Example R Script and R Markdown files

Introduction

The *.R and *.Rmd scripts on this page illustrate a range of possible approaches for building a “project” *.html document. The examples range from a very simple R Markdown Notebook to a multi-page website. This page focues on the scripts and not the procedures for constructing a GitHub repository with a GitHub Pages web page, nor for serving web pages on https://pages.uoregon.edu/.

The examples can be replicated by copying the scripts, and creating the appropriate files in RStudio (e.g. as alpha_plot_RScript.R for this first example).

Important: When replicating Example 5 (a multi-page *.html document), the file _site.yml must be present in the R working directory. This file describes the “navbar” (navigation bar) and the layout of the page. If it is present, it will influence the other examples. So, for example, if _site.yml is present, it will try to add a navbar to the *.html file created by, say, Example 4, which has its own formating information this will produce unexpected results. To repeat, _site.yml should be in the working directory only for Example 5, and should not be in the working directory for the other examples. (Note, instead of adding and deleting _site.yml, just rename it: not_site.yml.)

Example 1 – A simple R script

• Script file: [alpha_plot_RScript.R]
• Output is text in the Console pane and graphics in the Plots pane.

This is an example of “bare” code that reads a netCDF file, does some setup, and plots a map. The output could conceivably be collected from the Console and Plot windows, and used to make an *.html file, but, that’s what computers are for. This would involve:

• creating a *.md file, perhaps with VS Code,
• copying text from the Console pane into it,
• including saved images from the Plot pane (saving an image, say, as alpha.png and then including it in the Markdown file using the code fragment ![](alpha.png)), and then finally
• exporting the *.md file as an *.html file, or using Pandoc to render the *.md file.

That would be tedious.

It would still be worth running the script, chunk-by-chunk, to get an idea of what the basic task of inputing data, setting up, and plotting is.

Note: Copy everything in the boxes (except the first line if it’s blank).

  
# alpha_plot_RScript.R
# reads and plots "alpha" (Priestley-Taylor coefficient) (AE/PE)

# load libraries
library(maps)
library(sf)
library(stars)
library(ggplot2)

# get a world outline object for plotting

# world_sf
world_sf <- st_as_sf(maps::map("world", plot = FALSE, fill = TRUE))
world_otl_sf <- st_geometry(world_sf)

# ggplot map of world_outline
ggplot() + 
  geom_sf(data = world_otl_sf, fill = NA, col = "black") + 
  scale_x_continuous(breaks = seq(-180, 180, 30)) +
  scale_y_continuous(breaks = seq(-90, 90, 30)) +
  coord_sf(xlim = c(-180, +180), ylim = c(-90, 90), expand = FALSE) +
  theme_bw()

# read alpha from a netCDF file of bioclimatic variables using stars

# change path as necessary
nc_path <- "/Users/bartlein/Projects/RESS/data/nc_files/"
nc_name <- "cru10min30_bio.nc"
nc_file <- paste(nc_path, nc_name, sep="")
alpha <- read_ncdf(nc_file, var="alpha", proxy = FALSE)

# list alpha
alpha

# convert stars to sf
alpha_sf <- st_as_sf(alpha, as_points = TRUE)
alpha_sf
plot(alpha_sf, pch = 16, cex = 0.3)

# setup for plotting alpha

# make a data.frame
lon <- st_coordinates(alpha_sf)[,1]
lat <- st_coordinates(alpha_sf)[,2]
alpha <- as.vector(alpha_sf)
alpha_df <- data.frame(lon, lat, alpha)
dim(alpha_df)
head(alpha_df)

# set axis labels (breaks)
breaks_x <- c(seq(-180, 180, by = 60)) 
breaks_y <- c(seq(-90, 90, by = 30)) 
labels_x <- as.character(breaks_x) 
labels_y <- as.character(breaks_y) 

