# predict

##### Spatial model predictions

Make a Raster object with predictions from a fitted model object (for example, obtained with `lm`

, `glm`

). The first argument is a Raster object with the independent (predictor) variables. The `names`

in the Raster object should exactly match those expected by the model. This will be the case if the same Raster object was used (via `extract`

) to obtain the values to fit the model (see the example). Any type of model (e.g. glm, gam, randomForest) for which a predict method has been implemented (or can be implemented) can be used.

This approach (predict a fitted model to raster data) is commonly used in remote sensing (for the classification of satellite images) and in ecology, for species distribution modeling.

##### Usage

```
# S4 method for Raster
predict(object, model, filename="", fun=predict, ext=NULL,
const=NULL, index=1, na.rm=TRUE, inf.rm=FALSE, factors=NULL,
format, datatype, overwrite=FALSE, progress='', ...)
```

##### Arguments

- object
Raster* object. Typically a multi-layer type (RasterStack or RasterBrick)

- model
fitted model of any class that has a 'predict' method (or for which you can supply a similar method as

`fun`

argument. E.g. glm, gam, or randomForest- filename
character. Optional output filename

- fun
function. Default value is 'predict', but can be replaced with e.g. predict.se (depending on the type of model), or your own custom function.

- ext
Extent object to limit the prediction to a sub-region of

`x`

- const
data.frame. Can be used to add a constant for which there is no Raster object for model predictions. Particularly useful if the constant is a character-like factor value for which it is currently not possible to make a RasterLayer

- index
integer. To select the column(s) to use if predict.'model' returns a matrix with multiple columns

- na.rm
logical. Remove cells with

`NA`

values in the predictors before solving the model (and return a`NA`

value for those cells). This option prevents errors with models that cannot handle`NA`

values. In most other cases this will not affect the output. An exception is when predicting with a boosted regression trees model because these return predicted values even if some (or all!) variables are`NA`

- inf.rm
logical. Remove cells with values that are not finite (some models will fail with -Inf/Inf values). This option is ignored when

`na.rm=FALSE`

- factors
list with levels for factor variables. The list elements should be named with names that correspond to names in

`object`

such that they can be matched. This argument may be omitted for standard models such as 'glm' as the predict function will extract the levels from the`model`

object, but it is necessary in some other cases (e.g. cforest models from the party package)- format
character. Output file type. See writeRaster (optional)

- datatype
character. Output data type. See dataType (optional)

- overwrite
logical. If TRUE, "filename" will be overwritten if it exists

- progress
character. "text", "window", or "" (the default, no progress bar)

- ...
additional arguments to pass to the predict.'model' function

##### Value

RasterLayer or RasterBrick

##### Note

For more on the use of the predict function see this resource on species distribution modeling.

##### See Also

Use `interpolate`

if your model has 'x' and 'y' as implicit independent variables (e.g., in kriging).

