R/01_generics.r

In adamlilith/fasterRaster: Faster Raster and Spatial Vector Processing Using 'GRASS GIS'

# NB SQL WHERE queries can be up to 30000 character long... longer fails in GRASS

.restore <- NULL

# bad form:
# require(data.table)
# require(sf)
# require(terra)

# creates conflicts with terra::shift and data.table::shift
# #' @import terra
#' @importFrom data.table as.data.table
# #' @import terra

#' @import sf
#' @rawNamespace import(data.table, except = shift)
#' @rawNamespace import(terra, except = shift)
# #' @importFrom data.table as.data.table
# #' @importFrom methods new
# #' @importFrom methods setMethod
# #' @importFrom methods setValidity
# #' @importFrom methods validObject

### data.table
.datatable.aware <- TRUE

if (getRversion() >= "2.15.1") {
    utils::globalVariables(c(".", ".I", ".N", ".SD"), utils::packageName())
    utils::globalVariables(c("..ac", "..cols", "..i", "..j", "j", "i", "..fun"), utils::packageName())
}

### GENERICS
#' @importFrom data.table :=
# if (!isGeneric("[")) methods::setGeneric(name = "[", def = function(x, ...) standardGeneric("["))
# if (!isGeneric("[<-")) methods::setGeneric(name = "[<-", def = function(x, ...) standardGeneric("[<-"))

# $ is already generic
# $<- is already generic
# [ is already generic
# [<- is already generic
# [[ is already generic
# [[<- is already generic

methods::setGeneric(name = "%in%", package = "terra")
methods::setGeneric(name = "%notin%", def = function(x, ...) package = "omnibus")
methods::setGeneric(name = ".copyGSpatial", def = function(x, ...) standardGeneric(".copyGSpatial"))
methods::setGeneric(name = ".exists", def = function(x, ...) standardGeneric(".exists"))
methods::setGeneric(name = ".location", def = function(x, ...) standardGeneric(".location"))
methods::setGeneric(name = ".locationCreate", def = function(x, ...) standardGeneric(".locationCreate"))
methods::setGeneric(name = ".locationFind", def = function(x, ...) standardGeneric(".locationFind"))
methods::setGeneric(name = ".locationRestore", def = function(x, ...) standardGeneric(".locationRestore"))
methods::setGeneric(name = ".mapset", def = function(x, ...) standardGeneric(".mapset"))
methods::setGeneric(name = ".region", def = function(x, ...) standardGeneric(".region"))
methods::setGeneric(name = ".regionDim", def = function(x, ...) standardGeneric(".regionDim"))
methods::setGeneric(name = ".regionExt", def = function(x, ...) standardGeneric(".regionExt"))
methods::setGeneric(name = ".regionRes", def = function(x, ...) standardGeneric(".regionRes"))

# methods::setGeneric(name = "activeCat", package = "terra")
methods::setGeneric(name = "activeCat", def = function(x, ...) standardGeneric("activeCat"))
methods::setGeneric(name = "activeCats", def = function(x, ...) standardGeneric("activeCats"))
methods::setGeneric(name = "activeCat<-", package = "terra")
methods::setGeneric(name = "add<-", package = "terra")
methods::setGeneric(name = "addCats", package = "terra")
methods::setGeneric(name = "addCats<-", def = function(x, ..., value) standardGeneric("addCats<-"))
methods::setGeneric(name = "addTable<-", def = function(x, ..., value) standardGeneric("addTable<-"))
# methods::setGeneric(name = "andAndAnd", def = function(e1, e2) standardGeneric("andAndAnd"))
methods::setGeneric(name = "app", package = "terra")
# methods::setGeneric(name = "appFuns", def = function(x, ...) standardGeneric("appFuns"))
methods::setGeneric(name = "appCheck", def = function(x, fun, ...) standardGeneric("appCheck"))
methods::setGeneric(name = "as.contour", package = "terra")
methods::setGeneric("as.data.frame")
methods::setGeneric(name = "as.data.table", package = "data.table")
# methods::setGeneric(name = "as.data.table", def = function(x, ...) standardGeneric("as.data.table"))
methods::setGeneric(name = "as.doub", def = function(x, ...) standardGeneric("as.doub"))
methods::setGeneric(name = "as.float", def = function(x, ...) standardGeneric("as.float"))
# as.integer() is primitive
methods::setGeneric(name = "as.int", package = "terra")
setGeneric("as.lines", function(x,...) standardGeneric("as.lines"))
setGeneric("as.points", function(x,...) standardGeneric("as.points"))
setGeneric("as.polygons", function(x,...) standardGeneric("as.polygons"))
setGeneric("aggregate", function(x, ...) standardGeneric("aggregate"), package = "stats")

