simulator: An Engine for Running Simulations
Version 0.2.0

A framework for performing simulations such as those common in methodological statistics papers. The design principles of this package are described in greater depth in Bien, J. (2016) "The simulator: An Engine to Streamline Simulations," which is available at .

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AuthorJacob Bien [aut, cre]
Date of publication2016-07-12 10:55:18
MaintainerJacob Bien <jbien@cornell.edu>
LicenseGPL-3
Version0.2.0
URL http://github.com/jacobbien/simulator
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("simulator")

Man pages

add: Add a reference to a simulation
add_dref_to_list: Internal function to add DrawsRef to a list of DrawsRef...
add_eref_to_list: Internal function to add EvalsRef to a list of EvalsRef...
add_oref_to_list: Internal function to add OutputRef to a list of OutputRef...
aggregate_evals: Apply aggregator to a list of Evals objects
Aggregator-class: An S4 class for aggregating evaluated metrics
as.data.frame.Evals: Convert an Evals to a data.frame
as.data.frame.listofEvals: Convert a list of Evals to a data.frame
as.data.frame.listofModels: Convert a List of Models to a data.frame
as.data.frame.Model: Convert a Model to a data.frame
cash-Model-method: Get element of 'Model"s 'params' list
catsim: Concatenate and print for the simulator
Component: An S4 class representing a component of the simulator.
create: Create template for a new set of simulations
describe: Describe the contents of a simulator directory
do_in_parallel: Do a function in parallel.
draws: Get one or more draws from a simulation
Draws-class: An S4 class representing the random draws from a Model...
DrawsRef-class: An S4 class representing a reference to an object of class...
evals: Get one or more evals from a simulation
Evals-class: An S4 class representing the evaluation of a metric run by...
EvalsRef-class: An S4 class representing a reference to an object of class...
evaluate: Evaluate outputs of methods according to provided metrics.
evaluate_internal: Evaluate outputs of methods according to provided metrics.
evaluate_single: Run one or more metrics on outputs.
ExtendedMethod-class: An S4 class representing the extension of a method
generate_model: Generate a model.
get_contents: Get the contents of a simulator directory
get_files_not_in_simulations: Find files in simulator directory not referred to by any...
get_model_indices: Returns indices of a specified subset of sim@model_refs
get_relative_path: Get relative path
get_simulation_with_all_files: Returns a simulation object containing references to all...
ggplot_eval: Make a boxplot of a metric for each method using ggplot2
grapes-greater-than-grapes: This is not magrittr's pipe (actually it is)
load_draws: Load one or more draws objects from file.
load-DrawsRef-method: Load a DrawsRef
load_evals: Load one or more Evals objects from file.
load-EvalsRef-method: Load an EvalsRef
load_libraries_on_cluster: Load necessary libraries on a cluster
load-list-method: Load a list of reference objects
load_model: Load a model from file.
load-ModelRef-method: Load a ModelRef
load-OutputRef-method: Load an OutputRef
load_outputs: Load one or more output objects from file.
load_simulation: Load a simulation object
make_my_example_model: Make My Example Model
memory_as_string: Write memory in human readable way
Method-class: An S4 class representing a method to be run by simulator.
MethodExtension-class: An S4 class used to create an extended version of a method
Metric-class: An S4 class representing an evaluation metric to be used by...
model: Get one or more models from a simulation
Model-class: An S4 class representing the model component of the...
model_names: Get model names in a Simulation
ModelRef-class: An S4 class representing a reference to an object of class...
models_as_data.frame: Convert a list of Model objects into a data.frame
my_example_loss: My Example Loss
my_example_method: My Example Method
new_aggregator: Create an Aggregator object
new_extended_method: Create an ExtendedMethod object
new_method: Create a Method object
new_method_extension: Create an object that can be used to make an extended version...
new_metric: Create a Metric object
new_model: Create a Model object
new_simulation: Make a new simulation object
output: Get one or more outputs from a simulation
Output-class: An S4 class representing the output of a method run by...
OutputRef-class: An S4 class representing a reference to an object of class...
outputs_or_evals: Internal function used by both outputs and evals
plot_eval: Make a boxplot of a metric for each method
plot_eval_by: Plot a metric across multiple values of a model parameter
plot_evals: Plot one metric versus another for each method
plus-list-MethodExtension-method: Create a list of ExtendedMethod from a list of Methods and a...
plus-Method-MethodExtension-method: Create an ExtendedMethod from a Method and MethodExtension
recycle: Recycles elements to create vector of desired length
relabel: Give simulation a new label
rename: Give simulation a new name
run_extendedmethod_single: Run a single extended method on a single index of simulated...
run_extmethod_parallel: Run one or more extended methods on simulated data.
run_method: Run one or more methods on simulated data.
run_method_parallel: Run one or more methods on simulated data.
run_method_single: Run a single method on a single index of simulated data.
save_simulation: Save a simulation object
simulate_from_model: Simulate from a model.
simulate_from_model_single: Simulate from a model.
simulate_parallel: Simulate from a model in parallel.
Simulation: An S4 class representing a simulation.
subset_evals: Reduce an Evals object to a subset of methods and/or metrics
subset_models: Subset Models
subset_simulation: Create a simulation that is a subset of a preexisting...
tabulate_eval: Make a table of a metric for each pair of models and methods

