buildRMM {changeRangeR}

Create metadata objects from 'changeRangeR'

Description

Creates and populates a 'rangeModelMetadata' object from the output of 'changeRangeR'. See Merow et al. (2019) <doi:10.1111/geb.12993> for more details on the nature of the metadata and the 'rangeModelMetadata' package. To improve reproducibility of the study, this metadata object can be used as supplemental information for a manuscript, shared with collaborators, etc.

Usage

buildRMM(
  rmm = NULL,
  binaryRange = NULL,
  locs = NULL,
  AOOarea = NULL,
  PE = NULL,
  PhyloTree = NULL,
  complementarity = NULL,
  complementarity.of = NULL,
  complementarity.mask = NULL,
  envChange = NULL,
  envChange.rStack = NULL,
  envChange.binaryRange = NULL,
  envChange.threshold = NULL,
  envChange.bound = NULL,
  envChange.correlation = NULL,
  futureOverlap = NULL,
  futureOverlap.binRasters = NULL,
  futureOverlap.futures = NULL,
  mcp = NULL,
  mcpSDM = NULL,
  ratioOverlap = NULL,
  ratioOverlap.shape = NULL,
  ratioOverlap.field = NULL,
  SE = NULL,
  SE.ranges = NULL
)

Arguments

rmm

A 'rangemodelmetadata' object.

binaryRange

Raster layer of a binary SDM. Must be either unprojected in the WGS84 datum, or projected in a UTM projection measured in meters.

locs

'data.frame' of occurrence records: Longitude and latitude.

AOOarea

The output of the function 'AOOarea'.

PE

The output of the function 'calc_PE'.

PhyloTree

class phylo object of phylogenetic tree. The names on tree's tip labels need to match the column names on the matrix.

complementarity

The out put of the function 'complementarity'.

complementarity.of

'raster' of categorical values (e.g., a species richness map).

complementarity.mask

'raster' object representing areas of interest (e.g., protected areas).

envChange

The output of the function 'envChange'

envChange.rStack

'rasterStack' of environmental variable to measure within binary SDM through time.

envChange.binaryRange

'raster' object or shapefile of binary range (SDM, AOO, EOO) with same projection as rStack.

envChange.threshold

integer (or integers if bound = "both") of where rStack layers should be thresholded.

envChange.bound

character string characterizing the way the threshold should happen. "upper" removes values above the threshold (e.g., maximum human footprint)."lower" removes values below the threshold (e.g., minimum forest cover). "neither" does not threshold at any point. "both" thresholds at both threshold values (if provided; e.g., minimum and maximum temperature).

envChange.correlation

boolean. If FALSE, environmental variable will be converted to a binary map and used as a mask. If TRUE, environmental variable is only thresholded by bounds, but left continuous. Then, Pearson's correlation coefficient with SDM will be computed for overlapping areas.

futureOverlap

The output of the function 'futureOverlap'.

futureOverlap.binRasters

'list' of rasters of binary SDMs..

futureOverlap.futures

'list' of 'SpatialPolygons*' objects with same CRS as futureOverlap.binRasters.

mcp

The output of the function 'mcp'

mcpSDM

The output of the function 'mcpSDM'

ratioOverlap

The output of the function 'ratioOverlap'

ratioOverlap.shape

Either 1) a 'shapefile' of land cover features or 2) a continuous 'raster'. Must be in same projection as r parameter. If shp is a raster, then the number of cells within each quantile are calculated.

ratioOverlap.field

A character string representing the shapefile field attribute containing the features to compare (i.e., the column name).

SE

The output of the function 'SE'

SE.ranges

a 'rasterStack' of binary species presences

Value

Populated rmm object

Author(s)

[e-mail]

References

Merow, C., Maitner, B. S., Owens, H. L., Kass, J. M., Enquist, B. J., Jetz, W., & Guralnick, R. (2019). Species' range model metadata standards: RMMS. Global Ecology and Biogeography, 28: 1912-1924. doi:10.1111/geb.12993

Examples

buildRMM(binaryRange = NULL)