# plot alpha

# ggplot2 map of alpha
ggplot() +
  geom_tile(data = alpha_df, aes(x = lon, y = lat, fill = alpha)) +
  scale_fill_gradient2(low = "brown", mid="white", high = "darkgreen", midpoint = 0.50) +
  geom_sf(data = world_otl_sf, col = "black", fill = NA) +
  coord_sf(xlim = c(-180, +175.0), ylim = c(-90, 90), expand = FALSE) +
  scale_x_continuous(breaks = breaks_x) +
  scale_y_continuous(breaks = breaks_y) +
  labs(x = "Longitude", y = "Latitude", title="Priestley-Taylor Coefficient (alpha) (AE/PE)", fill="alpha") +
  theme_bw()

[Back to top]

Example 2 – An RMarkdown Notebook file

• Script file: [alpha_plot_RNotebook.Rmd]
• Output is a single-page R Notebook .html file.

This R Notebook *.Rmd file produces the simplest of .html output. Note that it does not do any Markdown-type formatting, but simply embeds the output in the document. What makes this an R Notebook file (despite having the *.Rmd extension), is the presence of a “YAML” (“Yet Another Markup Language/YAML Ain’t Markup Language”) header that looks like the following:

---
title: "Example 2 -- An RMarkdown Notebook file "
output: html_document
---

This header specifies that the output of “kniting” the file should be an *.html file. Here’s the code:

  
---
title: "Example 2 -- An RMarkdown Notebook file "
output: html_document
---

This RNotebook script reads a netCDF file consisting of several bioclimatic variables, and plots one of them, `alpha`

```{r alpha-plot-RNotebook-1 }
# load libraries
library(maps)
library(sf)
library(stars)
library(ggplot2)
```

Get a world outline object for plotting.

```{r alpha-plot-RNotebook-2 }
# world_sf
world_sf <- st_as_sf(maps::map("world", plot = FALSE, fill = TRUE))
world_otl_sf <- st_geometry(world_sf)
```

```{r alpha-plot-RNotebook-3 }
# ggplot map of world_outline
ggplot() + 
  geom_sf(data = world_otl_sf, fill = NA, col = "black") + 
  scale_x_continuous(breaks = seq(-180, 180, 30)) +
  scale_y_continuous(breaks = seq(-90, 90, 30)) +
  coord_sf(xlim = c(-180, +180), ylim = c(-90, 90), expand = FALSE) +
  theme_bw()
```

Read alpha from a netCDF file of bioclimatic variables using `stars`.

```{r alpha-plot-RNotebook-4 }
# change path as necessary
nc_path <- "/Users/bartlein/Projects/RESS/data/nc_files/"
nc_name <- "cru10min30_bio.nc"
nc_file <- paste(nc_path, nc_name, sep="")
alpha <- read_ncdf(nc_file, var="alpha", proxy = FALSE)
```

```{r alpha-plot-RNotebook-5 }
# list alpha
alpha
```

Convert to an `sf` object.

```{r alpha-plot-RNotebook-6 }
# convert stars to sf
alpha_sf <- st_as_sf(alpha, as_points = TRUE)
alpha_sf
plot(alpha_sf, pch = 16, cex = 0.3)
```

Setup for making a `{ggplot2}` map of alpha.

```{r alpha-plot-RNotebook-7 }
# make a data.frame
lon <- st_coordinates(alpha_sf)[,1]
lat <- st_coordinates(alpha_sf)[,2]
alpha <- as.vector(alpha_sf)
alpha_df <- data.frame(lon, lat, alpha)
dim(alpha_df)
head(alpha_df)
```

```{r alpha-plot-RNotebook-8 }
# set axis labels (breaks)
breaks_x <- c(seq(-180, 180, by = 60)) 
breaks_y <- c(seq(-90, 90, by = 30)) 
labels_x <- as.character(breaks_x) 
labels_y <- as.character(breaks_y)
```

Plot alpha.

```{r alpha-plot-RNotebook-9 }
# ggplot2 map of alpha
ggplot() +
  geom_tile(data = alpha_df, aes(x = lon, y = lat, fill = alpha)) +
  scale_fill_gradient2(low = "brown", mid="white", high = "darkgreen", midpoint = 0.50) +
  geom_sf(data = world_otl_sf, col = "black", fill = NA) +
  coord_sf(xlim = c(-180, +175.0), ylim = c(-90, 90), expand = FALSE) +
  scale_x_continuous(breaks = breaks_x) +
  scale_y_continuous(breaks = breaks_y) +
  labs(x = "Longitude", y = "Latitude", title="Priestley-Taylor Coefficient (alpha) (AE/PE)", fill="alpha") +
  theme_bw()
```

Some discussion could go here.

