Fill in some gaps in vignettes

_pkgdown.yml

@@ -5,3 +5,4 @@ repo:
     branch: 38-convert-to-r-pkg
 template:
   bootstrap: 5
+  bootswatch: yeti

pkgdown/extra.css

@@ -5,10 +5,10 @@
   font-size: 1.4rem;
 }
 
-/* h1 { */
-/*   font-size: 1.7rem; */
-/*   width: max-content; */
-/*   min-width: max-content; */
-/*   margin: 0; */
-/*   padding: 1.0rem 1.0rem 0.8rem 0; */
-/* } */
+h1 {
+  font-size: 2.2rem;
+  width: max-content;
+  min-width: max-content;
+  margin: 0;
+  padding: 0.8em 0;
+}

vignettes/config.qmd

@@ -53,23 +53,23 @@ A user-specific `.Renviron` would typically be stored at:
 
 - Windows:
 
-    ````
-    C:\Users\YourUsername\.Renviron
-    ````
+```
+C:\Users\YourUsername\.Renviron
+```
 
     Ensure the file name is exactly ".Renviron" (without any file extension like
     .txt)
 
 - Linux/macOS:
 
-    ````
-    ~/.Renviron
-    ````
+```
+~/.Renviron
+```
 
 Create this file if necessary. From within R, the `usethis` package can do this
 for you:
 
-```
+```{r, eval=FALSE}
 # Create a new user-level .Renviron file, or open an existing one for editing
 usethis::edit_r_environ("user")
 # Or, as this is the default:
@@ -86,7 +86,7 @@ contain such entries by default.)
 The `usethis` package supports creation/editing of a project-level `.Renviron`
 file too:
 
-```
+```{r, eval=FALSE}
 # Create a new project-level .Renviron file, or open an existing one for editing
 usethis::edit_r_environ("project")
 ```
@@ -99,19 +99,19 @@ effect. This can be achieved by doing one of the following:
 
 - Reload `.Renviron` in a running R session with, e.g.
 
-    ````
-    readRenviron("~/.Renviron")
-    ````
+```{r, eval=FALSE}
+readRenviron("~/.Renviron")
+```
 
     (where you shoul replace "~/.Renviron" with the appropriate path to your
     `.Renviron` file if it's not in your home directory)
 
 - A temporary alternative to reloading `.Renviron` is to manually override
   specific environment variables within the current R session:
 
-    ```
-    Sys.setenv(VAR_NAME = "value")
-    ```
+```{r, eval=FALSE}
+Sys.setenv(VAR_NAME = "value")
+```
 
     This can be helpful for testing specific changes without modifying the
     environment file.
@@ -120,11 +120,13 @@ effect. This can be achieved by doing one of the following:
 
 System environment variables for the `dimex` package start with 'DIMEX_'.
 
-[TODO: Add info about the act, ref and test root paths]
+```{=comment}
+[TODO: Add info about the main, ref and test root paths]
+```
 
-| Environment | Variable name   | Description                                      |
-|:------------|:----------------|:-------------------------------------------------|
-| act         | DIMEX_STORE     | Root path of the dimex Data and Output           |
+| Environment | Variable name   | Description                                        |
+|:------------|:----------------|:---------------------------------------------------|
+| main         | DIMEX_STORE     | Root path of the dimex Data and Output            |
 | ref         | DIMEX_STORE_REF | Root path of the dimex 'reference' Data and Output |
 
 ## The `config` object for package-level configuration {#pkg-config}
@@ -138,6 +140,8 @@ basis.
 
 ## The `config` template {#config-template}
 
+See also [development](#config-template).
+
 To create a default configuration for the first time and save it to your
 personal system, run:
 
@@ -166,7 +170,7 @@ so any custom changes would then need to be *manually re-applied*.
 
 ## Default `config` values and overriding them {#default-config-values}
 
-Defaults:
+### Defaults
 
 [TODO: Describe defaults]
 

vignettes/development.qmd

@@ -28,68 +28,85 @@ library(dimex)
 ## About this vignette
 
 This vignette deals with how to use the `dimex` package as a developer. See also
-the [introduction to dimex](dimex.html) and [configuration](config.html)
-vignettes.
+the [Get started](dimex.html) and [Configuration](config.html) vignettes.
+
+## Installation {#install-dev}
+
+Clone the GitHub repository:
+
+```
+$ git clone https://github.com/UoMResearchIT/SPFFinalReport.git
+```
 
 ## Setup
 
 For a development environment:
 
 ### devtools
 
-1.  Ensure `devtools` is installed. <br>
-    From the `R` console:
+1.  Ensure `devtools` is installed:
 
+    ```{r eval=FALSE}
+    install.packages("devtools")
     ```
-    > install.packages("devtools")
+
+2.  Ensure required packages are installed:
+
+    ```{r eval=FALSE}
+    install.packages(c("cli", "DescTools", "dplyr", "ggplot2", "gridExtra",
+                       "haven", "lubridate", "magrittr", "openair", "plyr",
+                       "proxy", "purrr", "rappdirs", "raster", "readr",
+                       "reshape2", "scales", "sf", "sp", "stringr",
+                       "truncnorm", "yaml"))
     ```
 
-2.  Ensure required packages are installed. <br>
-    [TODO: Implement `renv` and add setup instructions]
+```{=comment}
+[TODO: Implement `renv` and add setup instructions]
+```
 
-3.  See the [configuration](config.html) vignette for configuration information.
+3.  See the [Configuration](config.html) vignette for configuration information.
 
 ### Some useful dev commands
 
 These commands should be executed from the `R` console.
 
 (Note that when `devtools` is installed, the following commands are usually
 bound to keyboard shortcuts in RStudio; these are shown in the comments where
-applicable)
+applicable.)
 
--  Load the development version of the package:
+- Load the development version of the package:
 
