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

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Documentation for package ‘maxentcpp’ version 1.0.0

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C E F G L M P S

-- C --

clamp_grids Clamp Environmental Grids
compute_mess Compute MESS (Multivariate Environmental Similarity Surface)
compute_mess_range Compute MESS from Min/Max Ranges
compute_percent_contribution Compute Percent Contribution
compute_permutation_importance Compute Permutation Importance
compute_response_curve Compute Java-compatible Marginal Response Curve
compute_response_curve_fixed Compute Java-compatible Response Curve with Fixed Values
compute_variable_ranges Compute Variable Ranges from Grids
coords_to_rowcol Convert geographic coordinates to row/col
create_grid_dimension Create a GridDimension object
create_grid_float Create a float Grid object
create_hinge_feature Create a HingeFeature object
create_layer Create a Layer metadata object
create_linear_feature Create a LinearFeature object
create_product_feature Create a ProductFeature object
create_quadratic_feature Create a QuadraticFeature object
create_sample Create a Sample object
create_threshold_feature Create a ThresholdFeature object
csv_close Close a CsvReader
csv_headers Get CSV column headers
csv_next_record Read the next CSV record
csv_open Open a CSV file for reading
csv_read_double_column Read an entire named column as doubles
csv_writer_close Close a CsvWriter
csv_writer_open Open a CSV file for writing
csv_writer_print Write a value into the current row of a CSV
csv_writer_println Flush the current CSV row to disk
csv_writer_print_double Write a numeric value into the current row of a CSV

-- E --

eval_auc Compute AUC (Area Under the ROC Curve)
eval_correlation Compute Pearson Correlation
eval_logloss Compute Log-Loss
eval_misclassification Compute Misclassification Rate
eval_model Full Model Evaluation
eval_square_error Compute Mean Squared Error
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.
extract_predictions_raw Extract Java-compatible Raw Predictions at Sample Locations

-- F --

feature_eval Evaluate a feature at a given index
feature_get_info Get feature metadata

-- G --

generate_features Generate features from a list of environmental variable vectors
get_grid_dimension_info Get grid dimension properties
get_layer_info Get layer metadata
get_sample_info Get sample properties
grid_float_from_matrix Create a GridFloat from an R matrix
grid_float_info Get grid information for an ASC-loaded grid
grid_float_to_matrix Extract the data from a GridFloat as an R matrix
grid_from_matrix Set grid from matrix
grid_get_value Get grid value
grid_get_values_batch Extract multiple values from a Grid at given row/col indices (batch)
grid_has_data Check if grid cell has data
grid_read_asc Read an ESRI ASCII grid (.asc) file
grid_read_file Read a grid from file (auto-detect format)
grid_set_value Set grid value
grid_to_matrix Get grid as matrix
grid_write_asc Write a float Grid to an ESRI ASCII (.asc) file

