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Run a complete IDEA4 diagnosis

Source: R/diag_idea.R
diag_idea.Rd

This is a wrapper function designed to compute a complete IDEA4 diagnosis with a single function. According to the user's input, functions from IDEATools will be sequentially called to produce the desired output.

Usage

diag_idea(
  input,
  output_directory,
  type = "single",
  export_type = c("report", "local"),
  plot_choices = c("dimensions", "trees", "radars"),
  report_format = "pdf",
  prefix = NULL,
  dpi = 320,
  append = FALSE,
  quiet = FALSE
)

Arguments

input

a character vector with path names to a single file, multiple files or even a directory with IDEA data. File extensions can either be json or xls(x)

output_directory

the output directory for the rendered reports and/or plots. Defaults to "IDEATools_output"

type

the type of analysis to perform. Can be "single" for single farm-related results, "group" for group-related results, "group_reference" for anonymous group-related results, or a combination of the latter, provided that the number of farms is at least 3. Note that "group_reference" is a special option designed to work with an online platform using this package (WEBIDEA)

export_type

the type of output to produce. Can be either "report" to produce compiled reports and/or "local" to write raw plots. If NULL, the algorithm will not produce any plots on machine and will return a list with the IDEA results.

plot_choices

the type of plots to be produced. Can be either "dimensions", "trees" or "radars" or a combination of these 3. Ignored if the export type is "report".

report_format

a string indicating the output format if type = "report". Can be a single format (e.g "pdf") or multiple formats (e.g. c("pdf","xlsx")). Possible formats are "pdf", "docx", "pptx" and "xlsx"

prefix

a prefix which will be added to output files names. Typically, the name of the farm. Ignored if length(input) > 1 or in the case of a group analysis : the metadata$MTD_01 field will be used to identify each farm.

dpi

ggplot output resolution.

append

In the case of a single excel report and if the input is an xlsx file, should the results be appended to the original file ?

quiet

A command to remove console printing.

Value

Either reports and/or raw plots in output_directory or a named list with all the results.

Details

This function is designed to provide the user a single function to use for a full IDEA4 diagnosis.

If the input is a single file, then a simple "read_idea() |> compute_idea() |> plot_idea() |> write_idea()" or "old_idea() |> plot_idea() |> write_idea()" pipeline will be used. If export_type is NULL, then the output of plot_idea() will be returned.

If the input is a list of files and/or a directory, and if type is "single", then the single analysis pipelines are iterated over each file. If export_type is NULL, then the multiple outputs of plot_idea() are gathered in an unique list and returned.

If the input is a list of files and/or a directory, and if type is "group*", then the "import" (read_idea() |> compute_idea() or old_idea()) pipeline is iterated over each file and the results are gathered in an object of class "IDEA_group_data". This object introduced in the plot_idea() |> write_idea() pipeline will trigger a new algorithm suited to group analysis. If export_type is NULL, then the output of plot_idea() will be returned.

Examples

library(IDEATools)
path <- system.file("example_data/idea_example_1.json", package = "IDEATools")
group_path <- system.file("example_data", package = "IDEATools")

# Find your temporary directory (the output will be there)
tempdir <- tempdir()

# Run a full individual diagnosis with no export, with only trees
my_diagnosis <- diag_idea(
  input = path,
  output_directory = tempdir,
  type = "single",
  export_type = NULL,
  prefix = "Farm_A",
  plot_choices = "trees",
  dpi = 20,  ## Can be much higher
  quiet = TRUE
)