simulator: An Engine for Running Simulations

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 <http://faculty.bscb.cornell.edu/~bien/simulator.pdf>.

AuthorJacob Bien [aut, cre]
Date of publication2016-07-12 10:55:18
MaintainerJacob Bien <jbien@cornell.edu>
LicenseGPL-3
Version0.2.0
http://github.com/jacobbien/simulator

View on CRAN

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

\%>\% Man page
add Man page
add_dref_to_list Man page
add_eref_to_list Man page
add_oref_to_list Man page
add,Simulation,DrawsRef-method Man page
add,Simulation,EvalsRef-method Man page
add,Simulation,list-method Man page
add,Simulation,ModelRef-method Man page
add,Simulation,OutputRef-method Man page
aggregate_evals Man page
Aggregator-class Man page
as.data.frame.Evals Man page
as.data.frame.listofEvals Man page
as.data.frame.listofModels Man page
as.data.frame.Model Man page
catsim Man page
Component-class Man page
create Man page
describe Man page
do_in_parallel Man page
draws Man page
Draws-class Man page
DrawsRef-class Man page
evals Man page
Evals-class Man page
EvalsRef-class Man page
evaluate Man page
evaluate_internal Man page
evaluate_single Man page
ExtendedMethod-class Man page
generate_model Man page
get_contents Man page
get_files_not_in_simulations Man page
get_model_indices Man page
get_relative_path Man page
get_simulation_with_all_files Man page
ggplot_eval Man page
+,list,MethodExtension-method Man page
load_draws Man page
load,DrawsRef-method Man page
load_evals Man page
load_evals_from_ref Man page
load,EvalsRef-method Man page
load_libraries_on_cluster Man page
load,list-method Man page
load_model Man page
load,ModelRef-method Man page
load,OutputRef-method Man page
load_outputs Man page
load_outputs_from_ref Man page
load_simulation Man page
make_my_example_model Man page
memory_as_string Man page
Method-class Man page
MethodExtension-class Man page
+,Method,MethodExtension-method Man page
Metric-class Man page
model Man page
Model-class Man page
$,Model-method Man page
model_names Man page
ModelRef-class Man page
models_as_data.frame Man page
my_example_loss Man page
my_example_method Man page
new_aggregator Man page
new_extended_method Man page
new_method Man page
new_method_extension Man page
new_metric Man page
new_model Man page
new_simulation Man page
output Man page
Output-class Man page
OutputRef-class Man page
outputs_or_evals Man page
plot_eval Man page
plot_eval_by Man page
plot_evals Man page
recycle Man page
relabel Man page
rename Man page
run_extendedmethod_single Man page
run_extmethod_parallel Man page
run_method Man page
run_method_parallel Man page
run_method_single Man page
save_simulation Man page
simulate_from_model Man page
simulate_from_model_single Man page
simulate_parallel Man page
Simulation-class Man page
subset_evals Man page
subset_models Man page
subset_simulation Man page
tabulate_eval Man page

Files

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

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