Get output of a StoX process. — getProcessOutput • RstoxFramework

Gets the output of a process that has been run.

getProcessOutput(
  projectPath,
  modelName,
  processID,
  tableName = NULL,
  subFolder = NULL,
  flatten = FALSE,
  pretty = FALSE,
  pretty.json = FALSE,
  pageindex = integer(0),
  linesPerPage = 1000L,
  columnSeparator = " ",
  lineSeparator = NULL,
  na = "-",
  enable.auto_unbox = TRUE,
  drop = FALSE,
  drop.datatype = TRUE,
  splitGeoJson = TRUE,
  warn = TRUE,
  add.line.index = TRUE,
  returnBootstrapData = FALSE,
  selection = list(),
  BootstrapID = NA,
  unlistSingleTable = FALSE
)

getProcessTableOutput(
  projectPath,
  modelName,
  processID,
  tableName = NULL,
  flatten = FALSE,
  pretty = FALSE,
  pageindex = integer(0),
  linesPerPage = 1000L,
  columnSeparator = " ",
  na = "-",
  drop = FALSE,
  add.line.index = TRUE
)

getProcessGeoJsonOutput(
  projectPath,
  modelName,
  processID,
  geoJsonName = NULL,
  pretty = FALSE,
  splitGeoJson = TRUE
)

Arguments

projectPath: The path to the StoX project, i.e., the folder of the project with the sub folders "input", "output" and "process". Can possibly be the path to a file inside the project folder.
modelName: The name of the model (possible values are "baseline", "analysis" and "report").
processID: The ID of the process.
tableName: The name of the table to extract from the process.
subFolder: If the process returns subfolders (ReadBiotic and ReadAcoustic, where the subfolders represent files), specify the name of the folder with this parameter.
flatten: Logical: Should the output tables that contain cells of length > 1 be expanded to that the other columns are repeated, resulting in a regular table.
pretty: Logical: If TRUE pad with space in each cell to the maximum number of characters of the column including header.
pretty.json: Logical: If TRUE prettify the geojson.
pageindex: A vector of the pages to return with linesPerPage number of lines (rows). Default is to not split into pages.
linesPerPage: The number of lines per page if pageindex is given.
columnSeparator: The string to separate columns by, defaulted to a single space.
lineSeparator: The string to separate lines by, defaulted to a NULL, which keeps the output as a vector of strings.
na: The string to replace NAs by, defaulted to "-".
enable.auto_unbox: Logical: If TRUE wrap the output in a list if pretty is TRUE and the output is of length 1. This keeps the array when converting to JSON also for length 1.
drop: Logical: If TRUE drop the list if only one element.
drop.datatype: Logical: If TRUE drop the top level of the output if in a list, which is the level named by the data type.
splitGeoJson: Logical: If TRUE split the geojson into a vector of separate lines.
warn: Logical: If TRUE warn if the process has not bee run.
add.line.index: Logical: If TRUE (the default) print row indices as in data.table.
returnBootstrapData: Logical: If TRUE read the content of bootstrap NetCDF4 file.
selection: Hierarchical list of names of the groups/variables. The last element must be a vector of the variables to return from the table specified by the other elements. E.g., list("ImputeSuperIndividuals", "SuperIndividualsData", c("Stratum", "IndividualAge", "Abundance")) will return a data.table of the three columns "Stratum", "IndividualAge" and "Abundance", added the BootstrapID specified in BootstrapID.
BootstrapID: A sequence of bootstrap IDs, i.e., the indices of the bootstrap replicates. The default returns all bootstrap replicates.
unlistSingleTable: Logical: For use when only single table process outputs are among the requested processes in OutputProcesses of Bootstrap. If FALSE (default) return a list named by the selection with a sub-list named by the datatype holding the output data (e.g. $ImputeSuperIndividuals$SuperIndividualsData). If TRUE return a list named by the selection holding the output data, replicating the output of Bootstrap in StoX <= 3.6.2.
geoJsonName: The name of the GeoJSON object to extract from the process.