---
title: "Component-dose network meta-analysis with dose-dependent interactions"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Component-dose network meta-analysis with dose-dependent interactions}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
has_cmdstan <- requireNamespace("cmdstanr", quietly = TRUE) &&
  !is.null(tryCatch(cmdstanr::cmdstan_version(error_on_NA = FALSE),
                    error = function(e) NULL))
run_stan <- has_cmdstan || requireNamespace("rstan", quietly = TRUE)
```

This vignette shows the basic workflow for `cdtmbnma`. The example is the
sacubitril and valsartan sitting systolic blood-pressure dose plane. Each row is
one arm. `d_sac` and `d_val` are component dose columns; zero means absent.

```{r data}
library(cdtmbnma)
sv <- sacval_example()
head(sv)
```

## Building the single-timepoint design

`cdt_data()` turns the arm-level table into the model design. Studies with an
all-zero arm use that arm as the within-study reference. Studies without an
all-zero arm use their lowest-total-dose arm as the baseline and issue a warning.

```{r design}
d <- cdt_data(
  sv,
  study = "study",
  components = c("d_sac", "d_val"),
  outcome = "continuous",
  y = "y",
  se = "se",
  dstar = c(d_sac = 200, d_val = 320)
)
d
```

## Fitting the bilinear interaction model

`cdt_fit()` compiles the Stan model on first use and samples. The bilinear
interaction parameter is interpreted at the `dstar` corner: here, sacubitril 200
mg and valsartan 320 mg.

```{r fit, eval = run_stan}
fit <- cdt_fit(
  d,
  interaction = "bilinear",
  chains = 4,
  iter_warmup = 1000,
  iter_sampling = 1000,
  seed = 1
)
summary(fit)
```

The marginal component curves vary one component at a time while holding the
other at zero.

```{r plot, eval = run_stan, fig.width = 7, fig.height = 4}
plot(fit)
```

## Prediction at an unobserved dose pair

`predict()` returns the relative effect against the all-zero reference at any
component-dose combination, including dose pairs not directly observed in a
trial.

```{r predict, eval = run_stan}
predict(fit, newdata = data.frame(d_sac = 100, d_val = 160))
```

## Additive benchmark

The additive model is fitted by setting `interaction = "none"`.

```{r additive, eval = FALSE}
fit_add <- cdt_fit(d, interaction = "none")
```

If the `loo` package is installed, the pointwise log likelihood stored in Stan's
generated quantities can be used for information-criterion comparisons.

```{r loo, eval = FALSE}
loo::loo_compare(
  loo::loo(fit$fit$draws("log_lik")),
  loo::loo(fit_add$fit$draws("log_lik"))
)
```

## Stage-one longitudinal model

The package also contains a narrower two-component longitudinal interface. It is
useful when repeated arm means over time are available and an exponential
approach-to-asymptote is reasonable. The example below builds a small design but
does not fit it during vignette building.

```{r time-design}
long_dat <- data.frame(
  study = rep("trial1", 6),
  arm = rep(c("placebo", "A", "AB"), each = 2),
  week = rep(c(4, 8), 3),
  dose_A = rep(c(0, 10, 10), each = 2),
  dose_B = rep(c(0, 0, 20), each = 2),
  y = c(0, 0, -1, -2, -2, -3),
  se = rep(1, 6)
)

time_design <- cdt_time_data(
  long_dat,
  study = "study",
  arm = "arm",
  time = "week",
  components = c("dose_A", "dose_B"),
  y = "y",
  se = "se",
  dstar = c(dose_A = 10, dose_B = 20)
)
time_design
```

```{r time-fit, eval = FALSE}
fit_time <- cdt_time_fit(time_design)
predict(fit_time, data.frame(dose_A = 10, dose_B = 20))
```