[Back to top]

Example 3 – A single-page *.html file, with some styling

• Script file: [alpha_plot_RMarkdown_1Page.Rmd]
• Output is a single-page *.html file.

This example produces a single-page .html file as output, this time styled using the html-md-01.css stylesheet (the same one used for the course web page). The YAML header looks like

---
title: "Example 3 – A single-page *.html file, with some styling"
output:
  html_document:
    css: html-md-01.css
---

Here’s the code:

  
---
title: "Example 3 – A single-page *.html file, with some styling"
output:
  html_document:
    css: html-md-01.css
---

# Introduction #

This RMarkdown document describes reading a netCDF file consisting of several bioclimatic variables, and plots one of them, `alpha`.

## Load packages ## 

```{r alpha-plot-RMarkdown-1page-1 }
# load libraries
library(sf)
library(stars)
library(ggplot2)
```

# Read data #

## World outline ##

### Read map data from the `{maps}` package ###

Read a map file of  world coastlines and countries, and convert to an `sf` object.

```{r alpha-plot-RMarkdown-1page-2 }
# world_sf
world_sf <- st_as_sf(maps::map("world", plot = FALSE, fill = TRUE))
world_otl_sf <- st_geometry(world_sf)
```

### plot the world outline ###

```{r alpha-plot-RMarkdown-1page-3 }
# ggplot map of world_outline
ggplot() + 
  geom_sf(data = world_otl_sf, fill = NA, col = "black") + 
  scale_x_continuous(breaks = seq(-180, 180, 30)) +
  scale_y_continuous(breaks = seq(-90, 90, 30)) +
  coord_sf(xlim = c(-180, +180), ylim = c(-90, 90), expand = FALSE) +
  theme_bw()
```

## Read alpha ##

Now read in alpha alpha from a netCDF file of bioclimatic variables using stars.

```{r alpha-plot-RMarkdown-1page-4 }
# read alpha (AE/PE)
# change path as necessary
nc_path <- "/Users/bartlein/Projects/RESS/data/nc_files/"
nc_name <- "cru10min30_bio.nc"
nc_file <- paste(nc_path, nc_name, sep="")
alpha <- read_ncdf(nc_file, var="alpha", proxy = FALSE)
```

List alpha to show contents of the object.

```{r alpha-plot-RMarkdown-1page-5}
# list alpha
alpha
```

Convert the `stars` object to an `sf` object:

```{r alpha-plot-RMarkdown-1page-6}
# convert stars to sf
alpha_sf <- st_as_sf(alpha, as_points = TRUE)
alpha_sf
plot(alpha_sf, pch = 16, cex = 0.3)
```

# Plot the data #

## Setup ##

Do some setting up befor plotting.

```{r alpha-plot-RMarkdown-1page-7}
# setup for plotting alpha
# make a data.frame
lon <- st_coordinates(alpha_sf)[,1]
lat <- st_coordinates(alpha_sf)[,2]
alpha <- as.vector(alpha_sf)
alpha_df <- data.frame(lon, lat, alpha)
dim(alpha_df)
head(alpha_df)
```

Set axis labels or breaks:

```{r alpha-plot-RMarkdown-1page-8}
# set axis labels (breaks)
breaks_x <- c(seq(-180, 180, by = 60)) 
breaks_y <- c(seq(-90, 90, by = 30)) 
labels_x <- as.character(breaks_x) 
labels_y <- as.character(breaks_y)
```

