks_newcombe_hs(
  x1 = 36L, n1 = 54L,
  x2 = 41L, n2 = 56L
)
```

Stratified alternatives:

```{r}
ks_eairdiff_strata_mn(
  n1 = c(10, 5), n2 = c(5, 3),
  T1 = c(100, 80), T2 = c(100, 70)
)

ks_newcombe_hs_strata(
  x1 = c(36L, 10L), n1 = c(54L, 30L),
  x2 = c(41L, 8L),  n2 = c(56L, 30L)
)
```

## 2. Randomization Design

```{r}
w <- ks_williams(
  tmts_num = 4,
  tmt_names = c("Drug1A", "Drug2B", "ActCtrl", "Placebo"),
  sample_size = 24,
  seed_num = 20260408
)

w$design
head(w$schedule)
```

## 3. Data Loaders

```{r eval=FALSE}
# one-shot load of multiple domains from RDS directory (returns a named list)
dat <- ks_get_data(dm, ae, adlb, path = "data/rds")
dm  <- dat$dm

# case-insensitive lookup works too
dm <- ks_get_data(DM, path = "data/rds")  # matches dm.rds, DM.RDS, etc.

# or bulk by file type
x <- ks_batch_load("data/rds", type = "rds")
names(x)
```

These pieces can be mixed to build reproducible data review and reporting pipelines.