R/MapTaxaObs.R
In leppott/MBSStools: MBSS tool suite for calculations and data manipulation
Defines functions
MapTaxaObs
Documented in
MapTaxaObs
#' Taxa Observation Maps
#'
#' 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.
#'
#' 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.
#'
#' @param obs Excel file containing 3 columns: TaxaName, Latitude83, Longitude83
#' @param xWalk Crosswalk (Excel file) of taxa names between taxa name in
#' occurence file and file name outputs for maps. Three columns (CommonName,
#' Species, MapName).
#' @param dirMain Path for folder containing obs and xwalk. Optional.
#' Default = getwd().
#' @param onlymatches Flag for mapping obs taxa matching xwalk taxa, or all
#' taxa. Optional. Default = TRUE.
#' @param dirData Subdirectory of "dir" specified above with data files.
#' Default = "Data"
#' @param dirGIS Subdirectory of "dir" specified above with GIS files.
#' Default = "GIS"
#' @param dirMaps Subdirectory of "dir" specified above for map outputs.
#' Default = "Maps"
#' @param verbose Boolean value for including feedback to the user that the
#' script is working. Default = TRUE.
#'
#' @return 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)
#
#' @export
MapTaxaObs <- function(obs
, xWalk
, dirMain = getwd()
, onlymatches = TRUE
, dirData = "Data"
, dirGIS = "GIS"
, dirMaps = "Maps"
, verbose = TRUE
) {
# 0. QC
boo_QC <- FALSE
if(isTRUE(boo_QC)){
# Copy files
# 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(path.package("MBSStools"), "extdata", myFiles)
, file.path(wd, "Data", myFiles))
### GIS
utils::unzip(file.path(path.package("MBSStools"), "extdata", "MD_GIS.zip"),
exdir=file.path(wd, "GIS"))
# Function Inputs
obs <- "AllFish_95to16.xls"
xWalk <- "TaxaMapsCrossWalk20170731.xlsx"
dirMain <- tempdir()
onlymatches <- TRUE
dirData <- "Data"
dirGIS <- "GIS"
dirMaps <- "Maps"
verbose <- TRUE
i <- 1
# shell.exec(dirMain)
}## IF ~ boo_QC ~ END
# 2021-01-10
# Define missing variables
# bindings for global variables -----
CommonName <- MapName <- shp_strata_bugs <- shp_strata_fish <-
shp_strata_msw <- NULL
# 1. Define Parameters ####
#mainDir <- dir
if (verbose == TRUE) {
message(dirMain)
#flush.console()
}## IF ~ verbose ~ END
sh.state <- "MD_State_Boundary.shp"
sh.coast <- "MD_Coast_Hydrology.shp"
sh.county <- "MD_Boundary_County_Detailed.shp"
all.taxa <- file.path(dirMain, dirData ,obs)
taxa.lu <- file.path(dirMain, dirData, xWalk)
# 2. Testing ####
# Test for existence of required data subdirectory and data files
fl.files <-"\n"
if (!utils::file_test("-d", file.path(dirMain, dirData))) {
##IF.dirData.START
if (utils::file_test("-f", file.path(dirMain, dirData))) {
fl.files <- paste(fl.files
, "Path can't be created because a file with that name already exists."
, sep = "\n")
} else {
fl.files <- paste(fl.files
, "Data subdirectory does not exist."
, sep = "\n")
}
} else {
if (!utils::file_test("-f", file.path(dirMain, dirData, obs))) {
fl.files <- paste(fl.files
, "Observation file does not exist."
, sep="\n")
}
if (!utils::file_test("-f", file.path(dirMain, dirData, xWalk))) {
fl.files <- paste(fl.files
, "Crosswalk file does not exist."
, sep = "\n")
}
}##IF.dirData.END
# Test for existence of required data subdirectory and data files
if (!utils::file_test("-d", file.path(dirMain, dirGIS))) {##IF.dirGIS.START
if (utils::file_test("-f", file.path(dirMain, dirGIS))) {
fl.files <- paste(fl.files
, "Path can't be created because a file with that name already exists."
, sep = "\n")
} else {
fl.files <- paste(fl.files
, "GIS subdirectory does not exist."
, sep = "\n")
}
} else {
if (!utils::file_test("-f", file.path(dirMain, dirGIS, sh.state))) {
fl.files <- paste(fl.files
, "State boundary shapefile does not exist."
, sep = "\n")
}
if (!utils::file_test("-f", file.path(dirMain, dirGIS, sh.coast))) {
fl.files <- paste(fl.files
, "Coast boundary shapefile does not exist."
