---
title: "Finding other modules"
author: "Eliot McIntire"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Finding other modules}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
editor_options:
  chunk_output_type: console
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = TRUE
)

SuggestedPkgsNeeded <- c("SpaDES.core", "igraph", "visNetwork", "ellipsis", "terra", "raster")
hasSuggests <- all(sapply(SuggestedPkgsNeeded, require, character.only = TRUE, quietly = TRUE))
useSuggests <- !(tolower(Sys.getenv("_R_CHECK_DEPENDS_ONLY_")) == "true")

scalls <- sys.calls()
a <- format(scalls)

# Run everything during `pkgdown::build_*` (which uses rmarkdown::render)
knitr::opts_chunk$set(eval = hasSuggests && useSuggests &&
                        Sys.info()["user"] == "emcintir" && 
  any(grepl("rmarkdown::render", a)))# && interactive())

options(Ncpus = 1)
if (Sys.info()["user"] == "emcintir") {
  knitr::opts_knit$set(root.dir = Require::checkPath(file.path("c:/Eliot/tmp", "listModules"), create = TRUE ))
} else { 
  knitr::opts_knit$set(root.dir = Require::checkPath(file.path(tempdir(), "listModules"), create = TRUE ))
}

knitr::opts_chunk$set(fig.width=9, fig.height=7) # sets html figure height and width

# options(Require.clonePkgs = TRUE)

```

```{r setCRAN,echo=FALSE}
## cleanup / restore state
if (is.null(getOption("repos")) || !"CRAN" %in% names(getOption("repos"))) {
  options(repos = c(CRAN = "https://cloud.r-project.org"))
}
```

```{r install-spades-project}
if (!require("SpaDES.project")) {
  {install.packages("SpaDES.project", repos = c("predictiveecology.r-universe.dev", getOption("repos")))
   require("SpaDES.project")}
}
```



## Find other's modules

One powerful aspect of `SpaDES` is the ability to connect to other people's modules. It can be challenging to know where other modules are and what they do. Using the `listModules` function.

The command sequence we will use is:

- `listModule` to identify which modules exist on cloud storage systems,
- `getModules` to bring them (or a subset) to your local machine,
- `moduleDependencies` to do the metadata analysis, 
- `moduleDependenciesToGraph` converts them to a graph, 
- `moduleDependenciesToGraph` to visualize that graph.

A user can use only some of these steps if they do not want to produce the visuals.

### A small selection of SpaDES modules

#### **Some Biomass_* modules**
This will search the `PredictiveEcology` github.com repository for any SpaDES module whose name has `Biomass_species`, `Biomass_core`, `Biomass_regen` in it. The search will find any module that contains those keywords, i.e., `Biomass_regen` will find `Biomass_regeneration`

```{r clean13,echo=FALSE}
## cleanup / restore state
# SpaDES.project::.teardownProject(out$paths, origLibPaths)
```

```{r listModulesSmall,result='hide',message=FALSE}
Account <- "PredictiveEcology"
grepListShort <- "Biomass_species|Biomass_core|Biomass_regen"
mods <- listModules(grepListShort, accounts = Account)

modPath <- normPath(tempdir2())
getModule(mods, modulePath = modPath)

DT <- moduleDependencies(mods, modulePath = modPath)
graph <- moduleDependenciesToGraph(DT)
(vn <- PlotModuleGraph(graph))
```

#### **FireSense modules**

```{r FireSense,result='hide',message=FALSE}
Account <- "PredictiveEcology"
grepListShort <- "fireSense"
mods <- listModules(grepListShort, accounts = Account)

getModule(mods, modulePath = modPath)

DT <- moduleDependencies(mods, modulePath = modPath)
graph <- moduleDependenciesToGraph(DT)
(vn <- PlotModuleGraph(graph))
```


#### **LandR modules**

```{r LandR,result='hide',message=FALSE}
Account <- "PredictiveEcology"
grepListShort <- "Biomass_|LandR"
mods <- listModules(grepListShort, accounts = Account)

getModule(mods, modulePath = modPath)

DT <- moduleDependencies(mods, modulePath = modPath)
graph <- moduleDependenciesToGraph(DT)
(vn <- PlotModuleGraph(graph))
```



### A larger selection of "known" SpaDES modules

```{r listModulesAll,result='hide',message=FALSE,error=FALSE,warning=FALSE}
# Can do same, but with long list -- not done here -- can try
accountsListLong <- c("PredictiveEcology", "ianmseddy", "achubaty",
                       "FOR-CAST", "eliotmcintire", "tati-micheletti", "CeresBarros")
grepListLong <- c("Biomass", "WBI", "LandR", "fireSense", "CBM",
                  "LandMine", "LandWeb", "NRV", #"scfm",
                  "priority", "fire",
                  "dataPrep", "DataPrep", "RoF", "Ontario", "ROF")
modsLong <- listModules(grepListLong, accounts = accountsListLong)

# pass to listModules for much larger figure
getModule(modsLong, modulePath = modPath)

DT <- moduleDependencies(modsLong, modulePath = modPath)
graph <- moduleDependenciesToGraph(DT)
(vn <- PlotModuleGraph(graph))


```


### All SpaDES modules in a set of known accounts

This takes much longer to run as it scans all (open) repositories for each element of `accounts`. It will search for a relatively "lightweight" indicator of a SpaDES module, namely, a file at the top level that has the same name as the repository, but whose file extension is `.R`.

```{r listModulesReallyAll,result='hide',message=FALSE,error=FALSE,warning=FALSE,fig.height=12}
# Can do same, but with long list -- not done here -- can try
accountsListLong <- c("PredictiveEcology", "ianmseddy", "achubaty",
                       "FOR-CAST", "eliotmcintire", "tati-micheletti", "CeresBarros")
modsLong <- listModules(accounts = accountsListLong)

# pass to listModules for much larger figure
getModule(modsLong, modulePath = modPath)

DT <- moduleDependencies(modsLong, modulePath = modPath)
graph <- moduleDependenciesToGraph(DT)
(vn <- PlotModuleGraph(graph))


```