simulator: An Engine for Running Simulations

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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>.

Author
Jacob Bien [aut, cre]
Date of publication
2016-07-12 10:55:18
Maintainer
Jacob Bien <jbien@cornell.edu>
License
GPL-3
Version
0.2.0
URLs

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

Files in this package

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