startModelRun: startModelRun

In tbep-tech/tbepRSparrow: RSPARROW: An R system for SPARROW modeling

Description

executes sparrowSetup and sparrowExecution functions

Executed By:

• batchRun.R

• executeRSPARROW.R

Executes Routines:

• applyUserModify.R

• calcDemtareaClass.R

• calcIncremLandUse.R

• checkAnyMissingSubdataVars.R

• checkClassificationVars.R

• checkMissingSubdataVars.R

• controlFileTasksModel.R

• correlationMatrix.R

• createDataMatrix.R

• createMasterDataDictionary.R

• createSubdataSorted.R

• findMinMaxLatLon.R

• modelCompare.R

• named.list.R

• outputSettings.R

• readDesignMatrix.R

• readParameters.R

• selectCalibrationSites.R

• selectDesignMatrix.R

• selectParmValues.R

• selectValidationSites.R

• setNLLSWeights.R

• shinyMap2.R

• startEndmodifySubdata.R

• unPackList.R

Usage

startModelRun(file.output.list, if_estimate, if_estimate_simulation,
  if_boot_estimate, if_boot_predict, enable_interactiveMaps,
  filter_data1_conditions, data1, if_userModifyData, data_names,
  class.input.list, min.sites.list, if_validate, iseed, pvalidate,
  mapping.input.list, estimate.input.list, if_predict, biters,
  scenario.input.list, compare_models, modelComparison_name,
  if_spatialAutoCorr, add_vars, batch_mode, RSPARROW_errorOption)

Arguments

if_estimate	yes/no indicating whether or not estimation is run
if_estimate_simulation	character string setting from sparrow_control.R indicating whether estimation should be run in simulation mode only.
if_boot_estimate	yes/no control setting to specify if parametric bootstrap estimation (Monte Carlo) is to be executed
if_boot_predict	yes/no control setting to specify if bootstrap predictions (mean, SE, confidence intervals) are to be executed
enable_interactiveMaps	yes/no control setting indicating whether shiny app should be triggered at the end of the run
filter_data1_conditions	User specified additional DATA1 variables (and conditions) to be used to filter reaches from sparrow_control
data1	input data (data1)
if_userModifyData	yes/no indicating whether or not the userModifyData.R control file is to be applied
data_names	data.frame of variable metadata from data_Dictionary.csv file
if_validate	yes/no indicating whether or not validation is run
iseed	User specified initial seed for the bootstraps from sparrow_control
pvalidate	numeric control setting indicating a percentage of calibration sites to select for validation or if equal to 0 indicates that the user defined valsites variable should be used to select sites for validation. For more details see documentation Section 4.4.6
if_predict	yes/no indicating whether or not prediction is run
biters	User specified number of parametric bootstrap iterations from sparrow_control
compare_models	character string control setting indicated the run_ids of preivously run model to which the current model is to be compared
modelComparison_name	character string control setting that gives the name of the model comparision being executed
if_spatialAutoCorr	yes/no control setting to specifiy if the spatial autocorrelation diagnostic graphics for Moran's I test are to be output
add_vars	additional variables specified by the setting add_vars to be included in prediction, yield, and residuals csv and shape files
batch_mode	yes/no character string indicating whether RSPARROW is being run in batch mode
RSPARROW_errorOption

tbep-tech/tbepRSparrow documentation built on Oct. 9, 2020, 6:24 a.m.