Merge remote-tracking branch 'origin/development'

.github/.gitignore

@@ -0,0 +1,2 @@
+*.html
+

.github/workflows/render-module-rmd.yaml

@@ -0,0 +1,74 @@
+on:
+  pull_request:
+    branches:
+      - master
+      - development
+  push:
+    branches:
+      - master
+      - development
+    paths:
+      - .github/workflows/render-module-rmd.yaml
+      - Biomass_regeneration.Rmd
+      - Biomass_regeneration.R
+
+name: Render module Rmd
+
+jobs:
+  render:
+    if: "!contains(github.event.commits[0].message, '[skip-ci]')"
+    name: Render module Rmd
+    runs-on: ubuntu-20.04
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          Ncpus: 2
+
+      - name: Install additional system dependencies
+        run: |
+          sudo apt-get install -y \
+            libcurl4-openssl-dev \
+            libgdal-dev \
+            libgeos-dev \
+            libgit2-dev \
+            libglpk-dev \
+            libmagick++-dev \
+            libproj-dev \
+            libudunits2-dev \
+            libxml2-dev \
+            python3-gdal
+
+      - uses: PredictiveEcology/actions/install-Require@v0
+        with:
+          GitTag: '5c44205bf407f613f53546be652a438ef1248147'
+
+      - uses: PredictiveEcology/actions/install-SpaDES@v0
+
+      - uses: PredictiveEcology/actions/install-Rmd-pkgs@v0
+
+      - name: Install additional packages
+        run: |
+          options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest", CRAN = "https://cran.rstudio.com"))
+          Require::Require(c("PredictiveEcology/LandR@development"), require = FALSE)
+        shell: Rscript {0}
+
+      - name: Render module Rmd
+        run: |
+          rmarkdown::render("Biomass_regeneration.Rmd", encoding = "UTF-8")
+        shell: Rscript {0}
+
+      - name: Commit results
+        run: |
+          git config user.email "[email protected]"
+          git config user.name "GitHub Actions"
+          git commit Biomass_regeneration.html -m 'Re-build Biomass_regeneration.Rmd' || echo "No changes to commit"
+          git push https://${{github.actor}}:${{secrets.GITHUB_TOKEN}}@github.com/${{github.repository}}.git HEAD:${{github.ref}} || echo "No changes to commit"

.gitignore

@@ -2,3 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
+
+Biomass_regeneration2.Rmd

Biomass_regeneration.Rmd

@@ -1,11 +1,48 @@
 ---
-title: "Biomass_regeneration"
-author: ""
-date: "20 October 2019"
-output: pdf_document
+title: "LandR _Biomass_regeneration_ Manual"
+subtitle: "v.`r SpaDES.core::moduleMetadata(module = 'Biomass_regeneration', path = '..')$version`"
+date: "Last updated: `r Sys.Date()`"
+output:
+  bookdown::html_document2:
+    toc: true
+    toc_float: true
+    theme: sandstone
+    number_sections: false
+    df_print: paged
+    keep_md: yes
+editor_options:
+  chunk_output_type: console
+  bibliography: citations/references_Biomass_regeneration.bib
+link-citations: true
+always_allow_html: true
 ---
 
-# Overview
+<!-- the following are text references used in captions for LaTeX compatibility -->
+(ref:Biomass-regeneration) *Biomass_regeneration*
+
+```{r setup-Biomass-regeneration, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE, eval = FALSE, results = "hold") ## change to eval = TRUE if all chunks are to be evaluated
+
+if (!require(dplyr)) {
+  install.packages("dplyr")
+  library(dplyr)
+}
+
+dir.create("figures", showWarnings = FALSE)
+
+download.file(url = "https://img.shields.io/badge/Made%20with-Markdown-1f425f.png",
+              destfile = "figures/markdownBadge.png",
+              mode = 'wb')
+```
+
+#### Authors:
+
+`r paste(as.character(SpaDES.core::moduleMetadata(module = "Biomass_regeneration", path = '..')$authors), sep = ', ')`
+<!-- ideally separate authors with new lines, '\n' not working -->
+
+## Module Overview
+
+### Module summary
 
 Biomass_regeneration is a SpaDES module that simulates post-disturbance regeneration mechanisms for Biomass_core.
 As such, this module is mostly based on the post-disturbance regeneration mechanisms present in LANDIS-II Biomass Succession v3.2.1 extension (see [LANDIS-II Biomass Succession v3.2 User Guide](https://github.com/LANDIS-II-Foundation/Extension-Biomass-Succession/blob/master/docs/LANDIS-II%20Biomass%20Succession%20v3.2%20User%20Guide.docx) and [Scheller and Mladenoff (2004)](https://pdfs.semanticscholar.org/4d38/d0be6b292eccd444af399775d37a757d1967.pdf).
@@ -14,7 +51,8 @@ Post-fire mortality behaves in a stand-replacing fashion, i.e. should a pixel be
 
