# Gap analysis workflow for multiple species

This workflow demonstrates how to import your own point data (occurrences) and SDMs (rasters), check all inputs, and run the full gap analysis for multiple species using the GapAnalysis R package. We provide a general approach using a for-loop for processing and storing results for multiple species. Example Cucurbita data is provided within the package library.

> Note: This vignette recommends R version 4.5 or above. Windows users are also recommended to have Rtools 4.5 or above installed.

For each species, the workflow:

1. Runs SRSex on all records.
2. Checks inputs (occurrences, rasters, protected areas, ecoregions).
3. Runs gap analysis metrics.
4. Stores results as a table to an output excel file.
5. Creates a conservation priority summary figure as an output png file.
6. Generates interactive leaflet maps for both ex-situ and in-situ conservation as output HTML files.

At script end, the user is prompted to save the workflow by knitting to output HTML.

## Download GapAnalysis repository (ALTERNATIVE)

Copy the GapAnalysis GitHub repository locally as an alternative method to source functions and load example data if the GapAnalysis R package does not install properly in the step above. See the GitHub resource page on copying a repository.

> Easiest method: Download and extract the GapAnalysis repository. Select the green [Code] button on the main page to download as a ZIP.

> You can also clone the repository if you have a GitHub account.

## Data preparation

If you downloaded the repository locally, source functions and load data by removing the hashes below. Your specific path will differ based on your working directory and the relative path to the downloaded repository.

    # ── Load libraries ─────────────────────────────────────────────────────────────
    library(GapAnalysis)
    library(dplyr)

    ##
    ## Attaching package: 'dplyr'

    ## The following objects are masked from 'package:stats':
    ##
    ##     filter, lag

    ## The following objects are masked from 'package:base':
    ##
    ##     intersect, setdiff, setequal, union

    library(tidyr)
    library(stringr)
    library(terra)

    ## terra 1.9.34

    ##
    ## Attaching package: 'terra'

    ## The following object is masked from 'package:tidyr':
    ##
    ##     extract

    library(leaflet)
    library(openxlsx)
    library(ggplot2)
    library(ggtext)
    library(cowplot)
    library(htmltools)
    library(htmlwidgets)
    library(kableExtra)

    ##
    ## Attaching package: 'kableExtra'

    ## The following object is masked from 'package:dplyr':
    ##
    ##     group_rows

    # ── Set outputs folder ────────────────────────────────────────────────────────
    # NOTE: This path must match the path set in the knit: field in the YAML header
    # All files will be saved here. Update both locations if changing the path, e.g.:
    #outputs_folder <- "C:/Users/you/Desktop/GapAnalysis/outputs"
    outputs_folder <- "outputs"
    if (!dir.exists(outputs_folder)) dir.create(outputs_folder)

    # ── Source functions from GapAnalysis repo (alternative method) ───────────────
    #files <- list.files("R", pattern = "\\.[rR]$", full.names = TRUE)
    #for (f in files) source(f)

    # ── Load data from GapAnalysis repo (alternative method) ─────────────────────
    #load("data/CucurbitaData.rda")      # Occurrence data
    #load("data/CucurbitaRasts.rda")     # Raster list
    #load("data/ProtectedAreas.rda")     # Protected areas raster
    #load("data/ecoregions.rda")         # Ecoregions data

    # ── Load your own data ────────────────────────────────────────────────────────
    # NOTE: To use your own occurrence data and SDM rasters, remove the hashes
    # below and update the file paths.
    #occData <- read.csv("path/to/your_occurrences.csv") # Local occurrence data
    #sdms <- list(                                  # Local rasters read in as list
    #   rast("path/to/species1_sdm.tif"),
    #   rast("path/to/species2_sdm.tif"))
    # NOTE: To download protected areas and ecoregions data locally, run getDatasets().
    # This requires an active internet connection.
    #getDatasets()          # Local download of protected areas and ecoregions data

    # ── Load example Cucurbita data (GapAnalysis library) ────────────────────────
    # NOTE: To use your own data, hash out the two lines below.
    occData <- CucurbitaData
    sdms    <- terra::unwrap(CucurbitaRasts)

    # ── Prepare spatial layers ────────────────────────────────────────────────────
    ecos     <- terra::vect(ecoregions)
    proAreas <- terra::unwrap(ProtectedAreas)

    # Standardize CRS across all spatial layers to prevent mismatch warnings
    target_crs <- "+proj=longlat +datum=WGS84"
    ecos     <- terra::project(ecos, target_crs)
    proAreas <- terra::project(proAreas, target_crs)