Functions

$,Model-method Man page
+,Method,MethodExtension-method Man page
+,list,MethodExtension-method Man page
Aggregator-class Man page
Component-class Man page
Draws-class Man page
DrawsRef-class Man page
Evals-class Man page
EvalsRef-class Man page
ExtendedMethod-class Man page
Method-class Man page
MethodExtension-class Man page
Metric-class Man page
Model-class Man page
ModelRef-class Man page
Output-class Man page
OutputRef-class Man page
Simulation-class Man page
\%>\% Man page
add Man page Source code
add,Simulation,DrawsRef-method Man page
add,Simulation,EvalsRef-method Man page
add,Simulation,ModelRef-method Man page
add,Simulation,OutputRef-method Man page
add,Simulation,list-method Man page
add_dref_to_list Man page Source code
add_eref_to_list Man page Source code
add_oref_to_list Man page Source code
aggregate_evals Man page Source code
as.data.frame.Evals Man page Source code
as.data.frame.Model Man page Source code
as.data.frame.listofEvals Man page Source code
as.data.frame.listofModels Man page Source code
catsim Man page Source code
check_aggregator Source code
check_component Source code
check_draws Source code
check_drawsref Source code
check_evals Source code
check_evalsref Source code
check_extended_method Source code
check_method Source code
check_method_extension Source code
check_metric Source code
check_model Source code
check_modelref Source code
check_output Source code
check_outputref Source code
check_parallel_list Source code
check_simulation Source code
create Man page Source code
dcat Source code
describe Man page Source code
do_in_parallel Man page Source code
draws Man page Source code
evals Man page Source code
evaluate Man page Source code
evaluate_internal Man page Source code
evaluate_single Man page Source code
generate_model Man page Source code
generate_model_single Source code
get_contents Man page Source code
get_evals_list Source code
get_files_not_in_simulations Man page Source code
get_model_dir_and_file Source code
get_model_indices Man page Source code
get_relative_path Man page Source code
get_seeds_for_draws Source code
get_simulation_with_all_files Man page Source code
ggplot_eval Man page Source code
ggplot_evals Source code
hline Source code
is_valid_component_name Source code
is_valid_rij_list Source code
load,DrawsRef-method Man page
load,EvalsRef-method Man page
load,ModelRef-method Man page
load,OutputRef-method Man page
load,list-method Man page
load_draws Man page Source code
load_evals Man page Source code
load_evals_from_ref Man page Source code
load_libraries_on_cluster Man page Source code
load_model Man page Source code
load_outputs Man page Source code
load_outputs_from_ref Man page Source code
load_simulation Man page Source code
make_my_example_model Man page Source code
make_scalar_aggregator Source code
memory_as_string Man page Source code
model Man page Source code
model_names Man page Source code
models_as_data.frame Man page Source code
my_example_loss Man page
my_example_method Man page
new_aggregator Man page Source code
new_extended_method Man page Source code
new_method Man page Source code
new_method_extension Man page Source code
new_metric Man page Source code
new_model Man page Source code
new_simulation Man page Source code
onLoad Source code
output Man page Source code
outputs_or_evals Man page Source code
plot_eval Man page Source code
plot_eval_by Man page Source code
plot_evals Man page Source code
recycle Man page Source code
relabel Man page Source code
remove_slash Source code
rename Man page Source code
run_extendedmethod_single Man page Source code
run_extmethod_parallel Man page Source code
run_method Man page Source code
run_method_parallel Man page Source code
run_method_single Man page Source code
save_draws_to_file Source code
save_evals_to_file Source code
save_output_to_file Source code
save_simulation Man page Source code
simulate_from_model Man page Source code
simulate_from_model_single Man page Source code
simulate_parallel Man page Source code
subset_evals Man page Source code
subset_models Man page Source code
subset_output Source code
subset_simulation Man page Source code
tabulate_eval Man page Source code
write_evals Source code
write_main Source code
write_methods Source code
write_models Source code