## Plot alpha ##

Make a `{ggplot2}` maps of alpha.

```{r alpha-plot-RMarkdown-1page-9}
# ggplot2 map of alpha
ggplot() +
  geom_tile(data = alpha_df, aes(x = lon, y = lat, fill = alpha)) +
  scale_fill_gradient2(low = "brown", mid="white", high = "darkgreen", midpoint = 0.50) +
  geom_sf(data = world_otl_sf, col = "black", fill = NA) +
  coord_sf(xlim = c(-180, +175.0), ylim = c(-90, 90), expand = FALSE) +
  scale_x_continuous(breaks = breaks_x) +
  scale_y_continuous(breaks = breaks_y) +
  labs(x = "Longitude", y = "Latitude", title="Priestley-Taylor Coefficient (alpha) (AE/PE)", fill="alpha") +
  theme_bw()
```

# Discussion #

(A few paragraphs on map patterns, trends, etc.)

[Back to top]

Example 4 – A single-page *.html file, with styling and navigation

• Script file: [alpha_plot_RMarkdown.Rmd]
• Output is a single-page .html file, with styling and some navigation.

The YAML header is more elaborate now, speciying a code syntax-highlighting scheme (haddock), and a output “Bootstrap” theme (cerulean) (See [https://bookdown.org/yihui/rmarkdown/html-document.html#appearance-and-style])

---
title:  Raster mapping
output:
  html_document:
    css: html-md-01.css
    fig_caption: yes
    highlight: haddock
    number_sections: yes
    theme: cerulean
    toc: yes
    toc_float: true
    collapsed: no
---

There is also a “code-chunk” that sets some knitr options.

Here’s the code:

  
---
title:  "Example 4 – A single-page *.html file, with styling and navigation"
output:
  html_document:
    css: html-md-01.css
    fig_caption: yes
    highlight: haddock
    number_sections: yes
    theme: cerulean
    toc: yes
    toc_float: true
    collapsed: no
---

```{r set-options, echo=FALSE, strip.white=TRUE, style="background:  gray_80;"}
options(width = 105)
knitr::opts_chunk$set(dev='png', dpi=300, cache=TRUE)
pdf.options(useDingbats = TRUE)
```

# Introduction #

This RMarkdown document describes reading a netCDF file consisting of several bioclimatic variables, and plots one of them, `alpha`.

## Load packages ## 

```{r alpha-plot-RMarkdown-1 }
# load libraries
library(sf)
library(stars)
library(ggplot2)
```

# Read data #

## World outline ##

### Read map data from the `{maps}` package ###

Read a map file of  world coastlines and countries, and convert to an `sf` object.

```{r alpha-plot-RMarkdown-2 }
# world_sf
world_sf <- st_as_sf(maps::map("world", plot = FALSE, fill = TRUE))
world_otl_sf <- st_geometry(world_sf)
```

### Plot the world outline ###

```{r alpha-plot-RMarkdown-3 }
# ggplot map of world_outline
ggplot() + 
  geom_sf(data = world_otl_sf, fill = NA, col = "black") + 
  scale_x_continuous(breaks = seq(-180, 180, 30)) +
  scale_y_continuous(breaks = seq(-90, 90, 30)) +
  coord_sf(xlim = c(-180, +180), ylim = c(-90, 90), expand = FALSE) +
  theme_bw()
```

## Read alpha ##

Now read in alpha alpha from a netCDF file of bioclimatic variables using stars.

```{r alpha-plot-RMarkdown-4 }
# read alpha (AE/PE)
# change path as necessary
nc_path <- "/Users/bartlein/Projects/RESS/data/nc_files/"
nc_name <- "cru10min30_bio.nc"
nc_file <- paste(nc_path, nc_name, sep="")
alpha <- read_ncdf(nc_file, var="alpha", proxy = FALSE)
```

List alpha to show contents of the object.

```{r alpha-plot-RMarkdown-5 }
# list alpha
alpha
```

Convert the `stars` object to an `sf` object:

```{r alpha-plot-RMarkdown-6 }
# convert stars to sf
alpha_sf <- st_as_sf(alpha, as_points = TRUE)
alpha_sf
plot(alpha_sf, pch = 16, cex = 0.3)
```

