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Contribution of each predictor to model transferability

Source: R/rf_importance.R
rf_importance.Rd

Evaluates the contribution of the predictors to model transferability via spatial cross-validation. The function returns the median increase or decrease in a given evaluation metric (R2, pseudo R2, RMSE, nRMSE, or AUC) when a variable is introduced in a model, by comparing and evaluating via spatial cross-validation models with and without the given variable. This function was devised to provide importance scores that would be less sensitive to spatial autocorrelation than those computed internally by random forest on the out-of-bag data. This function is experimental.

Usage

rf_importance(
  model = NULL,
  xy = NULL,
  repetitions = 30,
  training.fraction = 0.75,
  metric = c("r.squared", "pseudo.r.squared", "rmse", "nrmse", "auc"),
  distance.step = NULL,
  distance.step.x = NULL,
  distance.step.y = NULL,
  fill.color = viridis::viridis(100, option = "F", direction = -1, alpha = 1, end = 0.9),
  line.color = "white",
  seed = 1,
  verbose = TRUE,
  n.cores = parallel::detectCores() - 1,
  cluster = NULL
)

Arguments

model

Model fitted with rf() and/or rf_spatial(). The function doesn't work with models fitted with rf_repeat(). Default: NULL

xy

Data frame or matrix with two columns containing coordinates and named "x" and "y". If NULL, the function will throw an error. Default: NULL

repetitions

Integer, number of spatial folds to use during cross-validation. Must be lower than the total number of rows available in the model's data. Default: 30

training.fraction

Proportion between 0.5 and 0.9 indicating the proportion of records to be used as training set during spatial cross-validation. Default: 0.75

metric

Character, nams of the performance metric to use. The possible values are: "r.squared" (cor(obs, pred) ^ 2), "pseudo.r.squared" (cor(obs, pred)), "rmse" (sqrt(sum((obs - pred)^2)/length(obs))), "nrmse" (rmse/(quantile(obs, 0.75) - quantile(obs, 0.25))), and "auc" (only for binary responses with values 1 and 0). Default: "r.squared"

distance.step

Numeric, argument distance.step of thinning_til_n(). distance step used during the selection of the centers of the training folds. These fold centers are selected by thinning the data until a number of folds equal or lower than repetitions is reached. Its default value is 1/1000th the maximum distance within records in xy. Reduce it if the number of training folds is lower than expected.

distance.step.x

Numeric, argument distance.step.x of make_spatial_folds(). Distance step used during the growth in the x axis of the buffers defining the training folds. Default: NULL (1/1000th the range of the x coordinates).

distance.step.y

Numeric, argument distance.step.x of make_spatial_folds(). Distance step used during the growth in the y axis of the buffers defining the training folds. Default: NULL (1/1000th the range of the y coordinates).

fill.color

Character vector with hexadecimal codes (e.g. "#440154FF" "#21908CFF" "#FDE725FF"), or function generating a palette (e.g. viridis::viridis(100)). Default: viridis::viridis(100, option = "F", direction = -1, alpha = 0.8, end = 0.9)

line.color

Character string, color of the line produced by ggplot2::geom_smooth(). Default: "white"

seed

Integer, random seed to facilitate reproduciblity. If set to a given number, the results of the function are always the same. Default: 1.

verbose

Logical. If TRUE, messages and plots generated during the execution of the function are displayed, Default: TRUE

n.cores

Integer, number of cores to use for parallel execution. Creates a socket cluster with parallel::makeCluster(), runs operations in parallel with foreach and %dopar%, and stops the cluster with parallel::clusterStop() when the job is done. Default: parallel::detectCores() - 1

cluster

A cluster definition generated with parallel::makeCluster(). If provided, overrides n.cores. When cluster = NULL (default value), and model is provided, the cluster in model, if any, is used instead. If this cluster is NULL, then the function uses n.cores instead. The function does not stop a provided cluster, so it should be stopped with parallel::stopCluster() afterwards. The cluster definition is stored in the output list under the name "cluster" so it can be passed to other functions via the model argument, or using the %>% pipe. Default: NULL

Value

The input model with new data in its "importance" slot. The new importance scores are included in the data frame model$importance$per.variable, under the column names "importance.cv" (median contribution to transferability over spatial cross-validation repetitions), "importance.cv.mad" (median absolute deviation of the performance scores over spatial cross-validation repetitions), "importance.cv.percent" ("importance.cv" expressed as a percent, taking the full model's performance as baseline), and "importance.cv.mad" (median absolute deviation of "importance.cv"). The plot is stored as "cv.per.variable.plot".

Examples

if(interactive()){

#loading example data
data(plant_richness_df)
data(distance_matrix)
xy <- plant_richness_df[, c("x", "y")]

#fitting random forest model
rf.model <- rf(
  data = plant_richness_df,
  dependent.variable.name = "richness_species_vascular",
  predictor.variable.names = colnames(plant_richness_df)[5:21],
  distance.matrix = distance_matrix,
  distance.thresholds = 0,
  xy = xy,
  n.cores = 1,
  verbose = FALSE
)

#computing predictor contribution to model transferability
rf.model <- rf_importance(rf.model)

}