diff options
Diffstat (limited to 'R/predict.R')
| -rw-r--r-- | R/predict.R | 45 |
1 files changed, 28 insertions, 17 deletions
diff --git a/R/predict.R b/R/predict.R index 68efbb7..37b9f87 100644 --- a/R/predict.R +++ b/R/predict.R @@ -25,8 +25,7 @@ setMethod("predict", "unmarkedFit", orig_formula <- get_formula(object, type) # 2. If newdata is raster, get newdata from raster as data.frame - if(inherits(newdata, c("RasterLayer","RasterStack"))){ - if(!require(raster)) stop("raster package required", call.=FALSE) + if(inherits(newdata, c("RasterLayer","RasterStack","SpatRaster"))){ is_raster <- TRUE orig_raster <- newdata newdata <- newdata_from_raster(newdata, all.vars(orig_formula)) @@ -95,8 +94,8 @@ setMethod("check_predict_arguments", "unmarkedFit", check_type(object, type) # Check newdata class - if(!inherits(newdata, c("unmarkedFrame", "data.frame", "RasterLayer", "RasterStack"))){ - stop("newdata must be unmarkedFrame, data.frame, RasterLayer, or RasterStack", call.=FALSE) + if(!inherits(newdata, c("unmarkedFrame", "data.frame", "RasterLayer", "RasterStack", "SpatRaster"))){ + stop("newdata must be unmarkedFrame, data.frame, RasterLayer, RasterStack, or SpatRaster", call.=FALSE) } invisible(TRUE) }) @@ -261,27 +260,39 @@ setMethod("predict_by_chunk", "unmarkedFit", # Raster handling functions---------------------------------------------------- # Convert a raster into a data frame to use as newdata -newdata_from_raster <- function(rst, vars){ - nd <- raster::as.data.frame(rst) - # Handle factor rasters - is_fac <- raster::is.factor(rst) - rem_string <- paste(paste0("^",names(rst),"_"), collapse="|") - names(nd)[is_fac] <- gsub(rem_string, "", names(nd)[is_fac]) +newdata_from_raster <- function(object, vars){ + if(inherits(object, "Raster")){ + if(!requireNamespace("raster", quietly=TRUE)) stop("raster package required", call.=FALSE) + nd <- raster::as.data.frame(object) + # Handle factor rasters + is_fac <- raster::is.factor(object) + rem_string <- paste(paste0("^",names(object),"_"), collapse="|") + names(nd)[is_fac] <- gsub(rem_string, "", names(nd)[is_fac]) + } else if(inherits(object, "SpatRaster")){ + if(!requireNamespace("terra", quietly=TRUE)) stop("terra package required", call.=FALSE) + nd <- terra::as.data.frame(object) + } # Check if variables are missing no_match <- vars[! vars %in% names(nd)] if(length(no_match) > 0){ - stop(paste0("Variable(s) ",paste(no_match, collapse=", "), " not found in raster stack"), + stop(paste0("Variable(s) ",paste(no_match, collapse=", "), " not found in raster(s)"), call.=FALSE) } return(nd) } -# Convert predict output into a raster -raster_from_predict <- function(pr, orig_rst, appendData){ - new_rast <- data.frame(raster::coordinates(orig_rst), pr) - new_rast <- raster::stack(raster::rasterFromXYZ(new_rast)) - raster::crs(new_rast) <- raster::crs(orig_rst) - if(appendData) new_rast <- raster::stack(new_rast, orig_rst) +raster_from_predict <- function(pr, object, appendData){ + if(inherits(object, "Raster")){ + new_rast <- data.frame(raster::coordinates(object), pr) + new_rast <- raster::stack(raster::rasterFromXYZ(new_rast)) + raster::crs(new_rast) <- raster::crs(object) + if(appendData) new_rast <- raster::stack(new_rast, object) + } else if(inherits(object, "SpatRaster")){ + new_rast <- data.frame(terra::crds(object), pr) + new_rast <- terra::rast(new_rast, type="xyz") + terra::crs(new_rast) <- terra::crs(object) + if(appendData) new_rast <- c(new_rast, object) + } new_rast } |