Generate maps of observed species richness and species presences by station

Generates maps of observed species richness and species presence by species and station. Output can be R graphics, PNG graphics or a shapefile for use in GIS software.

detectionMaps(
  CTtable,
  recordTable,
  Xcol,
  Ycol,
  backgroundPolygon,
  stationCol = "Station",
  speciesCol = "Species",
  speciesToShow,
  richnessPlot = TRUE,
  speciesPlots = TRUE,
  addLegend = TRUE,
  printLabels = FALSE,
  smallPoints,
  plotR = TRUE,
  writePNG = FALSE,
  plotDirectory,
  createPlotDir = FALSE,
  pngMaxPix = 1000,
  writeShapefile = FALSE,
  shapefileName,
  shapefileDirectory,
  shapefileProjection
)

Arguments

CTtable

data.frame. contains station IDs and coordinates

recordTable

data.frame. the record table created by recordTable

Xcol

character. name of the column specifying x coordinates in CTtable

Ycol

character. name of the column specifying y coordinates in CTtable

backgroundPolygon

SpatialPolygons or SpatialPolygonsDataFrame. Polygon to be plotted in the background of the map (e.g. project area boundary)

stationCol

character. name of the column specifying station ID in CTtable and recordTable

speciesCol

character. name of the column specifying species in recordTable

speciesToShow

character. Species to include in the maps. If missing, all species in recordTable will be included.

richnessPlot

logical. Generate a species richness plot?

speciesPlots

logical. Generate plots of all species number of independent events?

addLegend

logical. Add legends to the plots?

printLabels

logical. Add station labels to the plots?

smallPoints

numeric. Number by which to decrease point sizes in plots (optional).

plotR

logical. Create plots in R graphics device?

writePNG

logical. Create PNGs of the plots?

plotDirectory

character. Directory in which to save the PNGs

createPlotDir

logical. Create plotDirectory?

pngMaxPix

integer. number of pixels in pngs on the longer side

writeShapefile

logical. Create a shapefile from the output?

shapefileName

character. Name of the shapefile to be saved. If empty, a name will be generated automatically.

shapefileDirectory

character. Directory in which to save the shapefile.

shapefileProjection

character. A character string of projection arguments to use in the shapefile.

Value

An invisible data.frame with station coordinates, numbers of events by species at each station and total species number by station. In addition and optionally, R graphics or png image files.

Details

The column name stationCol must be identical in CTtable and recordTable and station IDs must match.

Shapefile creation depends on the packages sf. Argument shapefileProjection must be a valid argument of st_crs (one of (i) character: a string accepted by GDAL, (ii) integer, a valid EPSG value (numeric), or (iii) an object of class crs. If shapefileProjection is undefined, the resulting shapefile will lack a coordinate reference system.

References

A great resource for coordinate system information is https://spatialreference.org/. Use the Proj4 string as shapefileProjection argument.

Author

Juergen Niedballa

Examples

# load station information
data(camtraps)

# load record table
data(recordTableSample)


# create maps
Mapstest <- detectionMaps(CTtable           = camtraps,
                          recordTable       = recordTableSample,
                          Xcol              = "utm_x",
                          Ycol              = "utm_y",
                          stationCol        = "Station",
                          speciesCol        = "Species",
                          writePNG          = FALSE,
                          plotR             = TRUE,
                          printLabels       = TRUE,
                          richnessPlot      = TRUE,
                          addLegend         = TRUE
)









# with a polygon in the background, and for one species only

# make a dummy polygon for the background
library(sf)

Sr1 = st_polygon(list(cbind(c(521500,526500,527000, 521500, 521500),
                            c(607500, 608000, 603500, 603500, 607500))))
aoi <- data.frame(name = "My AOI")
st_geometry(aoi) <- st_geometry(Sr1)
st_crs(aoi) <- 32650  # assign CRS: UTM50N

Mapstest2 <- detectionMaps(CTtable           = camtraps,
                           recordTable       = recordTableSample,
                           Xcol              = "utm_x",
                           Ycol              = "utm_y",
                           backgroundPolygon = aoi,               # this was added
                           speciesToShow     = c("PBE", "VTA"),   # this was added
                           stationCol        = "Station",
                           speciesCol        = "Species",
                           writePNG          = FALSE,
                           plotR             = TRUE,
                           printLabels       = TRUE,
                           richnessPlot      = TRUE,
                           addLegend         = TRUE
)