🔨 update automating Rmd reports part 1

Author: erikaduan

figures/dv-creating_rmd_reports-dynamic_tabs.png

@@ -0,0 +1,110 @@
+---
+title: "Creating professional R Markdown reports"  
+author: "Erika Duan"
+date: "`r Sys.Date()`"
+output:
+  github_document:
+    toc: true
+---
+
+```{r setup, include=FALSE}
+# Set up global environment ----------------------------------------------------
+knitr::opts_chunk$set(echo=TRUE, results='hide', fig.show='hold', fig.align='center')  
+```
+
+```{r, echo=TRUE, message=FALSE, warning=FALSE}
+# Load required packages -------------------------------------------------------  
+if (!require("pacman")) install.packages("pacman")
+pacman::p_load(here,
+               tidyverse,
+               palmerpenguins)  
+```
+
+
+# Creating html tabs in R Markdown reports  
+
+Creating [html tabs](https://bookdown.org/yihui/rmarkdown-cookbook/html-tabs.html) is a handy way to organise parallel sections of information i.e. displaying multiple plots from the same dataset. We can use the dataset from the `palmerpenguin` R package to explore this.    
+
+```{r, results='hold'}
+# Preview palmerpenguin dataset ------------------------------------------------
+palmerpenguins::penguins %>%
+  head(3) %>%
+  knitr::kable()
+```
+
+
+## Creating tabs manually  
+
+Tabs can be created manually by adding the code `{.tabset}` next to an empty header one level higher than the header level that you want to display as a tab. Make sure you add the code `{-}` next to a second higher level header to signal where tab creation ends.  
+
+```{r, echo=FALSE, results='hold', out.width="70%"}
+knitr::include_graphics("../../figures/dv-creating_rmd_reports-manual_tabs_code.png")
+```
+
+The html output consists of interactive headers with titles corresponding to individual header names. 
+
+```{r, echo=FALSE, results='hold', out.width="100%"}
+knitr::include_graphics("../../figures/dv-creating_rmd_reports-manual_tabs.png")
+```
+
+
+## Creating tabs dynamically    
+
+There will be circumstances where you do not want to or cannot manually specify the number of tabs required. In these circumstances, dynamic tabs can be created through the following steps:    
+
+1. Create individual plots (using a function) and store them inside a list.   
+2. Create a chunk of code in between a higher level header labelled `{.tabset}` and another one labelled `{-}`.   
+3. Set this chunk of code with `echo=FALSE` and `results='asis'`.     
+
+```{r, echo=TRUE, results='hide'}
+# Create a list of plots -------------------------------------------------------
+plot_bill_length_vs_depth <- function(penguin_species) {
+  palmerpenguins::penguins %>%
+    filter(species == penguin_species) %>%
+    ggplot(aes(x = bill_length_mm,
+               y = bill_depth_mm)) +
+    geom_point() + 
+    labs(title = paste0("Species: ", penguin_species)) +  
+    theme_bw() +
+    theme(panel.grid = element_line(linetype = "dotted"))
+}
+
+# Extract distinct species names and create a plot per species  
+plots <- palmerpenguins::penguins %>%
+  distinct(species) %>%
+  pull(species) %>%
+  map(~ plot_bill_length_vs_depth(.x)) 
+
+# Set plot names  
+species_names <- palmerpenguins::penguins %>%
+  distinct(species) %>%
+  pull(species) 
+
+plots <- set_names(plots, species_names)
+```
+
+```{r, echo=TRUE, message=FALSE, warning=FALSE, fig.show='hide', results='hide'}
+# Use a for loop to print code for tab creation via R Markdown -----------------  
+# Set echo=FALSE and results='asis' in the code chunk   
+# Insert chunk between a header labelled `{.tabset}` and a header labelled `{-}`  
+# Store each plot as temp object and then print each temp object and two new lines  
+for (i in seq_along(plots)) {
+  temp <- plots[[i]]
+  cat("##", "Species: ", names(plots[i]), "\n") # Create tabs from plot names
+  print(temp) 
+  cat("\n\n")
+}
+```
+
+This will generate dynamically sized tabs as shown below.   
+
+```{r, echo=FALSE, results='hold', out.width='80%'}     
+knitr::include_graphics("../../figures/dv-creating_rmd_reports-dynamic_tabs.png")    
+```
+
+**Note:** The option `results='asis'` allows R code to be printed as a raw output (i.e. code is not printed inside fenced code blocks). This is handy for writing for loops to automate aspects of R Markdown report generation.       
+
+
+# Resources 
+
++ The definitive R Markdown [resource guide](https://bookdown.org/yihui/rmarkdown-cookbook/html-tabs.html) by Yihui Xie. 

