Package: maxentcpp 1.0.0

maxentcpp: Maximum Entropy Species Distribution Modeling ('C++' Implementation)

'C++' implementation of Maximum Entropy (Maxent) species distribution modeling with R bindings via 'Rcpp'. Provides a high-performance reimplementation of the Maxent algorithm for modeling species geographic distributions from occurrence data and environmental variables, following Phillips et al. (2006) <doi:10.1016/j.ecolmodel.2005.03.026>. Supports linear, quadratic, product, hinge, and threshold feature transformations, spatial projection in raw, logistic, and cloglog scales, and model diagnostics including Area Under the ROC Curve (AUC), variable importance, response curves, and Multivariate Environmental Similarity Surfaces (MESS) maps.

Authors:Angel Robles [aut, cre]

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manual.pdf |manual.html✨
card.svg |card.png
maxentcpp/json (API)
NEWS

# Install 'maxentcpp' in R:
install.packages('maxentcpp', repos = c('https://alrobles.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alrobles/maxentcpp/issues

Pkgdown/docs site:https://alrobles.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • example_occ_df - Species occurrence points from Abeillia abeillei presence points after download and clean from GBIF. This is a hummingbird example. A dataset with three variables. Contains scientific name, longitude and latitude.

On CRAN:

Conda:

cpp

3.11 score 13 scripts 148 exports 2 dependencies

Last updated from:88ddc4fdde. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK169
linux-devel-x86_64OK178
source / vignettesOK258
linux-release-arm64OK210
linux-release-x86_64OK169
macos-release-arm64OK199
macos-release-x86_64OK438
macos-oldrel-arm64OK119
macos-oldrel-x86_64OK216
windows-develOK188
windows-releaseOK175
windows-oldrelOK196
wasm-releaseOK152

Exports:clamp_gridscompute_messcompute_mess_rangecompute_percent_contributioncompute_permutation_importancecompute_response_curvecompute_response_curve_fixedcompute_variable_rangescoords_to_rowcolcreate_grid_dimensioncreate_grid_floatcreate_hinge_featurecreate_layercreate_linear_featurecreate_product_featurecreate_quadratic_featurecreate_samplecreate_threshold_featurecsv_closecsv_headerscsv_next_recordcsv_opencsv_read_double_columncsv_writer_closecsv_writer_opencsv_writer_printcsv_writer_print_doublecsv_writer_printlneval_auceval_correlationeval_loglosseval_misclassificationeval_modeleval_square_errorextract_predictions_rawfeature_evalfeature_get_infogenerate_featuresget_grid_dimension_infoget_layer_infoget_sample_infogrid_float_from_matrixgrid_float_infogrid_float_to_matrixgrid_from_matrixgrid_get_valuegrid_get_values_batchgrid_has_datagrid_read_ascgrid_read_filegrid_set_valuegrid_to_matrixgrid_write_asclayer_name_from_pathmaxent_append_results_csvmaxent_aucmaxent_background_indicesmaxent_clampmaxent_color_rampmaxent_correlationmaxent_csv_closemaxent_csv_headersmaxent_csv_nextmaxent_csv_openmaxent_csv_read_columnmaxent_csv_writemaxent_csv_write_closemaxent_csv_write_nummaxent_csv_write_openmaxent_csv_write_rowmaxent_dimensionmaxent_evaluatemaxent_extract_lambdasmaxent_extract_occurrence_env_terramaxent_extract_predictions_cloglogmaxent_extract_predictions_logisticmaxent_extract_predictions_rawmaxent_feature_evalmaxent_feature_infomaxent_featured_spacemaxent_featured_space_createmaxent_featured_space_from_callbackmaxent_featured_space_from_rastmaxent_featured_space_infomaxent_fitmaxent_generate_featuresmaxent_get_entropymaxent_get_lossmaxent_get_weightsmaxent_gridmaxent_grid_from_matrixmaxent_grid_from_terramaxent_grid_infomaxent_grid_to_matrixmaxent_grid_to_terramaxent_hinge_featuremaxent_layermaxent_layer_infomaxent_layer_namemaxent_linear_featuremaxent_load_lambdasmaxent_loglossmaxent_messmaxent_mess_rangemaxent_misclassificationmaxent_model_entropymaxent_model_lossmaxent_model_weightsmaxent_percent_contributionmaxent_permutation_importancemaxent_plot_response_curvesmaxent_plot_variable_importancemaxent_predictmaxent_predict_modelmaxent_print_resultsmaxent_product_featuremaxent_project_cloglogmaxent_project_logisticmaxent_project_rawmaxent_quadratic_featuremaxent_raster_sample_indicesmaxent_read_ascmaxent_read_gridmaxent_read_lambdasmaxent_read_occurrencesmaxent_response_curvemaxent_response_curve_fixedmaxent_runmaxent_samplemaxent_save_lambdasmaxent_sequential_fitmaxent_set_sample_expectationsmaxent_space_infomaxent_square_errormaxent_threshold_featuremaxent_trainmaxent_train_terramaxent_variable_rangesmaxent_write_ascmaxent_write_lambdasmaxent_write_omission_csvmaxent_write_prediction_pngmaxent_write_sample_predictionsproject_cloglogproject_logisticproject_rawsample_get_featuresample_set_feature