, sep = "\n")
}
if (!utils::file_test("-f", file.path(dirMain, dirGIS, sh.county))) {
fl.files <- paste(fl.files
, "County boundary shapefile does not exist."
, sep = "\n")
}
}##IF.dirGIS.END
if (fl.files != "\n") {##IF.!=.START
stop(fl.files)
}##IF.!=.END
# Make the Maps subdirectory if it doesn't exist
if (!utils::file_test("-d", file.path(dirMain, dirMaps))) {
if (utils::file_test("-f", file.path(dirMain, dirMaps))) {
stop("Path can't be created because a file with that name already
exists.")
} else {
dir.create(file.path(dirMain, dirMaps))
}
}##IF.dirMaps.END
# 3. Read Data ####
# Read in Taxon observations
df.taxa.obs <- readxl::read_excel(all.taxa
, sheet = 1
, col_names = TRUE
, skip = 0)
df.taxa.obs <- as.data.frame(df.taxa.obs)
df.taxa.obs[, 1] <- tolower(df.taxa.obs[, 1])
#df.taxa.obs <- as.data.frame(cbind(tolower(df.taxa.obs[,"TaxaName"])
#, df.taxa.obs[,2:3]))
colnames(df.taxa.obs)[1] <- "CommonName"
# Read in TaxaMapsCrossWalk.xlsx
df.lu.taxa <- readxl::read_excel(taxa.lu
, sheet = 1
, col_names = TRUE
, skip = 0)
df.lu.taxa <- as.data.frame(df.lu.taxa[, c("CommonName", "MapName")])
df.lu.taxa[, "CommonName"] <- tolower(df.lu.taxa[, "CommonName"])
# df.lu.taxa <- as.data.frame(cbind(tolower(df.lu.taxa[,"CommonName"])
#,df.lu.taxa[,"MapName"]))
# colnames(df.lu.taxa)[1:2] <- c("CommonName","MapName")
# 4. Munge Data ####
# Compare TaxaName to CommonName
taxa.names <- as.vector(df.lu.taxa[,"CommonName"])
matches <- as.vector(df.taxa.obs[,"CommonName"]) %in% taxa.names
df.taxa.nomatch <- as.data.frame(unique(sort(df.taxa.obs[
,"CommonName"][!matches])))
colnames(df.taxa.nomatch)[1] <- "CommonName"
df.taxa.match <- as.data.frame(unique(sort(df.taxa.obs[
,"CommonName"][matches])))
colnames(df.taxa.match)[1] <- "CommonName"
if (onlymatches == TRUE) {
# Create a data frame of common names and filenames for matching taxa
map.taxa <- subset(df.lu.taxa, CommonName %in% df.taxa.match[
,"CommonName"],
select = c(CommonName, MapName))
} else {
map.taxa.match <- subset(df.lu.taxa, CommonName %in% df.taxa.match[
,"CommonName"],
select = c(CommonName, MapName))
taxa.nomatch <- subset(df.taxa.obs, CommonName %in% df.taxa.nomatch[
,"CommonName"],
select = CommonName)
map.taxa.nomatch <- as.data.frame(unique(sort(taxa.nomatch$CommonName)))
map.taxa.nomatch <- cbind(map.taxa.nomatch, as.data.frame(paste0("zzz_",
#gsub("(\\s+)","",map.taxa.nomatch[,1]),".png")))
gsub("(\\s+)","",map.taxa.nomatch[,1]))))
colnames(map.taxa.nomatch) <- c("CommonName","MapName")
map.taxa <- rbind(map.taxa.match, map.taxa.nomatch)
}
# 5. Mapping ####
ppi <- 72
#dsn<-paste(dirMain,dirGIS,sep="/")
dsn <- file.path(dirMain, dirGIS)
# state <- rgdal::readOGR(dsn = dsn
# , layer = "MD_State_Boundary"
# , verbose=verbose)
# coastline <- rgdal::readOGR(dsn = dsn
# , layer = "MD_Coast_Hydrology"
# , verbose=verbose)
# counties <- rgdal::readOGR(dsn = dsn
# , layer = "MD_Boundary_County_Detailed"
# , verbose=verbose)
# sf version
state <- sf::st_read(dsn = dsn
, layer = "MD_State_Boundary")
coastline <- sf::st_read(dsn = dsn
, layer = "MD_Coast_Hydrology")
counties <- sf::st_read(dsn = dsn
, layer = "MD_Boundary_County_Detailed")
for (i in seq_len(nrow(map.taxa))) {
#
taxon <- as.character(map.taxa$CommonName[i])
filename <- map.taxa$MapName[i]
df.taxon.sites <- subset(df.taxa.obs, df.taxa.obs[,"CommonName"] == taxon)
df.taxon.sites <- subset(df.taxon.sites
, !is.na(df.taxon.sites["Latitude83"]))
##PLOT.START
grDevices::png(file = file.path(dirMain
, dirMaps
, paste0(filename, ".png"))
, width = 8.5 * ppi
, height = 5.5 * ppi
, pointsize = 12
, bg = "white")
plot(sf::st_geometry(state)
, col="white"
, border = "gray")
plot(sf::st_geometry(coastline)
, add = TRUE
, col = "light blue"
, border=FALSE)
plot(sf::st_geometry(counties)
, add = TRUE
, col = "white"
