View source: R/detectionMaps.R
detectionMaps | R Documentation |
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 )
CTtable |
data.frame. contains station IDs and coordinates |
recordTable |
data.frame. the record table created by
|
Xcol |
character. name of the column specifying x coordinates in
|
Ycol |
character. name of the column specifying y coordinates in
|
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
|
speciesCol |
character. name of the column specifying species in
|
speciesToShow |
character. Species to include in the maps. If missing,
all species in |
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 |
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. |
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.
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.
Juergen Niedballa
A great resource for coordinate system information
is https://spatialreference.org/. Use the Proj4 string as
shapefileProjection
argument.
# 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(sp) poly1 <- Polygon(cbind(c(521500,526500,527000, 521500),c(607500, 608000, 603500, 603500))) poly2 <- Polygons(list(poly1), "s1") poly3 <- SpatialPolygons(list(poly2)) Mapstest2 <- detectionMaps(CTtable = camtraps, recordTable = recordTableSample, Xcol = "utm_x", Ycol = "utm_y", backgroundPolygon = poly3, # this was added speciesToShow = c("PBE", "VTA"), # this was added stationCol = "Station", speciesCol = "Species", writePNG = FALSE, plotR = TRUE, printLabels = TRUE, richnessPlot = TRUE, addLegend = TRUE )
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