# Plot the data #

## Setup ##

Do some setting up befor plotting.

```{r alpha-plot-RMarkdown-7 }
# setup for plotting alpha
# make a data.frame
lon <- st_coordinates(alpha_sf)[,1]
lat <- st_coordinates(alpha_sf)[,2]
alpha <- as.vector(alpha_sf)
alpha_df <- data.frame(lon, lat, alpha)
dim(alpha_df)
head(alpha_df)
```

Set axis labels or breaks:

```{r alpha-plot-RMarkdown-8 }
# set axis labels (breaks)
breaks_x <- c(seq(-180, 180, by = 60)) 
breaks_y <- c(seq(-90, 90, by = 30)) 
labels_x <- as.character(breaks_x) 
labels_y <- as.character(breaks_y)
```

## Plot alpha ##

Make a `{ggplot2}` maps of alpha.

```{r alpha-plot-RMarkdown-9 }
# ggplot2 map of alpha
ggplot() +
  geom_tile(data = alpha_df, aes(x = lon, y = lat, fill = alpha)) +
  scale_fill_gradient2(low = "brown", mid="white", high = "darkgreen", midpoint = 0.50) +
  geom_sf(data = world_otl_sf, col = "black", fill = NA) +
  coord_sf(xlim = c(-180, +175.0), ylim = c(-90, 90), expand = FALSE) +
  scale_x_continuous(breaks = breaks_x) +
  scale_y_continuous(breaks = breaks_y) +
  labs(x = "Longitude", y = "Latitude", title="Priestley-Taylor Coefficient (alpha) (AE/PE)", fill="alpha") +
  theme_bw()
```

# Discussion #

(A few paragraphs on map patterns, trends, etc.)

Example 5 – A multi-page web site

Important To replicate this example, it would be best to creat an entirely new project in a differnt folder than the one you may have been working in.

• Script files:
  • [index.Rmd]
  • [intro.Rmd]
  • [alpha_plot_RMarkdown_Site.Rmd]
  • [about.Rmd]
  • [README.md]
  • [_site.yml]
• Output is a multi-page website.

A multi-page R Markdown website, as the name suggests, includes a collection of *.Rmd files (that are each knit to create *.html files, plus a support file (_site.yml) that controls the navigation bar layout. A sixth file is README.md file that appears on the main page of the GitHub repository. The steps below will create a minimalist multi-page web site. The site will include an index.html page with a brief overview, a “Topics” tab with two pages, one an introduction, and the other being the “Raster mapping” page, and an “About” tab, implemented by four *.Rmd files (plus the _site.yml file). Although R Studio contains great script-editing features, it’s a little clunky as a text editor compared to Markdown-specific editors. (In practice, if there is a lot of text to compose, edit, and format (as is the case with this page), it may be more efficient to do that in a Markdown editor, or VS Code, previewing while you go, and then include the contents of the *.md file created by the editor in a *.Rmd file using the Knitr “child document” chunk option (e.g. {r child="index.md"})).

Start by creating an R Markdown file that will produce a single-page .html file as output, which will be incorporated into the web site later:

1. Create a new R Markdown file in the projects folder (File > New File > R Markdown);
2. Delete the sample code in the new page;
3. Copy the contents of e.g. index.Rmd
4. Edit the paths in the script file as appropriate in alpha_plot_RMarkdown_Site.Rmd;
5. Knit the project to run the code and create the various *.html files.
6. Commit the changes, and push the website to the GitHub repository (explained elsewhere).