, border = "darkslategray"
, lwd = 0.5)
#xy <- df.taxon.sites[,2:3]
proj.sites <- rgdal::project(cbind(df.taxon.sites$Longitude83
, df.taxon.sites$Latitude83)
,
"+proj=lcc +lat_1=39.45 +lat_2=38.3 +lat_0=37.66666666666666 +lon_0=-77
+x_0=400000 +y_0=0 +datum=NAD83 +units=m +no_defs")
graphics::points(proj.sites[, 1]
, proj.sites[, 2]
, pch = 21
, col = "black"
, bg = "green"
, cex = 1.0)
grDevices::dev.off()
# user feedback
if (verbose == TRUE) {##IF.verbose.START
message(paste0("Saving map "
, i
, " of "
, nrow(map.taxa)
, "; "
, taxon
, "."))
#flush.console()
}##IF.verbose.END
##PLOT.END
}##FOR.i.END
#
# 6. Clean up ####
# Number on Non-Matches
n.nomatch <- nrow(df.taxa.nomatch)
# Save Non-Matches and inform user
if (n.nomatch == 0) {
message(paste0("There are no non-matching taxa names."))
} else {
file.output <- file.path(dirMain, dirMaps, "Taxa.NoMatch.csv")
utils::write.csv(df.taxa.nomatch, file.output)
message(paste0("There are "
, n.nomatch
, " non-matching taxa names.
The non-matches are saved in a table with the maps."))
#
}
#
}##FUNCTION.MapTaxaObs.END
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Defines functions MapTaxaObs
Documented in MapTaxaObs
#' Taxa Observation Maps
#'
#' 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.
#'
#' 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.
#'
#' @param obs Excel file containing 3 columns: TaxaName, Latitude83, Longitude83
#' @param xWalk Crosswalk (Excel file) of taxa names between taxa name in
#' occurence file and file name outputs for maps. Three columns (CommonName,
#' Species, MapName).
#' @param dirMain Path for folder containing obs and xwalk. Optional.
#' Default = getwd().
#' @param onlymatches Flag for mapping obs taxa matching xwalk taxa, or all
#' taxa. Optional. Default = TRUE.
#' @param dirData Subdirectory of "dir" specified above with data files.
#' Default = "Data"
#' @param dirGIS Subdirectory of "dir" specified above with GIS files.
#' Default = "GIS"
#' @param dirMaps Subdirectory of "dir" specified above for map outputs.
#' Default = "Maps"
#' @param verbose Boolean value for including feedback to the user that the
#' script is working. Default = TRUE.
#'
#' @return 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)
#
#' @export
MapTaxaObs <- function(obs
, xWalk
, dirMain = getwd()
, onlymatches = TRUE
, dirData = "Data"
, dirGIS = "GIS"
, dirMaps = "Maps"
, verbose = TRUE
) {
# 0. QC
boo_QC <- FALSE
if(isTRUE(boo_QC)){
# Copy files
# 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(path.package("MBSStools"), "extdata", myFiles)
, file.path(wd, "Data", myFiles))
### GIS
utils::unzip(file.path(path.package("MBSStools"), "extdata", "MD_GIS.zip"),
exdir=file.path(wd, "GIS"))
# Function Inputs
obs <- "AllFish_95to16.xls"
xWalk <- "TaxaMapsCrossWalk20170731.xlsx"
dirMain <- tempdir()
onlymatches <- TRUE
dirData <- "Data"
dirGIS <- "GIS"
dirMaps <- "Maps"
verbose <- TRUE
i <- 1
# shell.exec(dirMain)
}## IF ~ boo_QC ~ END
# 2021-01-10
# Define missing variables
# bindings for global variables -----
CommonName <- MapName <- shp_strata_bugs <- shp_strata_fish <-
shp_strata_msw <- NULL
# 1. Define Parameters ####
#mainDir <- dir
if (verbose == TRUE) {
message(dirMain)
#flush.console()
}## IF ~ verbose ~ END
sh.state <- "MD_State_Boundary.shp"
sh.coast <- "MD_Coast_Hydrology.shp"
sh.county <- "MD_Boundary_County_Detailed.shp"
all.taxa <- file.path(dirMain, dirData ,obs)
taxa.lu <- file.path(dirMain, dirData, xWalk)
# 2. Testing ####
# Test for existence of required data subdirectory and data files
fl.files <-"\n"
if (!utils::file_test("-d", file.path(dirMain, dirData))) {
##IF.dirData.START
if (utils::file_test("-f", file.path(dirMain, dirData))) {
fl.files <- paste(fl.files
, "Path can't be created because a file with that name already exists."