methods::setGeneric(name = "barplot", package = "terra")
methods::setGeneric(name = "bioclims", def = function(ppt, ...) standardGeneric("bioclims"))
methods::setGeneric(name = "bottom", def = function(x, ...) standardGeneric("bottom"))
methods::setGeneric(name = "breakPolys", def = function(x, ...) standardGeneric("breakPolys"))
methods::setGeneric(name = "buffer", package = "terra")

# c() is primitive
methods::setGeneric(name = "categories", package = "terra")
methods::setGeneric(name = "catNames", def = function(x, ...) standardGeneric("catNames"))
methods::setGeneric(name = "cats", package = "terra")
# methods::setGeneric(name = "cbind")
# from https://stackoverflow.com/questions/27886535/proper-way-to-use-cbind-rbind-with-s4-classes-in-package
# methods::getGeneric("cbind")
# methods::setGeneric(name = "cbind", signature = "...")
methods::setGeneric(name = "colbind", def = function(x, ...) standardGeneric("colbind"))
methods::setGeneric(name = "cellSize", package = "terra")
methods::setGeneric(name = "classify", package = "terra")
methods::setGeneric(name = "clump", def = function(x, ...) standardGeneric("clump"))
methods::setGeneric(name = "clusterPoints", def = function(x, ...) standardGeneric("clusterPoints"))
methods::setGeneric(name = "compareGeom", package = "terra")
methods::setGeneric("complete.cases", function(...) standardGeneric("complete.cases"), package = "stats")
methods::setGeneric(name = "compositeRGB", def = function(r, ...) standardGeneric("compositeRGB"))
methods::setGeneric(name = "combineCats", def = function(x, ...) standardGeneric("combineCats"))
methods::setGeneric(name = "combineLevels", def = function(x, ...) standardGeneric("combineLevels"))
methods::setGeneric(name = "connectors", def = function(x, y, ...) standardGeneric("connectors"))
methods::setGeneric(name = "convHull", package = "terra")
methods::setGeneric(name = "count", def = function(x, ...) standardGeneric("count"))
methods::setGeneric(name = "crds", package = "terra")
methods::setGeneric(name = "crs", package = "terra")
methods::setGeneric(name = "crop", package = "terra")


# dim() is primitive
methods::setGeneric(name = "datatype", def = function(x, ...) standardGeneric("datatype"))
methods::setGeneric(name = "delaunay", package = "terra")
methods::setGeneric(name = "denoise", def = function(x, ...) standardGeneric("denoise"))
methods::setGeneric(name = "dim3d", def = function(x, ...) standardGeneric("dim3d"))
methods::setGeneric(name = "disagg", package = "terra")
methods::setGeneric(name = "distance", def = function(x, y, ...) standardGeneric("distance"))
methods::setGeneric(name = "droplevels", package = "terra")
methods::setGeneric(name = "dropRows", def = function(x, ...) standardGeneric("dropRows"))
methods::setGeneric(name = "dropTable", def = function(x, ...) standardGeneric("dropTable"))

methods::setGeneric(name = "E", def = function(x, ...) standardGeneric("E"))
# methods::setGeneric(name = "elide", def = function(x, ...) standardGeneric("elide"))
methods::setGeneric(name = "erase", package = "terra") 
methods::setGeneric(name = "ext", package = "terra") 
methods::setGeneric(name = "extend", package = "terra")
methods::setGeneric(name = "expanse", package = "terra")
methods::setGeneric(name = "extract", package = "terra")