-- L --

layer_name_from_path Extract a layer name from a file path

-- M --

maxent_append_results_csv Append a Row to maxentResults.csv
maxent_auc Compute AUC (Area Under the ROC Curve)
maxent_background_indices Generate Background Sample Indices
maxent_clamp Clamp Environmental Grids
maxent_color_ramp Generate the Maxent Canonical Color Ramp
maxent_correlation Compute Pearson Correlation
maxent_csv_close Close a CSV Reader
maxent_csv_headers Get CSV Column Headers
maxent_csv_next Read the Next CSV Record
maxent_csv_open Open a CSV File for Reading
maxent_csv_read_column Read an Entire Column as Doubles
maxent_csv_write Write a String Value to the Current CSV Row
maxent_csv_write_close Close a CSV Writer
maxent_csv_write_num Write a Numeric Value to the Current CSV Row
maxent_csv_write_open Open a CSV File for Writing
maxent_csv_write_row Flush the Current Row to the CSV File
maxent_dimension Create a Grid Dimension Object
maxent_evaluate Full Model Evaluation
maxent_extract_lambdas Extract Lambda Values from a Maxent Run Result
maxent_extract_occurrence_env_terra Extract environmental values for occurrences from a terra SpatRaster
maxent_extract_predictions_cloglog Extract Cloglog Predictions at Sample Locations
maxent_extract_predictions_logistic Extract Logistic Predictions at Sample Locations
maxent_extract_predictions_raw Extract Raw Predictions at Sample Locations
maxent_featured_space Create a FeaturedSpace Object
maxent_featured_space_create Create a FeaturedSpace object
maxent_featured_space_from_callback Create a FeaturedSpace from a streaming background provider
maxent_featured_space_from_rast Create a FeaturedSpace directly from a terra SpatRaster
maxent_featured_space_info Get FeaturedSpace metadata
maxent_feature_eval Evaluate a Feature at a Given Index
maxent_feature_info Get Feature Properties
maxent_fit Train a MaxEnt Model
maxent_generate_features Generate Features from Environmental Variable Data
maxent_get_entropy Get entropy of a FeaturedSpace distribution
maxent_get_loss Get current loss of a FeaturedSpace
maxent_get_weights Get current distribution weights from a FeaturedSpace
maxent_grid Create a Grid Object
maxent_grid_from_matrix Create a Grid from an R Matrix
maxent_grid_from_terra Convert a terra SpatRaster to a maxentcpp GridFloat
maxent_grid_info Get Grid Information
maxent_grid_to_matrix Convert Grid to R Matrix
maxent_grid_to_terra Convert a maxentcpp GridFloat to a terra SpatRaster
maxent_hinge_feature Create a Hinge Feature
maxent_layer Create a Layer Metadata Object
maxent_layer_info Get Layer Metadata
maxent_layer_name Extract Layer Name from a File Path
maxent_linear_feature Create a Linear Feature
maxent_load_lambdas Load Model Lambdas from File
maxent_logloss Compute Log-Loss
maxent_mess Compute MESS (Multivariate Environmental Similarity Surface)
maxent_mess_range Compute MESS from Min/Max Ranges
maxent_misclassification Compute Misclassification Rate
maxent_model_entropy Get Model Entropy
maxent_model_loss Get Model Loss
maxent_model_weights Get Model Distribution Weights
maxent_percent_contribution Compute Percent Contribution
maxent_permutation_importance Compute Permutation Importance
maxent_plot_response_curves Write Response Curve PNGs for All Variables
maxent_plot_variable_importance Write a Variable Importance Bar Chart PNG
maxent_predict Predict with a trained FeaturedSpace model
maxent_predict_model Predict with a Trained MaxEnt Model
maxent_print_results Print Maxent Model Results
maxent_product_feature Create a Product Feature
maxent_project_cloglog Project Model onto Grids (Cloglog Output)
maxent_project_logistic Project Model onto Grids (Logistic Output)
maxent_project_raw Project Model onto Grids (Raw Output)
maxent_quadratic_feature Create a Quadratic Feature
maxent_raster_sample_indices Convert occurrence coordinates to 0-based stream indices
maxent_read_asc Read an ESRI ASCII Grid File
maxent_read_grid Read a Grid File (Auto-Detect Format)
maxent_read_lambdas Read feature lambdas from a file
maxent_read_occurrences Read Species Occurrence Data
maxent_response_curve Compute Marginal Response Curve
maxent_response_curve_fixed Compute Response Curve with Fixed Values
maxent_run Run a Complete Maxent Species Distribution Modelling Workflow
maxent_sample Create a MaxEnt Sample Object
maxent_save_lambdas Save Model Lambdas to File
maxent_sequential_fit Train a MaxEnt Model with the Java-Equivalent Sequential Optimizer
maxent_set_sample_expectations Set sample expectations for a FeaturedSpace
maxent_space_info Get FeaturedSpace Information
maxent_square_error Compute Mean Squared Error
maxent_threshold_feature Create a Threshold Feature
maxent_train Train a FeaturedSpace model
maxent_train_terra Train MaxEnt directly from a terra SpatRaster
maxent_variable_ranges Compute Variable Ranges from Grids
maxent_write_asc Write a Grid to ESRI ASCII Format
maxent_write_lambdas Write feature lambdas to a file
maxent_write_omission_csv Write an Omission / Threshold CSV
maxent_write_prediction_png Write a Maxent Prediction Grid as a PNG Image
maxent_write_sample_predictions Write Sample Predictions CSV

-- P --

print.maxent_sample Print Sample Information
project_cloglog Project Model onto Grids (Java-compatible cloglog output)
project_logistic Project Model onto Grids (Java-compatible logistic output)
project_raw Project Model onto Grids (Java-compatible raw output)

-- S --

sample_get_feature Get feature value from a sample
sample_set_feature Set feature value on a sample