util/prov_samples/prov_console_2021-01-12T13.31.09-03/scripts/console.R

In mmondelli/rdt2repr: rdt to reproduceme parser

library(modleR)
library(sp)
species <- names(example_occs)
occs <- example_occs[[1]]
test_folder <- "~/Dropbox/Reproducibility/prov2repr/prov_samples/modler_results"
sdmdata_1sp <- modleR::setup_sdmdata(species_name = species[1], 
    occurrences = occs, predictors = example_vars, models_dir = test_folder, 
    partition_type = "crossvalidation", cv_partitions = 5, cv_n = 1, 
    buffer_type = "mean", png_sdmdata = F, n_back = 500, clean_dupl = FALSE, 
    clean_uni = FALSE, clean_nas = FALSE, geo_filt = FALSE, geo_filt_dist = 10, 
    select_variables = TRUE, sample_proportion = 0.5, cutoff = 0.7)
many <- modleR::do_many(species_name = species[1], predictors = example_vars, 
    models_dir = test_folder, png_partitions = F, write_bin_cut = FALSE, 
    write_rda = TRUE, bioclim = FALSE, domain = FALSE, glm = FALSE, 
    svmk = FALSE, svme = FALSE, maxnet = F, rf = F, mahal = FALSE, 
    brt = TRUE, equalize = TRUE)
fm <- modleR::final_model(species_name = species[1], algorithms = NULL, 
    models_dir = test_folder, which_models = c("raw_mean", "bin_mean", 
        "bin_consensus"), consensus_level = 0.5, uncertainty = TRUE, 
    overwrite = TRUE, png_final = F)
ens <- modleR::ensemble_model(species_name = species[1], occurrences = occs, 
    performance_metric = "pROC", which_ensemble = c("average", 
        "best", "frequency", "weighted_average", "median", "pca", 
        "consensus"), consensus_level = 0.5, which_final = "raw_mean", 
    models_dir = test_folder, overwrite = TRUE, png_ensemble = F)