Plot Response Curve
Plot the Response Curve of the given environmental variable.
plotResponse( model, var, type = NULL, only_presence = FALSE, marginal = FALSE, fun = mean, rug = FALSE, color = "red" )
model |
SDMmodel or SDMmodelCV object. |
var |
character. Name of the variable to be plotted. |
type |
character. The output type used for "Maxent" and "Maxnet"
methods, possible values are "cloglog" and "logistic", default is |
only_presence |
logical, if |
marginal |
logical, if |
fun |
function used to compute the level of the other variables for
marginal curves, default is |
rug |
logical, if |
color |
The color of the curve, default is "red". |
Note that fun is not a character argument, you must use mean and
not "mean".
A ggplot object.
Sergio Vignali
# Acquire environmental variables
files <- list.files(path = file.path(system.file(package = "dismo"), "ex"),
pattern = "grd", full.names = TRUE)
predictors <- raster::stack(files)
# Prepare presence and background locations
p_coords <- virtualSp$presence
bg_coords <- virtualSp$background
# Create SWD object
data <- prepareSWD(species = "Virtual species", p = p_coords, a = bg_coords,
env = predictors, categorical = "biome")
# Train a model
model <- train(method = "Maxnet", data = data, fc = "lq")
# Plot cloglog response curve for a continuous environmental variable (bio1)
plotResponse(model, var = "bio1", type = "cloglog")
# Plot marginal cloglog response curve for a continuous environmental
# variable (bio1)
plotResponse(model, var = "bio1", type = "cloglog", marginal = TRUE)
# Plot logistic response curve for a continuous environmental variable
# (bio12) adding the rugs and giving a custom color
plotResponse(model, var = "bio12", type = "logistic", rug = TRUE,
color = "blue")
# Plot response curve for a categorical environmental variable (biome) giving
# a custom color
plotResponse(model, var = "biome", type = "logistic", color = "green")
# Train a model with cross validation
folds <- randomFolds(data, k = 4, only_presence = TRUE)
model <- train(method = "Maxnet", data = data, fc = "lq", folds = folds)
# Plot cloglog response curve for a continuous environmental variable (bio17)
plotResponse(model, var = "bio1", type = "cloglog")
# Plot logistic response curve for a categorical environmental variable
# (biome) giving a custom color
plotResponse(model, var = "biome", type = "logistic", color = "green")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.