write_rmd Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/getting-started.Rmd
inst/doc/getting-started.html
inst/doc/lasso.Rmd
inst/doc/getting-started.R
inst/doc/elastic-net.R
inst/doc/fdr.Rmd
inst/doc/james-stein.R
inst/doc/elastic-net.html
inst/doc/fdr.R
inst/doc/james-stein.Rmd
inst/doc/fdr.html
inst/doc/elastic-net.Rmd
inst/doc/james-stein.html
inst/doc/lasso.html
inst/doc/lasso.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test-utils.R
tests/testthat/test-simulator.files.R
tests/testthat/test-regex.R
tests/testthat/test-method.R
tests/testthat/test-method-extension.R
tests/testthat/test-create.R
tests/testthat/test-draws.R
tests/testthat/test-simulation.R
tests/testthat/test-models.R
tests/testthat/test-parallel.R
tests/testthat/test-evaluate.R
tests/testthat/test-table.R
NAMESPACE
R
R/method-extension-class.R
R/plot_eval.R
R/component-class.R
R/utils.R
R/load.R
R/models.R
R/method-class.R
R/reference-classes.R
R/parallel.R
R/manage.R
R/evaluate.R
R/create.R
R/draws.R
R/draws-class.R
R/simulation-class.R
R/plot_evals.R
R/plot_eval_by.R
R/add-to-simulation.R
R/get-from-simulation.R
R/methods.R
R/parallel-methods.R
R/model-class.R
R/extended-method-class.R
R/parallel-draws.R
R/metric-class.R
R/aggregator-class.R
R/examples.R
R/output-class.R
R/zzz.R
R/import_from.R
R/tables.R
R/evals-class.R
vignettes
vignettes/getting-started.Rmd
vignettes/lasso.Rmd
vignettes/false-discovery-rate
vignettes/false-discovery-rate/model_functions.R
vignettes/false-discovery-rate/eval_functions.R
vignettes/false-discovery-rate/method_functions.R
vignettes/false-discovery-rate/main.R
vignettes/fdr.Rmd
vignettes/lasso
vignettes/lasso/model_functions.R
vignettes/lasso/eval_functions.R
vignettes/lasso/method_functions.R
vignettes/lasso/main.R
vignettes/james-stein
vignettes/james-stein/model_functions.R
vignettes/james-stein/eval_functions.R
vignettes/james-stein/method_functions.R
vignettes/james-stein/main.R
vignettes/elastic-net
vignettes/elastic-net/model_functions.R
vignettes/elastic-net/eval_functions.R
vignettes/elastic-net/method_functions.R
vignettes/elastic-net/main.R
vignettes/james-stein.Rmd
vignettes/elastic-net.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/as.data.frame.Evals.Rd
man/grapes-greater-than-grapes.Rd
man/describe.Rd
man/run_method_single.Rd
man/add_oref_to_list.Rd
man/my_example_method.Rd
man/load_model.Rd
man/evaluate_internal.Rd
man/ExtendedMethod-class.Rd
man/add.Rd
man/catsim.Rd
man/new_extended_method.Rd
man/ggplot_eval.Rd
man/add_eref_to_list.Rd
man/run_extmethod_parallel.Rd
man/load_libraries_on_cluster.Rd
man/load-DrawsRef-method.Rd
man/ModelRef-class.Rd
man/EvalsRef-class.Rd
man/run_extendedmethod_single.Rd
man/DrawsRef-class.Rd
man/as.data.frame.listofModels.Rd
man/run_method.Rd
man/evaluate.Rd
man/plot_eval_by.Rd
man/load_evals.Rd
man/new_metric.Rd
man/model.Rd
man/new_method.Rd
man/make_my_example_model.Rd
man/new_aggregator.Rd
man/my_example_loss.Rd
man/Method-class.Rd
man/subset_models.Rd
man/Model-class.Rd
man/new_simulation.Rd
man/get_contents.Rd
man/as.data.frame.Model.Rd
man/run_method_parallel.Rd
man/model_names.Rd
man/new_model.Rd
man/memory_as_string.Rd
man/new_method_extension.Rd
man/Simulation.Rd
man/generate_model.Rd
man/aggregate_evals.Rd
man/subset_simulation.Rd
man/Aggregator-class.Rd
man/simulate_from_model.Rd
man/evals.Rd
man/load-EvalsRef-method.Rd
man/plot_eval.Rd
man/output.Rd
man/cash-Model-method.Rd
man/outputs_or_evals.Rd
man/rename.Rd
man/load-OutputRef-method.Rd
man/get_model_indices.Rd
man/evaluate_single.Rd
man/Output-class.Rd
man/add_dref_to_list.Rd
man/do_in_parallel.Rd
man/tabulate_eval.Rd
man/get_simulation_with_all_files.Rd
man/load_simulation.Rd
man/plus-Method-MethodExtension-method.Rd
man/draws.Rd
man/OutputRef-class.Rd
man/simulate_from_model_single.Rd
man/Metric-class.Rd
man/Draws-class.Rd
man/load_draws.Rd
man/get_files_not_in_simulations.Rd
man/plus-list-MethodExtension-method.Rd
man/simulate_parallel.Rd
man/save_simulation.Rd
man/Evals-class.Rd
man/plot_evals.Rd
man/MethodExtension-class.Rd
man/relabel.Rd
man/models_as_data.frame.Rd
man/subset_evals.Rd
man/load_outputs.Rd
man/load-list-method.Rd
man/as.data.frame.listofEvals.Rd
man/get_relative_path.Rd
man/create.Rd
man/recycle.Rd
man/Component.Rd
man/load-ModelRef-method.Rd
simulator documentation built on May 19, 2017, 8:28 a.m.