---
title: "Customize a PRISMA flow chart"
author: Lionel Duarte
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{PRISMA}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>", 
  dpi = 200, 
  warning = FALSE
)
library(prismadiagramR)
library(dplyr)
```

```{r setup}
library(prismadiagramR)
library(dplyr)
```



# Purpose
This package aids in rapidly creating a PRISMA diagram for use in meta-analysis from a simple dataframe tracking the use of publications in the analysis.

The minimal arguments needed are:
    1. Pub.ID: A unique publication ID.
    2. Source: A source identifier to describe where the study is from.
    3. Filter: A Filter identifier to describe how the study is filtered out or left NA if used.


# Simple StudySet input
From a dataframe with only the three arguments stated above we can get an initial PRISMA diagram.

```{r}

set.seed(25)
N <- 100
studyStatus <- data.frame(Pub.ID = seq(1:N),
                          Source = sample(letters[1:3], N, replace = TRUE),
                          Filter = sample(letters[1:5], N, replace = TRUE))
studyStatus$Filter[studyStatus$Filter=="e"] <- NA
getPrisma(studyStatus) %>% DiagrammeR::grViz(.)

```


## Switching Source
It is possible to re-order the sources and filters.

```{r}
studyStatus$Source <- ordered(studyStatus$Source , levels = c("c", "b", "a"))
studyStatus$Filter <- ordered(studyStatus$Filter , levels = c("d", "c", "b", "a"))

getPrisma(studyStatus) %>% DiagrammeR::grViz(.)
```





# Additional Formatting
We can also obtain a custom prismaFormat dataframe to modify to change items in the PRISMA as desired.
By default this dataframe has 3 arguments:
    1. prismaLvl: This describes the level the node is created at.
    2. nodeType: This describes the type of node it is.
    3. prismaTxt: The text used in the node for the PRISMA diagram.

```{r}
prismaFormat <- getPrismaFormat(studyStatus)
flextable::flextable(prismaFormat)

```


## Changing Text

```{r}
prismaFormat$prismaTxt[1] <- "Medline"
getPrisma(studyStatus = NULL, prismaFormat = prismaFormat) %>% DiagrammeR::grViz(.)

```

## Changing FonstSize
We can add the fontSize argument to the datatable to customize the fontsize in each node.

```{r}
prismaFormat$fontSize <- 15
prismaFormat$fontSize[1] <- 10
getPrisma(studyStatus = NULL, prismaFormat = prismaFormat) %>% DiagrammeR::grViz(.)
```


## From Scratch
It is also possible to create the PRISMA directly from prismaFormat and create nodes that do not need a filter. 
 
```{r}
prismaFormat <-
  data.frame(
    prismaLvl = c(1,2,3,3,4),
    nodeType =  c("Source", "Node", "Node", "Filter", "End"),
    prismaTxt = letters[1:5]
  )

getPrisma(studyStatus = NULL, prismaFormat = prismaFormat) %>% DiagrammeR::grViz(.)
```