methods::setGeneric(name = "fast", def = function(x, ...) standardGeneric("fast"))
methods::setGeneric(name = "fillHoles", package = "terra")
methods::setGeneric(name = "fillNAs", def = function(x, ...) standardGeneric("fillNAs"))
methods::setGeneric(name = "fixBridges", def = function(x, ...) standardGeneric("fixBridges"))
methods::setGeneric(name = "fixDangles", def = function(x, ...) standardGeneric("fixDangles"))
methods::setGeneric(name = "fixLines", def = function(x, ...) standardGeneric("fixLines"))
methods::setGeneric(name = "flow", def = function(x, ...) standardGeneric("flow"))
methods::setGeneric(name = "flowPath", def = function(x, ...) standardGeneric("flowPath"))
methods::setGeneric(name = "focal", package = "terra")
methods::setGeneric(name = "fractalRast", def = function(x, ...) standardGeneric("fractalRast"))
methods::setGeneric(name = "freq", package = "terra")
methods::setGeneric(name = "fragmentation", def = function(x, ...) standardGeneric("fragmentation"))

methods::setGeneric(name = "geomtype", package = "terra")
methods::setGeneric(name = "geomorphons", def = function(x, ...) standardGeneric("geomorphons"))
methods::setGeneric(name = "global", package = "terra")
methods::setGeneric(name = "grid", def = function(x, ...) standardGeneric("grid"))

methods::setGeneric(name = "head", package = "utils")
methods::setGeneric(name = "hexagons", def = function(x, ...) standardGeneric("hexagons"))
methods::setGeneric(name = "hillshade", def = function(x, ...) standardGeneric("hillshade"))
methods::setGeneric(name = "hist", package = "terra")
methods::setGeneric(name = "horizonHeight", def = function(x, ...) standardGeneric("horizonHeight"))

methods::setGeneric(name = "intersect", package = "terra")
methods::setGeneric(name = "intercept", def = function(x, ...) standardGeneric("intercept"))
methods::setGeneric(name = "interpIDW", package = "terra")
methods::setGeneric(name = "interpSplines", def = function(x, y, ...) standardGeneric("interpSplines"))
methods::setGeneric(name = "is.2d", def = function(x) standardGeneric("is.2d"))
methods::setGeneric(name = "is.3d", def = function(x) standardGeneric("is.3d"))
if (!isGeneric("is.factor")) { methods::setGeneric(name = "is.factor", def = function(x) standardGeneric("is.factor")) }
# is.double() is primitive and cannot be made generic
methods::setGeneric(name = "is.cell", def = function(x) standardGeneric("is.cell"))
methods::setGeneric(name = "is.doub", def = function(x) standardGeneric("is.doub"))
methods::setGeneric(name = "is.float", def = function(x) standardGeneric("is.float"))
# methods::setGeneric(name = "is.int", def = function(x) standardGeneric("is.int"))
methods::setGeneric(name = "is.int", package = "terra")
methods::setGeneric(name = "is.lines", package = "terra")
methods::setGeneric(name = "is.lonlat", package = "terra")
if (!isGeneric("is.na")) { methods::setGeneric(name = "is.na", def = function(x) standardGeneric("is.na")) }
methods::setGeneric(name = "is.points", package = "terra")
methods::setGeneric(name = "is.polygons", package = "terra")

# methods::setGeneric(name = "keepRows", def = function(x, ...) standardGeneric("keepRows"))
methods::setGeneric(name = "kernel", def = function(x, ...) standardGeneric("kernel"))
methods::setGeneric(name = "kurtosis", def = function(x, ...) standardGeneric("kurtosis"))

# levels (in base) is generic
# levels<- (in base) is primitive
methods::setGeneric(name = "layerCor", package = "terra")
methods::setGeneric(name = "ln", def = function(x, ...) standardGeneric("ln"))
methods::setGeneric(name = "longlat", def = function(x) standardGeneric("longlat"))
methods::setGeneric(name = "log10p", def = function(x) standardGeneric("log10p"))

methods::setGeneric(name = "mask", package = "terra")
methods::setGeneric(name = "maskNA", def = function(x, ...) standardGeneric("maskNA"))
methods::setGeneric(name = "match", package = "terra")
methods::setGeneric(name = "minmax", package = "terra")
methods::setGeneric(name = "missing.cases", def = function(...) standardGeneric("missing.cases"))
methods::setGeneric(name = "missingCats", def = function(x, ...) standardGeneric("missingCats"))
methods::setGeneric(name = "merge", package = "terra")
#' @importFrom terra median
methods::setGeneric(name = "median", def = function(x, na.rm) standardGeneric("median"))
methods::setGeneric(name = "mmode", def = function(x, ...) package = "omnibus")