-    ```
-    # Ctrl/Cmd + Shift + L
-    > devtools::load_all(".")
-    ```
+```{r eval=FALSE}
+# Ctrl/Cmd + Shift + L
+devtools::load_all(".")
+```
 
 -  Run the automated test suite:
 
-    ```
-    # Ctrl/Cmd + Shift + T
-    > devtools::test(".")
-    ```
+```{r eval=FALSE}
+# Ctrl/Cmd + Shift + T
+devtools::test(".")
+```
 
 -  Create package documentation:
 
-    ```
-    # Ctrl/Cmd + Shift + D
-    > devtools::document(roclets = c('rd', 'collate', 'namespace'))
-    ```
+```{r eval=FALSE}
+# Ctrl/Cmd + Shift + D
+devtools::document(roclets = c('rd', 'collate', 'namespace'))
+```
 
 -  Build the package vignettes:
 
-    ```
-    > devtools::build_vignettes()
-    ```
+```{r eval=FALSE}
+devtools::build_vignettes()
+```
 
 -  Run a package check:
 
-    ```
-    # Ctrl/Cmd + Shift + E
-    > devtools::check()
-    ```
+```{r eval=FALSE}
+# Ctrl/Cmd + Shift + E
+devtools::check()
+```
 
 - Test the current file:
 
@@ -145,14 +162,14 @@ applicable)
 - To temporarily set a specific high-level data test to run in the current R
   session, run (for e.g.):
 
-  ```
+  ```{r eval=FALSE}
   # Set the high-level data test for step "1a" to run
   Sys.setenv(DIMEX_RUN_HLDT_1A = "true")
   ```
 
   To reverse this, do one of the following:
 
-  ```
+  ```{r eval=FALSE}
   Sys.setenv(DIMEX_RUN_HLDT_1A = "false")
   # Or:
   Sys.unsetenv("DIMEX_RUN_HLDT_1A")
@@ -161,19 +178,19 @@ applicable)
 - To temporarily set all the high-level data tests to run in the current R
   session, use:
 
-  ```
+  ```{r eval=FALSE}
   Sys.setenv(DIMEX_RUN_ALL_HLDT = "true")
   ```
 
   To reverse this, do one of the following:
 
-  ```
+  ```{r eval=FALSE}
   Sys.setenv(DIMEX_RUN_ALL_HLDT = "false")
   # Or:
   Sys.unsetenv("DIMEX_RUN_ALL_HLDT")
   ```
-  
-### The config template
+
+### The config template {#config-template}
 
 To update the config template, edit the functions [generate_cfg_template()] and
 [get_cfg_template_keys()].
@@ -188,10 +205,13 @@ Note NB: <br>
 Changing the template will necessitate updating user config files that have
 already been created.
 
-<!-- [TODO: When a conversion utility has been implemented, update the following] -->
+```{=comment}
+[TODO: When a conversion utility has been implemented, update the following]
+```
 **There is currently no mechanism to convert the format of a user config file**
 *so until such time as this can be implemented, any local changes to a user
-config will need to be* **manually updated**.
+config will need to be* **manually applied**.
+
 To update the user config, run:
 ```{r, eval=FALSE}
 # NB: The following will *overwrite* any local changes to the user config!

vignettes/dimex.qmd

@@ -35,20 +35,20 @@ This package implements the DIMEX model. The package derived from the
 SPFFinalReport code (created for the case study and report for the final SPF
 reporting period).
 
-See also the [configuration](config.html) and [development](development.html)
+See also the [Configuration](config.html) and [Development](development.html)
 vignettes.
 
-### Installation
+### Installation {#install}
 
-[TODO: TBC]
+To install the development version of `dimex` from GitHub:
 
-```{=comment}
-<!-- You can install the development version of `dimex` from GitHub with: -->
-
-<!-- # install.packages("remotes") -->
-<!-- remotes::install_github("path/dimex") -->
+```{r, eval = FALSE}
+# install.packages("remotes")
+remotes::install_github("https://github.com/UoMResearchIT/SPFFinalReport")
 ```
 
+See [dimex](#install-dev) for doing development on the `dimex` package.
+
 ## Data workflow
 
 ### Data phases
@@ -82,13 +82,11 @@ For each of these data wrangling phases, there are three possible environments:
   - small enough to use for unit/integration tests
   - can be reliably reproduced
 
-## Getting started
-
-### Configuration
+## Configuration
 
 See [configuration](config.html) for configuration information.
 
-### Running the pipeline
+## Workflow: Running the pipeline
 
 The main entry point for running the code is the
 [run_workflow()](../reference/run_workflow.html)
@@ -114,15 +112,18 @@ run_workflow("4a, 4b")
 run_workflow(banner_only = TRUE)
 
 # Run steps 4a and 4b only, with the specified config
-# See the [configuration](config.html) vignette for information on
+# See the [Configuration](config.html) vignette for information on
 # how to create a non-default config
-# # [TODO: Show example of creating a config]
-# # cfg = ...
-# # cfg_overrides = ...
 run_workflow("4a, 4b", cfg = cfg, cfg_overrides = cfg_overrides)
 ```
 
+```{=comment}
+# [TODO: Show example of creating a config in the code chunk above]
+# cfg = ...
+# cfg_overrides = ...
+```
+
 ## Development
 
 For doing development work on the `dimex` package, see the
-[development](development.html) vignette.
+[Development](development.html) vignette.