figures/dv-creating_rmd_reports-manual_tabs.png

@@ -0,0 +1,120 @@
+Creating professional R Markdown reports
+================
+Erika Duan
+2022-05-22
+
+-   [Creating html tabs in R Markdown
+    reports](#creating-html-tabs-in-r-markdown-reports)
+    -   [Creating tabs manually](#creating-tabs-manually)
+    -   [Creating tabs dynamically](#creating-tabs-dynamically)
+-   [Resources](#resources)
+
+``` r
+# Load required packages -------------------------------------------------------  
+if (!require("pacman")) install.packages("pacman")
+pacman::p_load(here,
+               tidyverse,
+               palmerpenguins)  
+```
+
+# Creating html tabs in R Markdown reports
+
+Creating [html
+tabs](https://bookdown.org/yihui/rmarkdown-cookbook/html-tabs.html) is a
+handy way to organise parallel sections of information i.e. displaying
+multiple plots from the same dataset. We can use the dataset from the
+`palmerpenguin` R package to explore this.
+
+``` r
+# Preview palmerpenguin dataset ------------------------------------------------
+palmerpenguins::penguins %>%
+  head(3) %>%
+  knitr::kable()
+```
+
+| species | island    | bill_length_mm | bill_depth_mm | flipper_length_mm | body_mass_g | sex    | year |
+|:--------|:----------|---------------:|--------------:|------------------:|------------:|:-------|-----:|
+| Adelie  | Torgersen |           39.1 |          18.7 |               181 |        3750 | male   | 2007 |
+| Adelie  | Torgersen |           39.5 |          17.4 |               186 |        3800 | female | 2007 |
+| Adelie  | Torgersen |           40.3 |          18.0 |               195 |        3250 | female | 2007 |
+
+## Creating tabs manually
+
+Tabs can be created manually by adding the code `{.tabset}` next to an
+empty header one level higher than the header level that you want to
+display as a tab. Make sure you add the code `{-}` next to a second
+higher level header to signal where tab creation ends.
+
+<img src="../../figures/dv-creating_rmd_reports-manual_tabs_code.png" width="70%" style="display: block; margin: auto;" />
+
+The html output consists of interactive headers with titles
+corresponding to individual header names.
+
+<img src="../../figures/dv-creating_rmd_reports-manual_tabs.png" width="100%" style="display: block; margin: auto;" />
+
+## Creating tabs dynamically
+
+There will be circumstances where you do not want to or cannot manually
+specify the number of tabs required. In these circumstances, dynamic
+tabs can be created through the following steps:
+
+1.  Create individual plots (using a function) and store them inside a
+    list.  
+2.  Create a chunk of code in between a higher level header labelled
+    `{.tabset}` and another one labelled `{-}`.  
+3.  Set this chunk of code with `echo=FALSE` and `results='asis'`.
+
+``` r
+# Create a list of plots -------------------------------------------------------
+plot_bill_length_vs_depth <- function(penguin_species) {
+  palmerpenguins::penguins %>%
+    filter(species == penguin_species) %>%
+    ggplot(aes(x = bill_length_mm,
+               y = bill_depth_mm)) +
+    geom_point() + 
+    labs(title = paste0("Species: ", penguin_species)) +  
+    theme_bw() +
+    theme(panel.grid = element_line(linetype = "dotted"))
+}
+
+# Extract distinct species names and create a plot per species  
+plots <- palmerpenguins::penguins %>%
+  distinct(species) %>%
+  pull(species) %>%
+  map(~ plot_bill_length_vs_depth(.x)) 
+
+# Set plot names  
+species_names <- palmerpenguins::penguins %>%
+  distinct(species) %>%
+  pull(species) 
+
+plots <- set_names(plots, species_names)
+```
+
+``` r
+# Use a for loop to print code for tab creation via R Markdown -----------------  
+# Set echo=FALSE and results='asis' in the code chunk   
+# Insert chunk between a header labelled `{.tabset}` and a header labelled `{-}`  
+# Store each plot as temp object and then print each temp object and two new lines  
+for (i in seq_along(plots)) {
+  temp <- plots[[i]]
+  cat("##", "Species: ", names(plots[i]), "\n") # Create tabs from plot names
+  print(temp) 
+  cat("\n\n")
+}
+```
+
+This will generate dynamically sized tabs as shown below.
+
+<img src="../../figures/dv-creating_rmd_reports-dynamic_tabs.png" width="80%" style="display: block; margin: auto;" />
+
+**Note:** The option `results='asis'` allows R code to be printed as a
+raw output (i.e. code is not printed inside fenced code blocks). This is
+handy for writing for loops to automate aspects of R Markdown report
+generation.
+
+# Resources
+
+-   The definitive R Markdown [resource
+    guide](https://bookdown.org/yihui/rmarkdown-cookbook/html-tabs.html)
+    by Yihui Xie.