, sep = "\n")
} else {
fl.files <- paste(fl.files
, "Data subdirectory does not exist."
, sep = "\n")
}
} else {
if (!utils::file_test("-f", file.path(dirMain, dirData, obs))) {
fl.files <- paste(fl.files
, "Observation file does not exist."
, sep="\n")
}
if (!utils::file_test("-f", file.path(dirMain, dirData, xWalk))) {
fl.files <- paste(fl.files
, "Crosswalk file does not exist."
, sep = "\n")
}
}##IF.dirData.END
# Test for existence of required data subdirectory and data files
if (!utils::file_test("-d", file.path(dirMain, dirGIS))) {##IF.dirGIS.START
if (utils::file_test("-f", file.path(dirMain, dirGIS))) {
fl.files <- paste(fl.files
, "Path can't be created because a file with that name already exists."
, sep = "\n")
} else {
fl.files <- paste(fl.files
, "GIS subdirectory does not exist."
, sep = "\n")
}
} else {
if (!utils::file_test("-f", file.path(dirMain, dirGIS, sh.state))) {
fl.files <- paste(fl.files
, "State boundary shapefile does not exist."
, sep = "\n")
}
if (!utils::file_test("-f", file.path(dirMain, dirGIS, sh.coast))) {
fl.files <- paste(fl.files
, "Coast boundary shapefile does not exist."
, sep = "\n")
}
if (!utils::file_test("-f", file.path(dirMain, dirGIS, sh.county))) {
fl.files <- paste(fl.files
, "County boundary shapefile does not exist."
, sep = "\n")
}
}##IF.dirGIS.END
if (fl.files != "\n") {##IF.!=.START
stop(fl.files)
}##IF.!=.END
# Make the Maps subdirectory if it doesn't exist
if (!utils::file_test("-d", file.path(dirMain, dirMaps))) {
if (utils::file_test("-f", file.path(dirMain, dirMaps))) {
stop("Path can't be created because a file with that name already
exists.")
} else {
dir.create(file.path(dirMain, dirMaps))
}
}##IF.dirMaps.END
# 3. Read Data ####
# Read in Taxon observations
df.taxa.obs <- readxl::read_excel(all.taxa
, sheet = 1
, col_names = TRUE
, skip = 0)
df.taxa.obs <- as.data.frame(df.taxa.obs)
df.taxa.obs[, 1] <- tolower(df.taxa.obs[, 1])
#df.taxa.obs <- as.data.frame(cbind(tolower(df.taxa.obs[,"TaxaName"])
#, df.taxa.obs[,2:3]))
colnames(df.taxa.obs)[1] <- "CommonName"
# Read in TaxaMapsCrossWalk.xlsx
df.lu.taxa <- readxl::read_excel(taxa.lu
, sheet = 1
, col_names = TRUE
, skip = 0)
df.lu.taxa <- as.data.frame(df.lu.taxa[, c("CommonName", "MapName")])
df.lu.taxa[, "CommonName"] <- tolower(df.lu.taxa[, "CommonName"])
# df.lu.taxa <- as.data.frame(cbind(tolower(df.lu.taxa[,"CommonName"])
#,df.lu.taxa[,"MapName"]))
# colnames(df.lu.taxa)[1:2] <- c("CommonName","MapName")
# 4. Munge Data ####
# Compare TaxaName to CommonName
taxa.names <- as.vector(df.lu.taxa[,"CommonName"])
matches <- as.vector(df.taxa.obs[,"CommonName"]) %in% taxa.names
df.taxa.nomatch <- as.data.frame(unique(sort(df.taxa.obs[
,"CommonName"][!matches])))
colnames(df.taxa.nomatch)[1] <- "CommonName"
df.taxa.match <- as.data.frame(unique(sort(df.taxa.obs[
,"CommonName"][matches])))
colnames(df.taxa.match)[1] <- "CommonName"
if (onlymatches == TRUE) {
# Create a data frame of common names and filenames for matching taxa
map.taxa <- subset(df.lu.taxa, CommonName %in% df.taxa.match[
