forest_plot.qmd

---
title: "forest_plot"
author: "Kasandra Ascuña-Durand / Ariana Cardenas"
format: html
editor: visual
---

## Conjunto de datos

```{r}
forest <- readr::read_csv(
  "data/processed/forest_study.csv")
```

## Librerías

```{r}
library(tidyverse)
library(ggplot2)
library(grid)
library(forestploter)

```

## Exploración

```{r}
colnames(forest)
```

## Paso 1: Ajustar el df para el forest plot

```{r}

forest$var <- ifelse(is.na(forest$IRR1), 
                      forest$var,
                      paste0("   ", forest$var))

forest$model_type1 <- replace(as.character(forest$model_type1), is.na(forest$model_type1), "")
forest$pvalue1 <- replace(as.character(forest$pvalue1), is.na(forest$pvalue1), "")
forest$model_type2 <- replace(as.character(forest$model_type2), is.na(forest$model_type2), "")
forest$pvalue2 <- replace(as.character(forest$pvalue2), is.na(forest$pvalue2), "")

forest$`Adjusted model` <- paste(rep(" ", 20), collapse = " ")
forest$`Unadjusted model` <- paste(rep(" ", 20), collapse = " ")

# Create a confidence interval column to display

forest$`RR (95% CI)1` <- ifelse(is.na(forest$IRR1), "",
                             sprintf("%.2f (%.2f to %.2f)",
                                     forest$IRR1, forest$lower1, forest$upper1)) 

forest$`RR (95% CI)2` <- ifelse(is.na(forest$IRR2), "",
                             sprintf("%.2f (%.2f to %.2f)",
                                     forest$IRR2, forest$lower2, forest$upper2)) 

forest <- forest %>%
  relocate(`Adjusted model`, .after = `upper1`) %>%
  relocate(`RR (95% CI)1`, .after = `Adjusted model`) %>%
  relocate(`pvalue2`, .after = `RR (95% CI)2`)


head(forest)

#Adjusting the names - skeleton for the forest plot

g <- forest[,c(1, 6:8, 13:15)]
colnames(g) <- c("Centralities",
                      " ","RR (95% CI)","p-value"," ",
                      "RR (95% CI)","p-value")

```

## Graficar el forest plot

```{r fig.align="center", echo = FALSE,fig.height = 12, fig.width = 14}

tm <- forest_theme(core=list(
  #fg_params=list(hjust = 1, x = 0.9),
                             bg_params=list(fill = c("lightgray", "white", "white"))),
                   colhead=list(fg_params=list(hjust=0.5, x=0.5)))

study <- forestploter::forest(g,
            est = list(forest$IRR1,
                       forest$IRR2),
            lower = list(forest$lower1,
                         forest$lower2), 
            upper = list(forest$upper1,
                         forest$upper2),
            ci_column = c(2, 5),
            ref_line = c(1, 1),
            xlim = list(c(-1, 5), c(-1, 5)),
            theme = tm
           )


# Bold grouping text
study <- forestploter::edit_plot(study,
               row = c(1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40),
               gp = grid::gpar(fontface = "bold"))

# Insert text at the top
study <- insert_text(study,
                 text = "Adjusted model",
                 col = 2:4,
                 part = "header",
                 gp = grid::gpar(fontface = "bold"))

study <- add_text(study,
                 text = "Unadjusted model",
                 col = 5:7,
                 row = 1,
                 part = "header",
                 gp = grid::gpar(fontface = "bold"))

# Add underline at the bottom of the header
study <- add_border(study, part = "header", row = 1, where = "top")
study <- add_border(study, part = "header", row = 2, where = "bottom")
# study <- add_border(study, part = "header", row = 1, col = 2:4, 
#                 gp = gpar(lwd = 2))
# study <- add_border(study, part = "header", row = 1, col = 5:7, 
#                 gp = gpar(lwd = 2))

plot(study)


```

```{r fig.align="center", echo = FALSE,fig.height = 12, fig.width = 14}

```