Dependencies:RcppRcppEigen

Readme and manuals

Help Manual

Help pageTopics
Clamp Environmental Gridsclamp_grids
Compute MESS (Multivariate Environmental Similarity Surface)compute_mess
Compute MESS from Min/Max Rangescompute_mess_range
Compute Percent Contributioncompute_percent_contribution
Compute Permutation Importancecompute_permutation_importance
Compute Java-compatible Marginal Response Curvecompute_response_curve
Compute Java-compatible Response Curve with Fixed Valuescompute_response_curve_fixed
Compute Variable Ranges from Gridscompute_variable_ranges
Convert geographic coordinates to row/colcoords_to_rowcol
Create a GridDimension objectcreate_grid_dimension
Create a float Grid objectcreate_grid_float
Create a HingeFeature objectcreate_hinge_feature
Create a Layer metadata objectcreate_layer
Create a LinearFeature objectcreate_linear_feature
Create a ProductFeature objectcreate_product_feature
Create a QuadraticFeature objectcreate_quadratic_feature
Create a Sample objectcreate_sample
Create a ThresholdFeature objectcreate_threshold_feature
Close a CsvReadercsv_close
Get CSV column headerscsv_headers
Read the next CSV recordcsv_next_record
Open a CSV file for readingcsv_open
Read an entire named column as doublescsv_read_double_column
Close a CsvWritercsv_writer_close
Open a CSV file for writingcsv_writer_open
Write a value into the current row of a CSVcsv_writer_print
Write a numeric value into the current row of a CSVcsv_writer_print_double
Flush the current CSV row to diskcsv_writer_println
Compute AUC (Area Under the ROC Curve)eval_auc
Compute Pearson Correlationeval_correlation
Compute Log-Losseval_logloss
Compute Misclassification Rateeval_misclassification
Full Model Evaluationeval_model
Compute Mean Squared Erroreval_square_error
Species occurrence points from Abeillia abeillei presence points after download and clean from GBIF. This is a hummingbird example. A dataset with three variables. Contains scientific name, longitude and latitude.example_occ_df
Extract Java-compatible Raw Predictions at Sample Locationsextract_predictions_raw
Evaluate a feature at a given indexfeature_eval
Get feature metadatafeature_get_info
Generate features from a list of environmental variable vectorsgenerate_features
Get grid dimension propertiesget_grid_dimension_info
Get layer metadataget_layer_info
Get sample propertiesget_sample_info
Create a GridFloat from an R matrixgrid_float_from_matrix
Get grid information for an ASC-loaded gridgrid_float_info
Extract the data from a GridFloat as an R matrixgrid_float_to_matrix
Set grid from matrixgrid_from_matrix
Get grid valuegrid_get_value
Extract multiple values from a Grid at given row/col indices (batch)grid_get_values_batch
Check if grid cell has datagrid_has_data
Read an ESRI ASCII grid (.asc) filegrid_read_asc
Read a grid from file (auto-detect format)grid_read_file
Set grid valuegrid_set_value
Get grid as matrixgrid_to_matrix
Write a float Grid to an ESRI ASCII (.asc) filegrid_write_asc
Extract a layer name from a file pathlayer_name_from_path
Append a Row to maxentResults.csvmaxent_append_results_csv
Compute AUC (Area Under the ROC Curve)maxent_auc
Generate Background Sample Indicesmaxent_background_indices
Clamp Environmental Gridsmaxent_clamp
Generate the Maxent Canonical Color Rampmaxent_color_ramp
Compute Pearson Correlationmaxent_correlation
Close a CSV Readermaxent_csv_close
Get CSV Column Headersmaxent_csv_headers
Read the Next CSV Recordmaxent_csv_next
Open a CSV File for Readingmaxent_csv_open
Read an Entire Column as Doublesmaxent_csv_read_column
Write a String Value to the Current CSV Rowmaxent_csv_write
Close a CSV Writermaxent_csv_write_close
Write a Numeric Value to the Current CSV Rowmaxent_csv_write_num
Open a CSV File for Writingmaxent_csv_write_open
Flush the Current Row to the CSV Filemaxent_csv_write_row
Create a Grid Dimension Objectmaxent_dimension
Full Model Evaluationmaxent_evaluate
Extract Lambda Values from a Maxent Run Resultmaxent_extract_lambdas
Extract environmental values for occurrences from a terra SpatRastermaxent_extract_occurrence_env_terra
Extract Cloglog Predictions at Sample Locationsmaxent_extract_predictions_cloglog
