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

## Documentation for package ‘maxentcpp’ version 1.0.0

- DESCRIPTION file
- Package NEWS

## Help Pages

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