 As for post-fire regeneration, the module first evaluates whether any species present prior to fire are serotinous.
 If so, these species will germinate depending on light conditions and their shade tolerance, and depending on their (seed) establishment probability (i.e. germination success) in that pixel.
-The module then evaluates if any species present before fire are capable of resprouting. If so the model growth these species depending, again, on light conditions and their shade tolerance, and on their resprouting probability (i.e. resprouting success).
+The module then evaluates if any species present before fire are capable of resprouting.
+If so the model growth these species depending, again, on light conditions and their shade tolerance, and on their resprouting probability (i.e. resprouting success).
 For any given species in any given pixel, only serotiny or resprouting can occur.
 Hence, species that are capable of both will only resprout if serotiny was not activated.
 
@@ -30,63 +68,46 @@ According to the manual:
 This is no longer the case in Biomass_regeneration, where both serotinity and resprouting can occur in the same pixel, although not for the same species.
 We feel that this is more realistic ecologically, as resprouters will typically regenerate faster  after a fire, often shading serotinous species and creating interesting successional feedbacks (e.g. light-loving serotinous species having to "wait" for canopy gaps to germinate).
 
-## General flow of Biomass_regeneration processes - fire disturbances only
+### General flow of Biomass_regeneration processes - fire disturbances only
 
 1. Removal of biomass in disturbed, i.e. burnt, pixels
 2. Activation of serotiny for serotinous species present before the fire
 3. Activation of resprouting for resprouter species present before the fire and for which serotiny was not activated
 4. Establishment/growth of species for which serotiny or resprouting were activated
 
-# Usage
-
-```{r module_usage}
-library(SpaDES)
+### Module inputs and parameters
 
-setPaths()
-getPaths() # shows where the 4 relevant paths are
+Table \@ref(tab:moduleInputs-Biomass-regeneration) shows the full list of module inputs.
 
-times <- list(start = 0, end = 10)
-
-parameters <- list(
-  #.progress = list(type = "text", interval = 1), # for a progress bar
-  ## If there are further modules, each can have its own set of parameters:
-  #module1 = list(param1 = value1, param2 = value2),
-  #module2 = list(param1 = value1, param2 = value2)
-)
-modules <- list("Biomass_regeneration")
-objects <- list()
-inputs <- list()
-outputs <- list()
-
-mySim <- simInit(times = times, params = parameters, modules = modules,
-                 objects = objects)
-
-mySimOut <- spades(mySim)
+```{r moduleInputs-Biomass-regeneration, echo = FALSE, eval = TRUE, message = FALSE, warning = FALSE}
+df_inputs <- SpaDES.core::moduleInputs("Biomass_regeneration", "..")
+knitr::kable(df_inputs,
+             caption = "List of (ref:Biomass-regeneration) input objects and their description.") %>%
+  kableExtra::kable_styling(latex_options = "scale_down", full_width = TRUE)
 ```
 
-# Events
-
-Describe what happens for each event type.
-
-## Plotting
+Summary of user-visible parameters (Table \@ref(tab:moduleParams-Biomass-regeneration)):
 
-Write what is plotted.
-
-## Saving
-
-Write what is saved.
+```{r moduleParams-Biomass-regeneration, echo = FALSE, eval = TRUE, message = FALSE, warning = FALSE}
+df_params <- SpaDES.core::moduleParams("Biomass_regeneration", "..")
+knitr::kable(df_params, caption = "List of (ref:Biomass-regeneration) parameters and their description.") %>%
+  kableExtra::kable_styling(latex_options = "scale_down", full_width = TRUE)
+```
 
-# Data dependencies
+### Module outputs
 
-## Input data
+Description of the module outputs (Table \@ref(tab:moduleOutputs-Biomass-regeneration)).
 
-How to obtain input data, and a description of the data required by the module.
-If `sourceURL` is specified, `downloadData("Biomass_regeneration", "path/to/modules/dir")` may be sufficient.
+```{r moduleOutputs-Biomass-regeneration, echo = FALSE, eval = TRUE, message = FALSE, warning = FALSE}
+df_outputs <- SpaDES.core::moduleOutputs("Biomass_regeneration", "..")
+knitr::kable(df_outputs, caption = "List of (ref:Biomass-regeneration) outputs and their description.") %>%
+  kableExtra::kable_styling(latex_options = "scale_down", full_width = TRUE)
+```
 
-## Output data
+### Links to other modules
 
-Description of the module outputs.
+Primarily used with the LandR Biomass suite of modules, namely [Biomass_core](https://github.com/PredictiveEcology/Biomass_core).
 
-# Links to other modules
+## Getting help
 
-Describe any anticipated linkages to other modules.
+- <https://gitter.im/PredictiveEcology/LandR_Biomass>