Here is the code:

[index.Rmd]

  
---
title: "GEOG4/590: R for Earth-System Science"
output: 
  html_document:
    fig_caption: no
    number_sections: no
    toc: no
    toc_float: false
    collapsed: no
---

```{r set-options, echo=FALSE}
options(width = 105)
knitr::opts_chunk$set(dev='png', dpi=300, cache=TRUE)
pdf.options(useDingbats = TRUE)
```

## Project web page for GEOG 4/595 *R for Earth-System Science* ##
    
Topics covered here include:

- An introduction to the project
- A simple example of plotting a raster slice
- (more to come…)

[intro.Rmd]

  
---
title: "Introduction to the project"
output: 
  html_document:
    fig_caption: no
    number_sections: no
    toc: no
    toc_float: false
    collapsed: no
---

```{r set-options, echo=FALSE}
options(width = 105)
knitr::opts_chunk$set(dev='png', dpi=300, cache=TRUE)
pdf.options(useDingbats = TRUE)
```

The visualization developed here uses the `{terra}` and `{rasterVis}` packages to map the global 
pattern of alpha, calculated using the CRU CL2 climate data set.  The maps also include a 
world outline with coastlines and country borders.

More introductory material...

[alpha_plot_RMarkdown_Site.Rmd]

  
---
title:  Raster mapping
output:
  html_document:
    css: html-md-01.css
    fig_caption: yes
    highlight: haddock
    number_sections: yes
    theme: spacelab
    toc: yes
    toc_float: false
    collapsed: no
---

```{r set-options, echo=FALSE, strip.white=TRUE}
options(width = 105)
knitr::opts_chunk$set(dev='png', dpi=300, cache=TRUE)
pdf.options(useDingbats = TRUE)
```

# Introduction #

This RMarkdown document describes reading a netCDF file consisting of several bioclimatic variables, and plots one of them, `alpha`.

## Load packages ## 

```{r alpha-plot-RMarkdown_Site-1 }
# load libraries
library(sf)
library(stars)
library(ggplot2)
```

# Read data #

## World outline ##

### Read map data from the `{maps}` package ###

Read a map file of  world coastlines and countries, and convert to an `sf` object.

```{r alpha-plot-RMarkdown_Site-2 }
# world_sf
world_sf <- st_as_sf(maps::map("world", plot = FALSE, fill = TRUE))
world_otl_sf <- st_geometry(world_sf)
```

### Plot the world outline ###

```{r alpha-plot-RMarkdown_Site-3 }
# ggplot map of world_outline
ggplot() + 
  geom_sf(data = world_otl_sf, fill = NA, col = "blue") + 
  scale_x_continuous(breaks = seq(-180, 180, 30)) +
  scale_y_continuous(breaks = seq(-90, 90, 30)) +
  coord_sf(xlim = c(-180, +180), ylim = c(-90, 90), expand = FALSE) +
  theme_bw()
```

## Read alpha ##

Now read in alpha from a netCDF file of bioclimatic variables using stars.

```{r alpha-plot-RMarkdown_Site-4 }
# read alpha (AE/PE)
# change path as necessary
nc_path <- "/Users/bartlein/Projects/RESS/data/nc_files/"
nc_name <- "cru10min30_bio.nc"
nc_file <- paste(nc_path, nc_name, sep="")
alpha <- read_ncdf(nc_file, var="alpha", proxy = FALSE)
```

List alpha to show contents of the object.

```{r alpha-plot-RMarkdown_Site-5 }
# list alpha
alpha
```

Convert the `stars` object to an `sf` object:

```{r alpha-plot-RMarkdown_Site-6 }
# convert stars to sf
alpha_sf <- st_as_sf(alpha, as_points = TRUE)
alpha_sf
plot(alpha_sf, pch = 16, cex = 0.3)
```

# Plot the data #

## Setup ##

Do some setting up befor plotting.

```{r alpha-plot-RMarkdown_Site-7 }
# setup for plotting alpha
# make a data.frame
lon <- st_coordinates(alpha_sf)[,1]
lat <- st_coordinates(alpha_sf)[,2]
alpha <- as.vector(alpha_sf)
alpha_df <- data.frame(lon, lat, alpha)
dim(alpha_df)
head(alpha_df)
```

Set axis labels or breaks:

```{r alpha-plot-RMarkdown_Site-8 }
# set axis labels (breaks)
breaks_x <- c(seq(-180, 180, by = 60)) 
breaks_y <- c(seq(-90, 90, by = 30)) 
labels_x <- as.character(breaks_x) 
labels_y <- as.character(breaks_y)
```