# "names" (in base) is primitive
methods::setGeneric(name = "N", def = function(x, ...) standardGeneric("N"))
methods::setGeneric(name = "ncell", package = "terra")
methods::setGeneric(name = "ncell3d", def = function(x) standardGeneric("ncell3d"))
methods::setGeneric(name = "ncol", def = function(x) standardGeneric("ncol")) # in base
methods::setGeneric(name = "ndepth", def = function(x) standardGeneric("ndepth"))
methods::setGeneric(name = "new", package = "methods") 
methods::setGeneric(name = "nlyr", package = "terra")
methods::setGeneric(name = "nacell", def = function(x, ...) standardGeneric("nacell"))
methods::setGeneric(name = "ngeom", def = function(x, ...) standardGeneric("ngeom"))
methods::setGeneric(name = "nlevels", package = "terra")
methods::setGeneric(name = "noise", def = function(x, ...) standardGeneric("noise"))
methods::setGeneric(name = "nonnacell", def = function(x, ...) standardGeneric("nonnacell"))
methods::setGeneric(name = "not.na", def = function(x, ...) standardGeneric("not.na")) # in base
methods::setGeneric(name = "nrow", def = function(x) standardGeneric("nrow")) # in base
methods::setGeneric(name = "nsubgeom", def = function(x, ...) standardGeneric("nsubgeom"))
methods::setGeneric(name = "nunique", def = function(x, ...) standardGeneric("nunique"))

# methods::setGeneric(name = "orOrOr", def = function(e1, e2) standardGeneric("orOrOr"))
methods::setGeneric(name = "reorient", def = function(x, ...) standardGeneric("reorient"))

methods::setGeneric(name = "pairs", package = "terra")
methods::setGeneric(name = "pca", def = function(x, ...) standardGeneric("pca"))
methods::setGeneric(name = "plot", package = "terra")
methods::setGeneric(name = "plotRGB", package = "terra")
methods::setGeneric(name = "predict", package = "terra")
# methods::setGeneric(name = "print", def = function(x, ...) standardGeneric("print")) # base
methods::setGeneric(name = "print") # base
methods::setGeneric(name = "project", package = "terra")

methods::setGeneric(name = "quantile", package = "terra")

methods::setGeneric(name = "r2", def = function(x, ...) standardGeneric("r2"))
methods::setGeneric(name = "rast", package = "terra")
methods::setGeneric(name = "rasterize", package = "terra")
# methods::setGeneric(name = "rbind")

# from https://stackoverflow.com/questions/27886535/proper-way-to-use-cbind-rbind-with-s4-classes-in-package
methods::getGeneric("rbind")
methods::setGeneric(name = "rbind", signature = "...")

methods::setGeneric(name = "remove0", def = function(x, ...) standardGeneric("remove0"))
methods::setGeneric(name = "removeAngles", def = function(x, ...) standardGeneric("removeAngles"))
methods::setGeneric(name = "removeBridges", def = function(x, ...) standardGeneric("removeBridges"))
methods::setGeneric(name = "removeDangles", def = function(x, ...) standardGeneric("removeDangles"))
methods::setGeneric(name = "removeDupCentroids", def = function(x, ...) standardGeneric("removeDupCentroids"))
methods::setGeneric(name = "removeDups", def = function(x, ...) standardGeneric("removeDups"))
methods::setGeneric(name = "removeSmallPolys", def = function(x, ...) standardGeneric("removeSmallPolys"))
methods::setGeneric(name = "replaceNAs", def = function(x, ...) standardGeneric("replaceNAs"))
methods::setGeneric(name = "res", package = "terra")
methods::setGeneric(name = "res3d", def = function(x) standardGeneric("res3d"))
methods::setGeneric(name = "resample", package = "terra")
methods::setGeneric(name = "rnormRast", def = function(x, ...) standardGeneric("rnormRast"))
methods::setGeneric(name = "ruggedness", def = function(x, ...) standardGeneric("ruggedness"))
methods::setGeneric(name = "runifRast", def = function(x, ...) standardGeneric("runifRast"))
methods::setGeneric(name = "rvoronoi", def = function(x, ...) standardGeneric("rvoronoi"))