    # ── Prepare species list and SDM rasters ──────────────────────────────────────
    taxa    <- unique(occData$species)
    sdmList <- lapply(seq_along(taxa), function(i) {
      r <- sdms[[i]]
      if (terra::crs(r, proj = TRUE) != terra::crs(ecos, proj = TRUE)) {
        r <- terra::project(r, terra::crs(ecos))
      }
      r <- terra::subst(r, 0, NA)
      r[!(is.na(r) | r == 1)] <- NA
      r
    })
    names(sdmList) <- taxa

    # Confirm species names
    message("\nConfirm species for gap analysis:\n", paste(taxa, collapse = "\n"))

    ##
    ## Confirm species for gap analysis:
    ## Cucurbita_cordata
    ## Cucurbita_digitata
    ## Cucurbita_palmata

## Run gap analysis

Example gap analysis workflow using a named list and for-loop to process and store results for all species.

For details on each metric calculation, review the function documentation in the GapAnalysis R folder.

    results_list <- list()

    for (i in seq_along(taxa)) {
      taxon          <- taxa[i]
      occurrenceData <- occData[occData$species == taxon, ]
      sdm            <- sdms[[i]]

      if (terra::crs(sdm, proj = TRUE) != terra::crs(ecos, proj = TRUE)) {
        sdm <- terra::project(sdm, terra::crs(ecos))
      }
      sdm <- terra::subst(sdm, 0, NA)
      sdm[!(is.na(sdm) | sdm == 1)] <- NA

      # 1. Run SRSex first (on all records)
      srsex <- SRSex(taxon = taxon, occurrenceData = occurrenceData)

      # 2. Check inputs
      occurrences     <- checkOccurrences(csv = occurrenceData, taxon = taxon)
      if (!inherits(sdm, "SpatRaster")) stop("sdm is not a SpatRaster")
      sdm_checked     <- checksdm(sdm)
      proArea_cropped <- terra::crop(proAreas, terra::ext(sdm_checked))
      proArea_checked <- checkProtectedAreas(protectedArea = proArea_cropped,
                                             sdm           = sdm_checked)

      # Skip species if SDM raster has no values
      if (all(is.na(terra::values(sdm_checked)))) {
        message("Skipping ", taxon, ": SDM raster has no values.")
        next
      }

      # 3. Generate G buffers
      gBuffer <- generateGBuffers(
        taxon          = taxon,
        occurrenceData = occurrences$data,
        bufferDistM    = 50000
      )

      # 4. Ex-situ analysis
      grsex <- GRSex(taxon = taxon, sdm = sdm_checked, gBuffer = gBuffer)
      ersex <- ERSex(
        taxon          = taxon,
        sdm            = sdm_checked,
        occurrenceData = occurrences$data,
        gBuffer        = gBuffer,
        ecoregions     = ecos,
        idColumn       = "ECO_NAME",
        limitByPoints  = FALSE
      )
      fcsex <- FCSex(taxon = taxon, srsex = srsex, grsex = grsex, ersex = ersex)

      # 5. In-situ analysis
      srsin <- SRSin(
        taxon          = taxon,
        sdm            = sdm_checked,
        occurrenceData = occurrences$data,
        protectedAreas = proArea_checked
      )
      grsin <- GRSin(taxon = taxon, sdm = sdm_checked, protectedAreas = proArea_checked)
      ersin <- ERSin(
        taxon          = taxon,
        sdm            = sdm_checked,
        occurrenceData = occurrences$data,
        protectedAreas = proArea_checked,
        ecoregions     = ecos,
        idColumn       = "ECO_NAME",
        limitByPoints  = FALSE
      )
      fcsin   <- FCSin(taxon = taxon, srsin = srsin, grsin = grsin, ersin = ersin)
      fcsmean <- FCSc_mean(taxon = taxon, fcsin = fcsin, fcsex = fcsex)

      # 6. Store results
      results_list[[taxon]] <- list(
        srsex           = srsex,
        occurrences     = occurrences,
        sdm_checked     = sdm_checked,
        proArea_checked = proArea_checked,
        eco_checked     = ecoregions,
        grsex           = grsex,
        ersex           = ersex,
        fcsex           = fcsex,
        srsin           = srsin,
        grsin           = grsin,
        ersin           = ersin,
        fcsin           = fcsin,
        fcsmean         = fcsmean
      )
    }

    ## A total of  139  out of the  139 contained records for  Cucurbita_cordata

    ## Removed   0  records because lat values were outside the range of -90 to 90 or lonitude values were outside the range of -180-180 or there is a no value present for latitude or longitude for a record.

