---
title: "Cost-effectiveness plane"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Cost-effectiveness plane}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 6
)
```
```{r setup, results='hide', message=FALSE, warning=FALSE, echo=FALSE}
library(BCEA)
library(dplyr)
library(reshape2)
library(ggplot2)
library(purrr)
```
## Introduction
The intention of this vignette is to show how to plot different styles of cost-effectiveness acceptability curves using the BCEA package.
#### R code
To calculate these in BCEA we use the `bcea()` function.
```{r}
data("Vaccine")
he <- bcea(eff, cost)
```
The plot defaults to base R plotting. Type of plot can be set explicitly using the `graph` argument.
```{r}
ceplane.plot(he, graph = "base")
ceplane.plot(he, graph = "ggplot2")
# ceac.plot(he, graph = "plotly")
```
Other plotting arguments can be specified such as title, line colours and theme.
```{r}
ceplane.plot(he,
graph = "ggplot2",
title = "my title",
line = list(color = "green", size = 3),
point = list(color = "blue", shape = 10, size = 5),
icer = list(color = "orange", size = 5),
area = list(fill = "grey"),
theme = theme_linedraw())
```
If you only what the mean point then you can suppress the sample points by passing size `NA`.
```{r}
ceplane.plot(he,
graph = "ggplot2",
point = list(size = NA),
icer = list(size = 5))
```
## Multiple interventions
This situation is when there are more than two interventions to consider.
#### R code
```{r}
data("Smoking")
he <- bcea(eff, cost, ref = 4)
# str(he)
```
Basic plots with defaults.
```{r}
ceplane.plot(he)
ceplane.plot(he, graph = "ggplot2")
```
The font size can be adjusted using the `text` argument.
```{r}
ceplane.plot(he, graph = "ggplot2", text = list(size = 20))
ceplane.plot(he, graph = "ggplot2", text = list(size = rel(2))) # relative scaling, double size
# equivalent but more flexible and direct
ceplane.plot(he, graph = "ggplot2") +
theme(axis.text = element_text(size = 18),
axis.title.x = element_text(size = 20),
axis.title.y = element_text(size = 20))
```
Numerous different styling arguments can be provided.
```{r}
ceplane.plot(he,
graph = "ggplot2",
title = "my title",
line = list(color = "red", size = 1),
point = list(color = c("plum", "tomato", "springgreen"), shape = 3:5, size = 2),
icer = list(color = c("red", "orange", "black"), size = 5))
```
There are various different ways to reposition the legend.
```{r}
ceplane.plot(he, pos = FALSE) # bottom right
ceplane.plot(he, pos = c(0, 0))
ceplane.plot(he, pos = c(0, 1))
ceplane.plot(he, pos = c(1, 0))
ceplane.plot(he, pos = c(1, 1))
```
### Willingness-to-pay label
For `{ggplot2}` we can modify the willingness-to-pay label e.g. "k = 25000".
The default is
```{r}
ceplane.plot(he, graph = "ggplot2")
```
The simplest argument is to set the value of the willingness-to-pay threshold using `wtp`.
```{r}
ceplane.plot(he, graph = "ggplot2", wtp = 10000)
```
Alternatively, we can pass a list of arguments to `wtp` to modify the appearance of the label.
```{r}
ceplane.plot(he, graph = "ggplot2", wtp = list(value = 10000))
ceplane.plot(he, graph = "ggplot2", wtp = list(value = 10000, colour = "blue"))
ceplane.plot(he, graph = "ggplot2", wtp = list(colour = "blue"))
ceplane.plot(he, graph = "ggplot2", wtp = list(size = 5))
```
To hide the text assign `size = 0`.
```{r}
ceplane.plot(he, graph = "ggplot2", wtp = list(size = 0))
```
The label is placed at the left hand side of the plot next to the willingness-to-pay line by default. When this would mean the label is off the bottom of the plot it is positioned at the bottom left corner.
```{r}
data("Vaccine")
he <- bcea(eff, cost, ref=2)
ceplane.plot(he, graph = "ggplot2")
ceplane.plot(he, graph = "ggplot2", wtp = 1000, xlim = c(-0.0005, 0.0015))
ceplane.plot(he, graph = "ggplot2", wtp = 10000, xlim = c(-0.0005, 0.0015))
ceplane.plot(he, graph = "ggplot2", wtp = 25000, xlim = c(-0.0005, 0.0015))
ceplane.plot(he, graph = "ggplot2", wtp = 50000, xlim = c(-0.0005, 0.0015))
```
The position of the label can be adjusted using the `label.pos` argument and a logical value.