methods::setGeneric(name = "S", def = function(x, ...) standardGeneric("S"))
methods::setGeneric(name = "sampleRast", def = function(x, ...) standardGeneric("sampleRast"))
methods::setGeneric(name = "scale", package = "terra")
methods::setGeneric(name = "scalepop", def = function(x, ...) standardGeneric("scalepop"))
methods::setGeneric(name = "sdpop", def = function(x, ...) standardGeneric("sdpop"))
methods::setGeneric(name = "selectRange", def = function(x, ...) standardGeneric("selectRange"))
methods::setGeneric(name = "show", package = "methods")
methods::setGeneric(name = "simplifyGeom", package = "terra")
methods::setGeneric(name = "sineRast", def = function(x, ...) standardGeneric("sineRast"))
methods::setGeneric(name = "smoothGeom", def = function(x, ...) standardGeneric("smoothGeom"))
methods::setGeneric(name = "skewness", def = function(x, ...) standardGeneric("skewness"))
methods::setGeneric(name = "slope", def = function(x, ...) standardGeneric("slope"))
methods::setGeneric(name = "snap", package = "terra")
methods::setGeneric(name = "sources", package = "terra")
methods::setGeneric(name = "spatSample", package = "terra")
methods::setGeneric(name = "rSpatialDepRast", def = function(x, ...) standardGeneric("rSpatialDepRast"))

methods::setGeneric(name = "streams", def = function(x, ...) standardGeneric("streams"))
methods::setGeneric(name = "stretch", package = "terra")
methods::setGeneric(name = "st_as_sf", package = "sf")
# methods::setGeneric(name = "st_bbox", package = "sf")
methods::setGeneric(name = "st_buffer", package = "sf")
methods::setGeneric(name = "st_crs", package = "sf")
# methods::setGeneric(name = "st_distance", package = "sf")
methods::setGeneric(name = "stdev", package = "terra")
methods::setGeneric(name = "subst", package = "terra")
methods::setGeneric(name = "summary", def = function(object, ...) standardGeneric("summary"))

methods::setGeneric(name = "terrain", package = "terra")
methods::setGeneric(name = "thinLines", def = function(x, ...) standardGeneric("thinLines"))
methods::setGeneric(name = "thinPoints", def = function(x, y, ...) standardGeneric("thinPoints"))
methods::setGeneric(name = "tiles", def = function(x, ...) standardGeneric("tiles"))
methods::setGeneric(name = "top", def = function(x, ...) standardGeneric("top"))
methods::setGeneric(name = "topology", def = function(x, ...) standardGeneric("topology"))
methods::setGeneric(name = "trim", package = "terra")
methods::setGeneric(name = "tvalue", def = function(x, ...) standardGeneric("tvalue"))

methods::setGeneric(name = "update", package = "terra")
methods::setGeneric(name = "union", package = "terra")
methods::setGeneric(name = "unscale", def = function(x, ...) standardGeneric("unscale"))

methods::setGeneric(name = "varpop", def = function(x, ...) standardGeneric("varpop"))
methods::setGeneric(name = "vegIndex", def = function(x, ...) standardGeneric("vegIndex"))
methods::setGeneric(name = "vect", package = "terra")
methods::setGeneric(name = "voronoi", package = "terra")

methods::setGeneric(name = "W", def = function(x, ...) standardGeneric("W"))
methods::setGeneric(name = "wetness", def = function(x, ...) standardGeneric("wetness"))
methods::setGeneric(name = "workDir", def = function(x, ...) standardGeneric("workDir"))
methods::setGeneric(name = "writeRaster", package = "terra")
methods::setGeneric(name = "writeVector", package = "terra")

methods::setGeneric(name = "xres", package = "terra")
methods::setGeneric(name = "xor", def = function(x, y, ...) standardGeneric("xor"))

methods::setGeneric(name = "yres", package = "terra")

methods::setGeneric(name = "zext", def = function(x) standardGeneric("zext"))
methods::setGeneric(name = "zonal", package = "terra")
methods::setGeneric(name = "zonalGeog", def = function(x, ...) standardGeneric("zonalGeog"))
methods::setGeneric(name = "zres", def = function(x) standardGeneric("zres"))