,"CommonName"],
select = c(CommonName, MapName))
} else {
map.taxa.match <- subset(df.lu.taxa, CommonName %in% df.taxa.match[
,"CommonName"],
select = c(CommonName, MapName))
taxa.nomatch <- subset(df.taxa.obs, CommonName %in% df.taxa.nomatch[
,"CommonName"],
select = CommonName)
map.taxa.nomatch <- as.data.frame(unique(sort(taxa.nomatch$CommonName)))
map.taxa.nomatch <- cbind(map.taxa.nomatch, as.data.frame(paste0("zzz_",
#gsub("(\\s+)","",map.taxa.nomatch[,1]),".png")))
gsub("(\\s+)","",map.taxa.nomatch[,1]))))
colnames(map.taxa.nomatch) <- c("CommonName","MapName")
map.taxa <- rbind(map.taxa.match, map.taxa.nomatch)
}
# 5. Mapping ####
ppi <- 72
#dsn<-paste(dirMain,dirGIS,sep="/")
dsn <- file.path(dirMain, dirGIS)
# state <- rgdal::readOGR(dsn = dsn
# , layer = "MD_State_Boundary"
# , verbose=verbose)
# coastline <- rgdal::readOGR(dsn = dsn
# , layer = "MD_Coast_Hydrology"
# , verbose=verbose)
# counties <- rgdal::readOGR(dsn = dsn
# , layer = "MD_Boundary_County_Detailed"
# , verbose=verbose)
# sf version
state <- sf::st_read(dsn = dsn
, layer = "MD_State_Boundary")
coastline <- sf::st_read(dsn = dsn
, layer = "MD_Coast_Hydrology")
counties <- sf::st_read(dsn = dsn
, layer = "MD_Boundary_County_Detailed")
for (i in seq_len(nrow(map.taxa))) {
#
taxon <- as.character(map.taxa$CommonName[i])
filename <- map.taxa$MapName[i]
df.taxon.sites <- subset(df.taxa.obs, df.taxa.obs[,"CommonName"] == taxon)
df.taxon.sites <- subset(df.taxon.sites
, !is.na(df.taxon.sites["Latitude83"]))
##PLOT.START
grDevices::png(file = file.path(dirMain
, dirMaps
, paste0(filename, ".png"))
, width = 8.5 * ppi
, height = 5.5 * ppi
, pointsize = 12
, bg = "white")
plot(sf::st_geometry(state)
, col="white"
, border = "gray")
plot(sf::st_geometry(coastline)
, add = TRUE
, col = "light blue"
, border=FALSE)
plot(sf::st_geometry(counties)
, add = TRUE
, col = "white"
, border = "darkslategray"
, lwd = 0.5)
#xy <- df.taxon.sites[,2:3]
proj.sites <- rgdal::project(cbind(df.taxon.sites$Longitude83
, df.taxon.sites$Latitude83)
,
"+proj=lcc +lat_1=39.45 +lat_2=38.3 +lat_0=37.66666666666666 +lon_0=-77
+x_0=400000 +y_0=0 +datum=NAD83 +units=m +no_defs")
graphics::points(proj.sites[, 1]
, proj.sites[, 2]
, pch = 21
, col = "black"
, bg = "green"
, cex = 1.0)
grDevices::dev.off()
# user feedback
if (verbose == TRUE) {##IF.verbose.START
message(paste0("Saving map "
, i
, " of "
, nrow(map.taxa)
, "; "
, taxon
, "."))
#flush.console()
}##IF.verbose.END
##PLOT.END
}##FOR.i.END
#
# 6. Clean up ####
# Number on Non-Matches
n.nomatch <- nrow(df.taxa.nomatch)
# Save Non-Matches and inform user
if (n.nomatch == 0) {
message(paste0("There are no non-matching taxa names."))
} else {
file.output <- file.path(dirMain, dirMaps, "Taxa.NoMatch.csv")
utils::write.csv(df.taxa.nomatch, file.output)
message(paste0("There are "
, n.nomatch
, " non-matching taxa names.
The non-matches are saved in a table with the maps."))
#
}
#
}##FUNCTION.MapTaxaObs.END
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