## Plot alpha ##

Make a `{ggplot2}` maps of alpha.

```{r alpha-plot-RMarkdown_Site-9 }
# ggplot2 map of alpha
ggplot() +
  geom_tile(data = alpha_df, aes(x = lon, y = lat, fill = alpha)) +
  scale_fill_gradient2(low = "brown", mid="white", high = "darkgreen", midpoint = 0.50) +
  geom_sf(data = world_otl_sf, col = "black", fill = NA) +
  coord_sf(xlim = c(-180, +175.0), ylim = c(-90, 90), expand = FALSE) +
  scale_x_continuous(breaks = breaks_x) +
  scale_y_continuous(breaks = breaks_y) +
  labs(x = "Longitude", y = "Latitude", title="Priestley-Taylor Coefficient (alpha) (AE/PE)", fill="alpha") +
  theme_bw()
```

# Discussion #

(A few paragraphs on map patterns, trends, etc.)

[about.Rmd]

  
---
title: "GEOG 4/590:  R for Earth-System Science"
output: 
  html_document:
    fig_caption: no
    number_sections: no
    toc: no
    toc_float: false
    collapsed: no
---

```{r set-options, echo=FALSE}
options(width = 105)
knitr::opts_chunk$set(dev='png', dpi=300, cache=TRUE)
pdf.options(useDingbats = TRUE)
```
P.J. Bartlein  
Dept. Geography  
Univ. Oregon  
bartlein@uoregon.edu

The GitHub repository for this web site is at:  
[https://github.com/pjbartlein/geog490](https://github.com/pjbartlein/geog490)

[README.md]

  
# geog490project
GEOG 4/590 *R for Earth-System Science*
Project Web Page Repository

The web page is at:  [https://pjbartlein.github.io/geog490project/](https://pjbartlein.github.io/geog490project/)

[_site.yml]

  
name: GEOG 4/590
navbar:
  title: "Project Web Page:  R for Earth-System Science"
  left:
  - text: Topics
    menu:
    - text: "Introduction"
      href: intro.html
    - text: "Raster mapping example"
      href: alpha_plot_RMarkdown_Site.html
  right:
  - text: "About"
    href: about.html
output:
  html_document:
    theme: cosmo
    version: 4
    highlight: haddock
    css: html-md-01.css
    fig_caption: no
    number_sections: yes
    toc: yes
    toc_float: no
    collapsed: no
    lib_dir: site_libs
    self_contained: no
output_dir: docs

The GitHub repository

The knitr() package is quite fussy about formatting of the _site.yml file so check it first in the case of later errors.

In RStudio, the “build tools” needed to create the web site will need to be configured. On the RStudio menu, click on Build. If there is a menu choice that says “Install Tools” do that first, otherwise click on “Configure Build Tools…” A “Project Options” dialog will open. On the “Project build tools:” dropdown box, select “Website” The initial choices are probably fine, with the “Site directory” set to “(Project Root)” and the “Preview” and “Re-knit” checkboxes checked. Upon clicking OK, a “Build” tab should appear in the upper-right pane. If it doesn’t, restart R Studio (Session > Restart R). Select the build tab, and click on “Build Website”.

At this point, the project folder should contain:

/.git
/.Rproj.user
/docs
/alpha_plot_RMarkdown_Site_cache
/alpha_plot_RMarkdown_Site_files

html-md-01.css

.gitignore
.RData
.Rhistory

about.Rmd
index.Rmd
intro.Rmd
alpha_plot_RMarkdown_Site.Rmd

geog490.Rproj

README.md
_site.yml

… and the docs folder,

/site_libs
/plot_alpha_RMarkdown_Site_files

html-md-01.css

about.html
index.html
intro.html
alpha_plot_RMarkdown_Site.html
README.html

The website should be viewable at: https://pjbartlein.github.io/geog490/index.html (the project’s web page)

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