In Yu-Group/simChef: Intensive Computational Experiments Made Easy

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  # disable R chunk evaluation when using macOS in GH Actions
  # see https://github.com/tidyverse/ggplot2/issues/2252#issuecomment-1006713187
  # and https://github.com/lcolladotor/biocthis/issues/27 and
  # https://github.com/bodkan/slendr/commit/f0f5ae18452cc9df5d151874e41b0b8fd5f29aa2#
  eval = Sys.getenv("RUNNER_OS") != "macOS"
)

library(simChef)

set.seed(12345)

{width="100%" #fig:fit-eval-viz-figure}

DGP

• Inputs
• Any number of named parameters (e.g., dgp_param1, dgp_param2, ...)
• Outputs
• A list of named elements to be passed onto the method(s) (e.g., dgp_out1, dgp_out2, ...)

Method

• Inputs
• Named parameters matching all names in the list returned by the DGP function (e.g., dgp_out1, dgp_out2, ...)
• Any number of additional named parameters (e.g., method_param1, method_param2, ...)
• Outputs
• A list of named elements (e.g., method_out1, method_out2, ...)

Evaluator

• Inputs
• fit_results (optional): output of fit_experiment()
• vary_params (optional): character vector of parameter names that are varied across in the experiment
• Any number of additional named parameters (e.g., eval_param1, eval_param2, ...)
• Outputs
• Typically a tibble or data.frame

Visualizer

• Inputs
• fit_results (optional): output of fit_experiment()
• eval_results (optional): output of evaluate_experiment()
• vary_params (optional): character vector of parameter names that are varied across in the experiment
• Any number of additional named parameters (e.g., viz_param1, viz_param2, ...)
• Outputs
• Typically a plot (e.g., a ggplot or plotly object). Can also return tables or more generally, any R Markdown snippet (e.g., verbatim text)

Outputs of *_experiment

• fit_results: output of fit_experiment()
• A tibble of results from each (replicate, DGP, Method) combination with the following columns:
  • .rep: replicate ID
  • .dgp_name: name of DGP
  • .method_name: name of Method
  • vary_across parameter columns (if applicable): value of the specified vary_across parameter
  • A column corresponding to each named component in the list returned by Method (e.g., method_out1, method_out2, ...)
• eval_results: output of evaluate_experiment()
• A named list of elements, with one element for each Evaluator in the Experiment
  • The list names correspond to the names given to each Evaluator in create_evaluator(.name = ...)
  • The list elements are exactly the return values from each Evaluator function
• viz_results: output of visualize_experiment()
• A named list of elements, with one element for each Visualizer in the Experiment
  • The list names correspond to the names given to each Visualizer in create_visualizer(.name = ...)
  • The list elements are exactly the return values from each Visualizer function

Yu-Group/simChef documentation built on March 25, 2024, 3:22 a.m.