```{r}
ceplane.plot(he, graph = "ggplot2", wtp = 1000, xlim = c(-0.0005, 0.0015), label.pos = TRUE)
ceplane.plot(he, graph = "ggplot2", wtp = 1000, xlim = c(-0.0005, 0.0015), label.pos = FALSE)
```
A direct way of specifying the position of the label is to use the `wtp` argument and set the `y` value in a list.
```{r}
ceplane.plot(he, graph = "ggplot2", wtp = list(y = 8))
```
For base `R`
```{r}
ceplane.plot(he) # default
```
```{r}
ceplane.plot(he, wtp = 1000, xlim = c(-0.0005, 0.0015))
ceplane.plot(he, wtp = 10000, xlim = c(-0.0005, 0.0015))
ceplane.plot(he, wtp = 25000, xlim = c(-0.0005, 0.0015))
ceplane.plot(he, wtp = 50000, xlim = c(-0.0005, 0.0015))
```
```{r}
ceplane.plot(he, wtp = 1000, xlim = c(-0.0005, 0.0015), label.pos = TRUE)
ceplane.plot(he, wtp = 1000, xlim = c(-0.0005, 0.0015), label.pos = FALSE)
```
```{r}
##TODO: not yet implemented ggplot syntax for base R
# ceplane.plot(he, wtp = list(value = 10000))
# ceplane.plot(he, wtp = list(value = 10000, colour = "blue"))
# ceplane.plot(he, wtp = list(colour = "blue"))
# ceplane.plot(he, wtp = list(y = 8))
# ceplane.plot(he, wtp = list(size = 5))
#
# # to hide text
# ceplane.plot(he, wtp = list(size = 0))
```
<!-- ```{r} -->
<!-- ceac.plot(he, graph = "ggplot2", pos = c(0, 0)) -->
<!-- ceac.plot(he, graph = "ggplot2", pos = c(0, 1)) -->
<!-- ceac.plot(he, graph = "ggplot2", pos = c(1, 0)) -->
<!-- ceac.plot(he, graph = "ggplot2", pos = c(1, 1)) -->
<!-- ``` -->
<!-- Define colour palette. -->
<!-- ```{r} -->
<!-- mypalette <- RColorBrewer::brewer.pal(3, "Accent") -->
<!-- ceac.plot(he, -->
<!-- graph = "base", -->
<!-- title = "my title", -->
<!-- line = list(colors = mypalette), -->
<!-- pos = FALSE) -->
<!-- ceac.plot(he, -->
<!-- graph = "ggplot2", -->
<!-- title = "my title", -->
<!-- line = list(colors = mypalette), -->
<!-- pos = FALSE) -->
<!-- ``` -->
<!-- ### Pair-wise comparisons -->
<!-- Again, without loss of generality, if we assume that we are interested in intervention $i=1$, the we wish to calculate -->
<!-- $$ -->
<!-- p(NB_1 = \max\{NB_i : i \in S\} | k) -->
<!-- $$ -->
<!-- This can be approximated by the following. -->
<!-- $$ -->
<!-- \frac{1}{N} \sum_j^N \prod_{i \in S} \mathbb{I} (k \Delta e_{1,i}^j - \Delta c_{1,i}^j) -->
<!-- $$ -->
<!-- #### R code -->
<!-- In BCEA we first we must determine all combinations of paired interventions using the `multi.ce()` function. -->
<!-- ```{r} -->
<!-- he <- multi.ce(he) -->
<!-- ``` -->
<!-- We can use the same plotting calls as before i.e. `ceac.plot()` and BCEA will deal with the pairwise situation appropriately. -->
<!-- Note that in this case the probabilities at a given willingness to pay sum to 1. -->
<!-- ```{r} -->
<!-- ceac.plot(he, graph = "base") -->
<!-- ceac.plot(he, -->
<!-- graph = "base", -->
<!-- title = "my title", -->
<!-- line = list(colors = "green"), -->
<!-- pos = FALSE) -->
<!-- mypalette <- RColorBrewer::brewer.pal(4, "Dark2") -->
<!-- ceac.plot(he, -->
<!-- graph = "base", -->
<!-- title = "my title", -->
<!-- line = list(colors = mypalette), -->
<!-- pos = c(0,1)) -->
<!-- ``` -->
<!-- ```{r} -->
<!-- ceac.plot(he, -->
<!-- graph = "ggplot2", -->
<!-- title = "my title", -->
<!-- line = list(colors = mypalette), -->
<!-- pos = c(0,1)) -->
<!-- ``` -->
<!-- ```{r echo=FALSE} -->
<!-- # create output docs -->
<!-- # rmarkdown::render(input = "vignettes/ceac.Rmd", output_format = "pdf_document", output_dir = "vignettes") -->
<!-- # rmarkdown::render(input = "vignettes/ceac.Rmd", output_format = "html_document", output_dir = "vignettes") -->
<!-- ``` -->