Man pages for kevinwolz/hisafer
An R Toolbox for the Hi-sAFe Biophysical Agroforestry Model

addGridAdd grid to hisafe_root3D() plot
add_historic_dataAdd historic data
add_phantom_treesAdd phantom trees
add_treesAdd trees & canopies to hisafe tile plots
analyze_hisafeShortcut to Hi-sAFe analysis
annotatorAdd labels to plot panels
augment_with_systemAugment hop elements with system name
build_cluster_scriptBuilds a cluster shell script
build_hisafeBuild a Hi-sAFe simulation or experiment
build_structureBuilds the structure of a Hi-sAFe simulation
build_white_boxes_sliceBuild white boxes to cover phantom trees
build_white_boxes_tileBuild white boxes to cover phantom trees
call_hisafeCalls Hi-sAFe from command line
check_acceptedCheck validity of Hi-sAFe accepted values
check_input_valuesCheck validity of all Hi-sAFe inputs
check_rangeCheck validity of Hi-sAFe input ranges
check_typeCheck validity of Hi-sAFe input numeric types
compress_batch_arrayCompress a batch array into a character string
copy_hisafe_templateCopy a Hi-sAFe template to specified location
create_faceCombine hop objects into a face object
create_tile_dataGenerate tree data for hisafe tile plots
create_tree_dataGenerate tree data for hisafe tile plots
cycle_summaryPlot summary dashboard of daily and annual cycles
define_hisafeDefine a Hi-sAFe experiment
define_hisafe_fileDefine a Hi-sAFe experiment from a file
diag_hisafeShortcut to Hi-sAFe diagnostics
diag_hisafe_annualcellsPlot annualCells diagnostics of Hi-sAFe output
diag_hisafe_cellsPlot cells diagnostics of Hi-sAFe output
diag_hisafe_monthcellsPlot monthCells diagnostics of Hi-sAFe output
diag_hisafe_tsPlot timeseries diagnostics of Hi-sAFe output
diag_hisafe_voxelsPlot timeseries diagnostics of Hi-sAFe voxels output
diag_output_pathDetermine diagnostic output path
edit_param_elementEdit an individual parameter element
edit_param_fileEdits parameter files
extract_complete_datesExtract complete dates
get_carbon_allocationGet tree carbon above vs. belowground allocation from a hop...
get_carbon_incrementGet tree carbon increment from a hop object
get_carbon_poolsGet tree carbon pools from a hop object
get_dimsFind overall dimensions of a ggplot
get_light_fluxesGet light fluxes from a hop object
get_nitrogen_fluxesGet nitrogen fluxes in and out of soil from a hop object
get_param_namesGet names of template parameters
get_param_valsGet values/constraints of template parameters
get_pheno_datesGet dates of tree phenological stage changes from a hop
get_pruning_datesGet branch pruning dates from a hop
get_stics_budgetGet stics budget values from .bil export files
get_template_paramsRead all template parameters
get_unitsGet variable units
get_used_paramsComplies list of parameters actually used
get_water_fluxes#' Get water fluxes from a hop object
get_yieldsGet yields from a hop object
ggsave_fitmaxSave ggplot to correctly-shaped image file
hip_paramsDisplay supported Hi-sAFe input parameters
hisafe_budgetCalculate water and nitrogen budgets
hisafe_infoDisplay version numbers of Hi-sAFe and Java
hisafe_profilesDisplay supported Hi-sAFe output profiles
hisaferhisafer: A package of tools for interacting with the Hi-sAFe...
hisafe_root3DCreate a 3D plot of tree coarse root topology
hisafe_slicePlot a "sliced" profile of the simulated Hi-sAFe scene
hisafe_snapshotCreate daily plots combining hisafe_slice() &...
hop_filterFilter a hop object by SimulationName, Date, and idTree
hop_mergeMerge multiple hop objects
hop_paramsDisplay Hi-sAFe output variables
hop_renameChange SimulationNames in a hop object
is_faceCheck if an object is of class face
is_hipCheck if an object is of class hip
is_hopCheck if an object is of class hop
join_profilesJoin multiple hop profiles together
layer_init_paramsGenerate soil layer initialization table for define_hisafe
layer_paramsGenerate soil layer table for define_hisafe
LERPlot LER for yield, light, water, or nitrogen
LER_summaryPlot LER for yield, light, water, or nitrogen
make_rel_yearsConvert absolute years to relative years in a hop
modify_tableBuild tables for table param functions
plot_hisafe_annualcellsTile plot of Hi-sAFe annualCells output variable
plot_hisafe_bgPlot belowground tree root depth & water table
plot_hisafe_cellsTile plot of Hi-sAFe cells output variable
plot_hisafe_cycle_barPlot annual barchart of major cycles
plot_hisafe_cycle_tsPlot daily timeseries of major cycles
plot_hisafe_monthcellsTile plot of Hi-sAFe monthCells output variable
plot_hisafe_scenePlot a map of the simulated Hi-sAFe scene
plot_hisafe_tsPlot timeseries of Hi-sAFe output variable
plot_hisafe_tstressPlot crop temperature and temperature stress regions
plot_hisafe_voxelsTile plot of Hi-sAFe voxels output variable
profile_checkCheck for existiance of profiles in a hop object
read_hisafeRead output from one or more Hi-sAFe simulations
read_hisafe_exampleRead example Hi-sAFe experiment output
read_hisafe_output_fileRead a single Hi-sAFe output profile
read_param_fileReads parameter files
read_profileRead a Hi-sAFe output profile
read_simulationRead output from a single Hi-sAFe simulation
read_tree_infoRead tree information from a Hi-sAFe pld file
read_weatherRead weather data from a Hi-sAFe .WTH file.
root_init_paramsGenerate root initialization table for define_hisafe
run_hisafeRun one or more Hi-sAFe simulations
shift_sceneFlip scene about cell row
shift_yearShift Year column based on a provided JulianDay
stics_budget_compCompare Hi-sAFe and STICS budget calcualations
theme_hisafe_tileA 'ggplot2' theme for Hi-sAFe monthCells tile plots
theme_hisafe_tsA 'ggplot2' theme for Hi-sAFe timeseries plots
tree_init_paramsGenerate tree initialization table for define_hisafe
variable_checkCheck for existiance of variables in a hop object
vars_to_diagDetermine diagnostic variables to plot
visual_legendCreate a legend for hisafe_visual()
warn_unequal_lengthsProvide warning if simulation lengths are unequal
which_profilesGet which profiles exist in a hop
write_hopWrite hop profiles to CSV files
write_param_fileWrites parameter files
write_weatherWrite weather data to a Hi-sAFe .WTH file.
kevinwolz/hisafer documentation built on Nov. 19, 2018, 9:22 p.m.