# Canonical Associative Learning Models and their Representations

## Documentation for package ‘calmr’ version 0.7.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G L M N P R S T

## -- A --

aggregate | CalmrExperiment methods
aggregate-method | CalmrExperiment methods
AIC | CalmrFit methods
AIC-method | CalmrFit methods

## -- B --

BIC | CalmrFit methods
BIC-method | CalmrFit methods

## -- C --

CalmrDesign-class | S4 class for calmr designs
CalmrDesign-methods | CalmrDesign methods
CalmrExperiment-class | S4 class for calmr experiments.
CalmrExperiment-methods | CalmrExperiment methods
CalmrExperimentResult-class | S4 class for calmr experiment results
CalmrFit-class | S4 class for calmr Fit
CalmrFit-methods | CalmrFit methods
CalmrResult-class | S4 class for calmr results
CalmrResult-methods | CalmrResult methods
CalmrRSA-class | S4 class for calmr representational similarity analysis
CalmrRSA-methods | CalmrRSA methods
calmr_model_graph | Create a graph with calmr data
calmr_model_plot | Create a plot with calmr data
calmr_verbosity | Set verbosity options for calmr
compare_models | Run models given a set of parameters

## -- D --

design | CalmrExperiment methods
design-method | CalmrExperiment methods

## -- E --

experiences | CalmrExperiment methods
experiences-method | CalmrExperiment methods
experiences<- | CalmrExperiment methods
experiences<--method | CalmrExperiment methods

## -- F --

filter | CalmrExperiment methods
filter-method | CalmrExperiment methods
fit_model | Fit model to data

## -- G --

get_design | Get basic designs
get_graph_opts | Create a graph with calmr data
get_model | Model information functions
get_optimizer_opts | Get optimizer options
get_parameters | Get model parameters
get_plot_opts | Create a plot with calmr data
get_timings | Get timing design parameters
graph | CalmrExperiment methods
graph-method | CalmrExperiment methods

## -- L --

length-method | CalmrExperiment methods

## -- M --

make_experiment | Make CalmrExperiment
mapping | CalmrDesign methods
mapping-method | CalmrDesign methods
model_information | Model information functions
model_outputs | Model information functions
model_parameters | Model information functions

## -- N --

NLL | CalmrFit methods
NLL-method | CalmrFit methods

## -- P --

parameters | CalmrExperiment methods
parameters-method | CalmrExperiment methods
parameters<- | CalmrExperiment methods
parameters<--method | CalmrExperiment methods
parse | CalmrExperiment methods
parse-method | CalmrExperiment methods
parsed_results | CalmrExperiment methods
parsed_results-method | CalmrExperiment methods
parse_design | Parse design data.frame
patch_graphs | Create a graph with calmr data
patch_plots | Create a plot with calmr data
pati | Rat responses from Patittucci et al. 2016
phase_parser | Parses a phase string
plot | CalmrExperiment methods
plot-method | CalmrExperiment methods
plot-method | CalmrRSA methods
plotting_functions | General plotting functions
plot_common_scale | Create a plot with calmr data
plot_targetted_complex_trials | General plotting functions
plot_targetted_tbins | General plotting functions
plot_targetted_trials | General plotting functions
plot_targetted_typed_trials | General plotting functions
plot_tbins | General plotting functions
plot_trials | General plotting functions
predict | CalmrFit methods
predict-method | CalmrFit methods

## -- R --

raw_results | CalmrExperiment methods
raw_results-method | CalmrExperiment methods
results | CalmrExperiment methods
results-method | CalmrExperiment methods
rsa | Perform representational similarity analysis
run_experiment | Run experiment

## -- S --

set_calmr_palette | Get/set the colour/fill palette for plots
set_reward_parameters | Set reward parameters for ANCCR model
show-method | CalmrDesign methods
show-method | CalmrExperiment methods
show-method | CalmrFit methods
show-method | CalmrRSA methods
show-method | CalmrResult methods
supported_families | Model information functions
supported_models | Model information functions
supported_optimizers | Model information functions
supported_plots | Model information functions
supported_timed_models | Model information functions

## -- T --

test | CalmrRSA methods
test-method | CalmrRSA methods
timings | CalmrExperiment methods
timings-method | CalmrExperiment methods
timings<- | CalmrExperiment methods
timings<--method | CalmrExperiment methods
trials | CalmrExperiment methods
trials-method | CalmrDesign methods
trials-method | CalmrExperiment methods