MapTaxaObs: Taxa Observation Maps

In leppott/MBSStools: MBSS tool suite for calculations and data manipulation

Taxa Observation Maps

Description

Map taxonomic observations in Maryland. Inputs are 3 GIS shapefiles (State, County, and Hydrology) for Maryland, Observations (taxa names and Lat/Longs), and #' a crosswalk table of taxa names and map names. Input files are assumed to be Excel with the data on the first worksheet.

Usage

MapTaxaObs(
  obs,
  xWalk,
  dirMain = getwd(),
  onlymatches = TRUE,
  dirData = "Data",
  dirGIS = "GIS",
  dirMaps = "Maps",
  verbose = TRUE
)

Arguments

obs	Excel file containing 3 columns: TaxaName, Latitude83, Longitude83
xWalk	Crosswalk (Excel file) of taxa names between taxa name in occurence file and file name outputs for maps. Three columns (CommonName, Species, MapName).
dirMain	Path for folder containing obs and xwalk. Optional. Default = getwd().
onlymatches	Flag for mapping obs taxa matching xwalk taxa, or all taxa. Optional. Default = TRUE.
dirData	Subdirectory of "dir" specified above with data files. Default = "Data"
dirGIS	Subdirectory of "dir" specified above with GIS files. Default = "GIS"
dirMaps	Subdirectory of "dir" specified above for map outputs. Default = "Maps"
verbose	Boolean value for including feedback to the user that the script is working. Default = TRUE.

Details

The example data is fish but can be used for benthic macroinvertebrates as well. Maps are output as PNG. There is a flag for "only" matches between the data and the crosswalk table (this is the default). There is also a "verbose" flag for printing status messages to the user (this is the default). Tests for existence of Data, GIS directories and required files. On failure, stops and prints missing directories/files to screen.

The R libraries 'rgdal', 'sf', and 'readxl' are required for this function. The 'rgdal' package was deprecated in 2023. In 2024 revised this fucntion to use functions from the 'sf' package.

Value

Saves the maps and a dataframe of observed taxa not matching xwalk taxa to the dirMaps folder.

Examples

# Set Working Directory
wd <- tempdir()
# Create Example Data if Needed
## Create Directories
myDir.create <- file.path(wd, "Data")
ifelse(dir.exists(myDir.create) == FALSE
       , dir.create(myDir.create)
       , "Directory already exists")
myDir.create <- file.path(wd,"GIS")
ifelse(dir.exists(myDir.create) == FALSE
       , dir.create(myDir.create)
       , "Directory already exists")
myDir.create <- file.path(wd,"Maps")
ifelse(dir.exists(myDir.create) == FALSE
       , dir.create(myDir.create)
       , "Directory already exists")
## Create Data
### Taxa Data
myFiles <- c("AllFish_95to16.xls", "TaxaMapsCrossWalk20170731.xlsx")
file.copy(file.path(find.package("MBSStools", .libPaths())
         , "extdata"
         , myFiles),
file.path(wd, "Data", myFiles))
### GIS
unzip(file.path(find.package("MBSStools", .libPaths()), "extdata", "MD_GIS.zip")
      , exdir = file.path(wd, "GIS"))

# Inputs
obs     <- "AllFish_95to16.xls"
xWalk   <- "TaxaMapsCrossWalk20170731.xlsx"
dirMain <- tempdir()

# Create maps
MapTaxaObs(obs, xWalk, dirMain)

# Open folder (Windows only)
# shell.exec(tempdir())

leppott/MBSStools documentation built on March 5, 2025, 5:33 p.m.