    ## All checks completed
    ## All checks completed
    ## All checks completed

    ## A total of  253  out of the  253 contained records for  Cucurbita_digitata

    ## Removed   0  records because lat values were outside the range of -90 to 90 or lonitude values were outside the range of -180-180 or there is a no value present for latitude or longitude for a record.

    ## All checks completed
    ## All checks completed
    ## All checks completed

    ## A total of  811  out of the  811 contained records for  Cucurbita_palmata

    ## Removed   0  records because lat values were outside the range of -90 to 90 or lonitude values were outside the range of -180-180 or there is a no value present for latitude or longitude for a record.

    ## All checks completed
    ## All checks completed
    ## All checks completed

## Summary metrics tables

Results are organized as a named list, allowing review of individual species metrics. The tables below summarize the main metrics for all species.

    # ── Ex-situ metrics ───────────────────────────────────────────────────────────
    exsitu_table <- do.call(rbind, lapply(names(results_list), function(taxon) {
      r <- results_list[[taxon]]
      data.frame(
        Species          = taxon,
        SRS_exsitu       = r$srsex$`SRS exsitu`,
        GRS_exsitu       = r$fcsex$`GRS exsitu`,
        ERS_exsitu       = r$fcsex$`ERS exsitu`,
        FCS_exsitu       = r$fcsex$`FCS exsitu`,
        FCS_exsitu_score = r$fcsex$`FCS exsitu score`
      )
    }))

    # ── In-situ metrics ───────────────────────────────────────────────────────────
    insitu_table <- do.call(rbind, lapply(names(results_list), function(taxon) {
      r <- results_list[[taxon]]
      data.frame(
        Species          = taxon,
        SRS_insitu       = r$fcsin$`SRS insitu`,
        GRS_insitu       = r$fcsin$`GRS insitu`,
        ERS_insitu       = r$fcsin$`ERS insitu`,
        FCS_insitu       = r$fcsin$`FCS insitu`,
        FCS_insitu_score = r$fcsin$`FCS insitu score`
      )
    }))

    # ── Combined metrics ──────────────────────────────────────────────────────────
    combined_table <- do.call(rbind, lapply(names(results_list), function(taxon) {
      r <- results_list[[taxon]]
      data.frame(
        Species         = taxon,
        FCSc_min        = r$fcsmean$FCSc_min,
        FCSc_max        = r$fcsmean$FCSc_max,
        FCSc_mean       = r$fcsmean$FCSc_mean,
        FCSc_min_class  = r$fcsmean$FCSc_min_class,
        FCSc_max_class  = r$fcsmean$FCSc_max_class,
        FCSc_mean_class = r$fcsmean$FCSc_mean_class
      )
    }))

    knitr::kable(exsitu_table,   digits = 2, caption = "<span style='text-align:left; display:block;'>Ex-situ gap analysis metrics</span>",  format = "html") %>% kableExtra::kable_styling()

Ex-situ gap analysis metrics
Species | SRS_exsitu | GRS_exsitu | ERS_exsitu | FCS_exsitu | FCS_exsitu_score
--- | --- | --- | --- | --- | ---
Cucurbita_cordata | 0.72 | 9.75 | 22.22 | 10.90 | UP
Cucurbita_digitata | 8.12 | 25.95 | 40.00 | 24.69 | UP
Cucurbita_palmata | 4.11 | 30.52 | 50.00 | 28.21 | HP

    knitr::kable(insitu_table,   digits = 2, caption = "<span style='text-align:left; display:block;'>In-situ gap analysis metrics</span>",   format = "html") %>% kableExtra::kable_styling()

In-situ gap analysis metrics
Species | SRS_insitu | GRS_insitu | ERS_insitu | FCS_insitu | FCS_insitu_score
--- | --- | --- | --- | --- | ---
Cucurbita_cordata | 79.13 | 62.33 | 75.00 | 72.15 | MP
Cucurbita_digitata | 12.56 | 20.86 | 100.00 | 44.47 | HP
Cucurbita_palmata | 68.64 | 49.23 | 85.71 | 67.86 | MP

    knitr::kable(combined_table, digits = 2, caption = "<span style='text-align:left; display:block;'>Combined gap analysis metrics</span>",  format = "html") %>% kableExtra::kable_styling()

Combined gap analysis metrics
Species | FCSc_min | FCSc_max | FCSc_mean | FCSc_min_class | FCSc_max_class | FCSc_mean_class
--- | --- | --- | --- | --- | --- | ---
Cucurbita_cordata | 10.90 | 72.15 | 41.53 | UP | MP | HP
Cucurbita_digitata | 24.69 | 44.47 | 34.58 | UP | HP | HP
Cucurbita_palmata | 28.21 | 67.86 | 48.04 | HP | MP | HP