Extract Logistic Predictions at Sample Locationsmaxent_extract_predictions_logistic
Extract Raw Predictions at Sample Locationsmaxent_extract_predictions_raw
Evaluate a Feature at a Given Indexmaxent_feature_eval
Get Feature Propertiesmaxent_feature_info
Create a FeaturedSpace Objectmaxent_featured_space
Create a FeaturedSpace objectmaxent_featured_space_create
Create a FeaturedSpace from a streaming background providermaxent_featured_space_from_callback
Create a FeaturedSpace directly from a terra SpatRastermaxent_featured_space_from_rast
Get FeaturedSpace metadatamaxent_featured_space_info
Train a MaxEnt Modelmaxent_fit
Generate Features from Environmental Variable Datamaxent_generate_features
Get entropy of a FeaturedSpace distributionmaxent_get_entropy
Get current loss of a FeaturedSpacemaxent_get_loss
Get current distribution weights from a FeaturedSpacemaxent_get_weights
Create a Grid Objectmaxent_grid
Create a Grid from an R Matrixmaxent_grid_from_matrix
Convert a terra SpatRaster to a maxentcpp GridFloatmaxent_grid_from_terra
Get Grid Informationmaxent_grid_info
Convert Grid to R Matrixmaxent_grid_to_matrix
Convert a maxentcpp GridFloat to a terra SpatRastermaxent_grid_to_terra
Create a Hinge Featuremaxent_hinge_feature
Create a Layer Metadata Objectmaxent_layer
Get Layer Metadatamaxent_layer_info
Extract Layer Name from a File Pathmaxent_layer_name
Create a Linear Featuremaxent_linear_feature
Load Model Lambdas from Filemaxent_load_lambdas
Compute Log-Lossmaxent_logloss
Compute MESS (Multivariate Environmental Similarity Surface)maxent_mess
Compute MESS from Min/Max Rangesmaxent_mess_range
Compute Misclassification Ratemaxent_misclassification
Get Model Entropymaxent_model_entropy
Get Model Lossmaxent_model_loss
Get Model Distribution Weightsmaxent_model_weights
Compute Percent Contributionmaxent_percent_contribution
Compute Permutation Importancemaxent_permutation_importance
Write Response Curve PNGs for All Variablesmaxent_plot_response_curves
Write a Variable Importance Bar Chart PNGmaxent_plot_variable_importance
Predict with a trained FeaturedSpace modelmaxent_predict
Predict with a Trained MaxEnt Modelmaxent_predict_model
Print Maxent Model Resultsmaxent_print_results
Create a Product Featuremaxent_product_feature
Project Model onto Grids (Cloglog Output)maxent_project_cloglog
Project Model onto Grids (Logistic Output)maxent_project_logistic
Project Model onto Grids (Raw Output)maxent_project_raw
Create a Quadratic Featuremaxent_quadratic_feature
Convert occurrence coordinates to 0-based stream indicesmaxent_raster_sample_indices
Read an ESRI ASCII Grid Filemaxent_read_asc
Read a Grid File (Auto-Detect Format)maxent_read_grid
Read feature lambdas from a filemaxent_read_lambdas
Read Species Occurrence Datamaxent_read_occurrences
Compute Marginal Response Curvemaxent_response_curve
Compute Response Curve with Fixed Valuesmaxent_response_curve_fixed
Run a Complete Maxent Species Distribution Modelling Workflowmaxent_run
Create a MaxEnt Sample Objectmaxent_sample
Save Model Lambdas to Filemaxent_save_lambdas
Train a MaxEnt Model with the Java-Equivalent Sequential Optimizermaxent_sequential_fit
Set sample expectations for a FeaturedSpacemaxent_set_sample_expectations
Get FeaturedSpace Informationmaxent_space_info
Compute Mean Squared Errormaxent_square_error
Create a Threshold Featuremaxent_threshold_feature
Train a FeaturedSpace modelmaxent_train
Train MaxEnt directly from a terra SpatRastermaxent_train_terra
Compute Variable Ranges from Gridsmaxent_variable_ranges
Write a Grid to ESRI ASCII Formatmaxent_write_asc
Write feature lambdas to a filemaxent_write_lambdas
Write an Omission / Threshold CSVmaxent_write_omission_csv
Write a Maxent Prediction Grid as a PNG Imagemaxent_write_prediction_png
Write Sample Predictions CSVmaxent_write_sample_predictions
Print Sample Informationprint.maxent_sample
Project Model onto Grids (Java-compatible cloglog output)project_cloglog
Project Model onto Grids (Java-compatible logistic output)project_logistic
Project Model onto Grids (Java-compatible raw output)project_raw
Get feature value from a samplesample_get_feature
Set feature value on a samplesample_set_feature