Man pages for kevinwolz/hisafer
An R Toolbox for the Hi-sAFe Biophysical Agroforestry Model
| addGrid | Add grid to hisafe_root3D() plot |
| add_historic_data | Add historic data |
| add_phantom_trees | Add phantom trees |
| add_trees | Add trees & canopies to hisafe tile plots |
| analyze_hisafe | Shortcut to Hi-sAFe analysis |
| annotator | Add labels to plot panels |
| augment_with_system | Augment hop elements with system name |
| build_cluster_script | Builds a cluster shell script |
| build_hisafe | Build a Hi-sAFe simulation or experiment |
| build_structure | Builds the structure of a Hi-sAFe simulation |
| build_white_boxes_slice | Build white boxes to cover phantom trees |
| build_white_boxes_tile | Build white boxes to cover phantom trees |
| call_hisafe | Calls Hi-sAFe from command line |
| check_accepted | Check validity of Hi-sAFe accepted values |
| check_input_values | Check validity of all Hi-sAFe inputs |
| check_range | Check validity of Hi-sAFe input ranges |
| check_type | Check validity of Hi-sAFe input numeric types |
| compress_batch_array | Compress a batch array into a character string |
| copy_hisafe_template | Copy a Hi-sAFe template to specified location |
| create_face | Combine hop objects into a face object |
| create_tile_data | Generate tree data for hisafe tile plots |
| create_tree_data | Generate tree data for hisafe tile plots |
| cycle_summary | Plot summary dashboard of daily and annual cycles |
| define_hisafe | Define a Hi-sAFe experiment |
| define_hisafe_file | Define a Hi-sAFe experiment from a file |
| diag_hisafe | Shortcut to Hi-sAFe diagnostics |
| diag_hisafe_annualcells | Plot annualCells diagnostics of Hi-sAFe output |
| diag_hisafe_cells | Plot cells diagnostics of Hi-sAFe output |
| diag_hisafe_monthcells | Plot monthCells diagnostics of Hi-sAFe output |
| diag_hisafe_ts | Plot timeseries diagnostics of Hi-sAFe output |
| diag_hisafe_voxels | Plot timeseries diagnostics of Hi-sAFe voxels output |
| diag_output_path | Determine diagnostic output path |
| edit_param_element | Edit an individual parameter element |
| edit_param_file | Edits parameter files |
| extract_complete_dates | Extract complete dates |
| get_carbon_allocation | Get tree carbon above vs. belowground allocation from a hop... |
| get_carbon_increment | Get tree carbon increment from a hop object |
| get_carbon_pools | Get tree carbon pools from a hop object |
| get_dims | Find overall dimensions of a ggplot |
| get_light_fluxes | Get light fluxes from a hop object |
| get_nitrogen_fluxes | Get nitrogen fluxes in and out of soil from a hop object |
| get_param_names | Get names of template parameters |
| get_param_vals | Get values/constraints of template parameters |
| get_pheno_dates | Get dates of tree phenological stage changes from a hop |
| get_pruning_dates | Get branch pruning dates from a hop |
| get_stics_budget | Get stics budget values from .bil export files |
| get_template_params | Read all template parameters |
| get_units | Get variable units |
| get_used_params | Complies list of parameters actually used |
| get_water_fluxes | #' Get water fluxes from a hop object |
| get_yields | Get yields from a hop object |
| ggsave_fitmax | Save ggplot to correctly-shaped image file |
| hip_params | Display supported Hi-sAFe input parameters |
| hisafe_budget | Calculate water and nitrogen budgets |
| hisafe_info | Display version numbers of Hi-sAFe and Java |
| hisafe_profiles | Display supported Hi-sAFe output profiles |
| hisafer | hisafer: A package of tools for interacting with the Hi-sAFe... |
| hisafe_root3D | Create a 3D plot of tree coarse root topology |
| hisafe_slice | Plot a "sliced" profile of the simulated Hi-sAFe scene |
| hisafe_snapshot | Create daily plots combining hisafe_slice() &... |
| hop_filter | Filter a hop object by SimulationName, Date, and idTree |
| hop_merge | Merge multiple hop objects |
| hop_params | Display Hi-sAFe output variables |
| hop_rename | Change SimulationNames in a hop object |
| is_face | Check if an object is of class face |
| is_hip | Check if an object is of class hip |
| is_hop | Check if an object is of class hop |
| join_profiles | Join multiple hop profiles together |
| layer_init_params | Generate soil layer initialization table for define_hisafe |
| layer_params | Generate soil layer table for define_hisafe |
| LER | Plot LER for yield, light, water, or nitrogen |
| LER_summary | Plot LER for yield, light, water, or nitrogen |
| make_rel_years | Convert absolute years to relative years in a hop |
| modify_table | Build tables for table param functions |
| plot_hisafe_annualcells | Tile plot of Hi-sAFe annualCells output variable |
| plot_hisafe_bg | Plot belowground tree root depth & water table |
| plot_hisafe_cells | Tile plot of Hi-sAFe cells output variable |
| plot_hisafe_cycle_bar | Plot annual barchart of major cycles |
| plot_hisafe_cycle_ts | Plot daily timeseries of major cycles |
| plot_hisafe_monthcells | Tile plot of Hi-sAFe monthCells output variable |
| plot_hisafe_scene | Plot a map of the simulated Hi-sAFe scene |
| plot_hisafe_ts | Plot timeseries of Hi-sAFe output variable |
| plot_hisafe_tstress | Plot crop temperature and temperature stress regions |
| plot_hisafe_voxels | Tile plot of Hi-sAFe voxels output variable |
| profile_check | Check for existiance of profiles in a hop object |
| read_hisafe | Read output from one or more Hi-sAFe simulations |
| read_hisafe_example | Read example Hi-sAFe experiment output |
| read_hisafe_output_file | Read a single Hi-sAFe output profile |
| read_param_file | Reads parameter files |
| read_profile | Read a Hi-sAFe output profile |
| read_simulation | Read output from a single Hi-sAFe simulation |
| read_tree_info | Read tree information from a Hi-sAFe pld file |
| read_weather | Read weather data from a Hi-sAFe .WTH file. |
| root_init_params | Generate root initialization table for define_hisafe |
| run_hisafe | Run one or more Hi-sAFe simulations |
| shift_scene | Flip scene about cell row |
| shift_year | Shift Year column based on a provided JulianDay |
| stics_budget_comp | Compare Hi-sAFe and STICS budget calcualations |
| theme_hisafe_tile | A 'ggplot2' theme for Hi-sAFe monthCells tile plots |
| theme_hisafe_ts | A 'ggplot2' theme for Hi-sAFe timeseries plots |
| tree_init_params | Generate tree initialization table for define_hisafe |
| variable_check | Check for existiance of variables in a hop object |
| variety_params | Generate variety table for define_hisafe |
| vars_to_diag | Determine diagnostic variables to plot |
| visual_legend | Create a legend for hisafe_visual() |
| warn_unequal_lengths | Provide warning if simulation lengths are unequal |
| which_profiles | Get which profiles exist in a hop |
| write_hop | Write hop profiles to CSV files |
| write_param_file | Writes parameter files |
| write_weather | Write weather data to a Hi-sAFe .WTH file. |