##### Examples

```
# NOT RUN {
# A simple model to predict the location of the R in the R-logo using 20 presence points
# and 50 (random) pseudo-absence points. This type of model is often used to predict
# species distributions. See the dismo package for more of that.
# create a RasterStack or RasterBrick with with a set of predictor layers
logo <- brick(system.file("external/rlogo.grd", package="raster"))
names(logo)
# }
# NOT RUN {
# the predictor variables
par(mfrow=c(2,2))
plotRGB(logo, main='logo')
plot(logo, 1, col=rgb(cbind(0:255,0,0), maxColorValue=255))
plot(logo, 2, col=rgb(cbind(0,0:255,0), maxColorValue=255))
plot(logo, 3, col=rgb(cbind(0,0,0:255), maxColorValue=255))
par(mfrow=c(1,1))
# }
# NOT RUN {
# known presence and absence points
p <- matrix(c(48, 48, 48, 53, 50, 46, 54, 70, 84, 85, 74, 84, 95, 85,
66, 42, 26, 4, 19, 17, 7, 14, 26, 29, 39, 45, 51, 56, 46, 38, 31,
22, 34, 60, 70, 73, 63, 46, 43, 28), ncol=2)
a <- matrix(c(22, 33, 64, 85, 92, 94, 59, 27, 30, 64, 60, 33, 31, 9,
99, 67, 15, 5, 4, 30, 8, 37, 42, 27, 19, 69, 60, 73, 3, 5, 21,
37, 52, 70, 74, 9, 13, 4, 17, 47), ncol=2)
# extract values for points
xy <- rbind(cbind(1, p), cbind(0, a))
v <- data.frame(cbind(pa=xy[,1], extract(logo, xy[,2:3])))
#build a model, here an example with glm
model <- glm(formula=pa~., data=v)
#predict to a raster
r1 <- predict(logo, model, progress='text')
plot(r1)
points(p, bg='blue', pch=21)
points(a, bg='red', pch=21)
# use a modified function to get a RasterBrick with p and se
# from the glm model. The values returned by 'predict' are in a list,
# and this list needs to be transformed to a matrix
predfun <- function(model, data) {
v <- predict(model, data, se.fit=TRUE)
cbind(p=as.vector(v$fit), se=as.vector(v$se.fit))
}
# predfun returns two variables, so use index=1:2
r2 <- predict(logo, model, fun=predfun, index=1:2)
# }
# NOT RUN {
# You can use multiple cores to speed up the predict function
# by calling it via the clusterR function (you may need to install the snow package)
beginCluster()
r1c <- clusterR(logo, predict, args=list(model))
r2c <- clusterR(logo, predict, args=list(model=model, fun=predfun, index=1:2))
# }
# NOT RUN {
# principal components of a RasterBrick
# here using sampling to simulate an object too large
# too feed all its values to prcomp
sr <- sampleRandom(logo, 100)
pca <- prcomp(sr)
# note the use of the 'index' argument
x <- predict(logo, pca, index=1:3)
plot(x)
# }
# NOT RUN {
# partial least square regression
library(pls)
model <- plsr(formula=pa~., data=v)
# this returns an array:
predict(model, v[1:5,])
# write a function to turn that into a matrix
pfun <- function(x, data) {
y <- predict(x, data)
d <- dim(y)
dim(y) <- c(prod(d[1:2]), d[3])
y
}
pp <- predict(logo, model, fun=pfun, index=1:3)
# Random Forest
library(randomForest)
rfmod <- randomForest(pa ~., data=v)
## note the additional argument "type='response'" that is
## passed to predict.randomForest
r3 <- predict(logo, rfmod, type='response', progress='window')
## get a RasterBrick with class membership probabilities
vv <- v
vv$pa <- as.factor(vv$pa)
rfmod2 <- randomForest(pa ~., data=vv)
r4 <- predict(logo, rfmod2, type='prob', index=1:2)
spplot(r4)
# cforest (other Random Forest implementation) example with factors argument
v$red <- as.factor(round(v$red/100))
logo$red <- round(logo[[1]]/100)
library(party)
m <- cforest(pa~., control=cforest_unbiased(mtry=3), data=v)
f <- list(levels(v$red))
names(f) <- 'red'
# the second argument in party:::predict.RandomForest
# is "OOB", and not "newdata" or similar. We need to write a wrapper
# predict function to deal with this
predfun <- function(m, d, ...) predict(m, newdata=d, ...)
pc <- predict(logo, m, OOB=TRUE, factors=f, fun=predfun)
# knn example, using calc instead of predict
library(class)
cl <- factor(c(rep(1, nrow(p)), rep(0, nrow(a))))
train <- extract(logo, rbind(p, a))
k <- calc(logo, function(x) as.integer(as.character(knn(train, x, cl))))
# }
```

*Documentation reproduced from package raster, version 2.9-5, License: GPL (>= 3)*