Running experiments in parallel | Why run things in parallel? | Running an experiment in parallel
Package: calmr 0.8.1
calmr: Canonical Associative Learning Models and their Representations
Implementations of canonical associative learning models, with tools to run experiment simulations, estimate model parameters, and compare model representations. Experiments and results are represented using S4 classes and methods.
Authors:
calmr_0.8.1.tar.gz
calmr_0.8.1.zip(r-4.7-any)calmr_0.8.1.zip(r-4.6-any)calmr_0.8.1.zip(r-4.5-any)
calmr_0.8.1.tgz(r-4.6-any)calmr_0.8.1.tgz(r-4.5-any)
calmr_0.8.1.tar.gz(r-4.7-any)calmr_0.8.1.tar.gz(r-4.6-any)
calmr_0.8.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
calmr/json (API)
| # Install 'calmr' in R: |
| install.packages('calmr', repos = c('https://victor-navarro.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/victor-navarro/calmr/issues
Pkgdown/docs site:https://victornavarro.org
Datasets:
- pati - Rat responses from Patittucci et al. 2016
Last updated from:050acf0d61. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 209 | ||
| source / vignettes | OK | 318 | ||
| linux-release-x86_64 | OK | 193 | ||
| macos-release-arm64 | OK | 208 | ||
| macos-oldrel-arm64 | OK | 174 | ||
| windows-devel | OK | 129 | ||
| windows-release | OK | 124 | ||
| windows-oldrel | OK | 127 | ||
| wasm-release | OK | 163 |
Exports:aggregateAICBICcalmr_model_graphcalmr_verbositycompare_modelsdesignexperiencesexperiences<-filterfit_modelget_designget_graph_optsget_modelget_optimizer_optsget_parametersget_plot_optsget_timingsgraphmake_experimentmappingmodel_outputsmodel_parametersNLLparametersparameters<-parseparse_designparsed_resultspatch_graphspatch_plotsphase_parserplotplot_common_scaleplot_targeted_complex_trialsplot_targeted_tbinsplot_targeted_trialsplot_targeted_typed_trialsplot_tbinsplot_trialspredictraw_resultsresultsrsarunrun_experimentset_calmr_paletteset_reward_parametersshowsupported_familiessupported_modelssupported_optimizerssupported_plotssupported_timed_modelstesttimingstimings<-trials
Dependencies:clicodacodetoolscpp11crayondata.tabledigestfarverforeachfuturefuture.applyGAggnetworkggplot2ggrepelglobalsgluegtableigraphisobanditeratorslabelinglatticelifecyclelistenvmagrittrMatrixnetworkparallellypatchworkpillarpkgconfigprogressrR6RColorBrewerRcppRcppArmadillorlangS7scalessnastatnet.commontibbleutf8vctrsviridisLitewithr
parallelism_in_calmr
Last update: 2025-07-07
Started: 2024-02-27
directional_models
The behaviour of directional models | Denoting directional trials | Expression | Learning | A simple example | A more complex example | Conclusion | References
Last update: 2025-07-07
Started: 2025-05-07
model_parameters
RW1972 | MAC1975 | PKH1982 | SM2007 | HDI2020/HD2022 | TD | ANCCR | RAND
Last update: 2025-05-10
Started: 2025-05-10
TD
The mathematics behind TD | 1 - Maintaining stimulus representations | 2 - Generating expectations | 3 - Learning associations | 4 - Generating responses | References
Last update: 2025-05-10
Started: 2024-04-08
PKH1982
The mathematics behind PKH1982 | 1 - Generating expectations | 2 - Learning associations | 3 - Learning to attend | 4 - Generating responses | References
Last update: 2025-05-07
Started: 2024-02-22
calmr_fits
Fitting HeiDI to empirical data | The data | Writing the model function | Fitting the model | A final note
Last update: 2024-11-13
Started: 2022-12-12
Getting started with calmr
The design data.frame | The parameters list | Simulating | Plotting | Stimulus associations | Responding | Graphing | Final thoughts
Last update: 2024-11-13
Started: 2024-04-08
heidi_similarity
Simulating similarity effects | Reproducing the simulation presented in the paper | Plotting the similarity between saliencies | Plotting the distribution of responding | Some final notes
Last update: 2024-11-13
Started: 2022-03-03
using_time_models
Time models in calmr | Changes to trial-based models | Specifying a design for time-based models | References
Last update: 2024-11-13
Started: 2024-02-26
calmr_app
A companion package for calmr | For non-programmers | For programmers | A final message
Last update: 2024-04-10
Started: 2023-01-30
ANCCR
The mathematics behind ANCCR | 1 - Maintaining stimulus representations | 2 - Learning stimulus associations: | 3 - Releasing Dopamine | 4 - Generating responses | A diagram | Note | References
Last update: 2024-04-09
Started: 2024-02-28
RAND
The mathematics behind RAND
Last update: 2024-04-07
Started: 2024-02-24
SM2007
The mathematics behind SOCR | 1 - Learning associations | 2 - Activating stimuli | 3 - Generating responses and comparison processes | 4 - Switching between facilitation and competition | References
Last update: 2024-03-10
Started: 2024-02-22
HD2022
The mathematics behind HeiDI | 1 - Acquiring reciprocal associations | 1.1 - The stimulus expectation rule | 1.2 - Learning rule | 2 - Pooling the strength of associations | 2.1 - Combined associative strength | 2.2 - Chained associative strength | 3 - Distributing strength into stimulus-specific response units | 4 - Generating responses
Last update: 2024-03-10
Started: 2024-02-22
MAC1975
The mathematics behind MAC1975 | 1 - Generating expectations | 2 - Learning associations | 3 - Learning to attend | 4 - Generating responses | References
Last update: 2024-03-10
Started: 2024-02-22
RW1972
The mathematics behind RW1972 | 1 - Generating expectations | 2 - Learning associations | 3 - Generating responses | References
Last update: 2024-03-10
Started: 2024-02-22
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create a graph with calmr data | calmr_model_graph get_graph_opts patch_graphs |
| Set verbosity options for calmr | calmr_verbosity |
| S4 class for calmr designs | CalmrDesign-class |
| CalmrDesign methods | CalmrDesign-methods mapping mapping,CalmrDesign-method show,CalmrDesign-method trials,CalmrDesign-method |
| S4 class for calmr experiments. | CalmrExperiment-class |
| CalmrExperiment methods | aggregate aggregate,CalmrExperiment-method CalmrExperiment-methods design design,CalmrExperiment-method experiences experiences,CalmrExperiment-method experiences<- experiences<-,CalmrExperiment-method filter filter,CalmrExperiment-method graph graph,CalmrExperiment-method length,CalmrExperiment-method parameters parameters,CalmrExperiment-method parameters<- parameters<-,CalmrExperiment-method parse parse,CalmrExperiment-method parsed_results parsed_results,CalmrExperiment-method plot plot,CalmrExperiment-method raw_results raw_results,CalmrExperiment-method results results,CalmrExperiment-method show,CalmrExperiment-method timings timings,CalmrExperiment-method timings<- timings<-,CalmrExperiment-method trials trials,CalmrExperiment-method |
| S4 class for calmr Fit | CalmrFit-class |
| CalmrFit methods | AIC AIC,CalmrFit-method BIC BIC,CalmrFit-method CalmrFit-methods NLL NLL,CalmrFit-method predict predict,CalmrFit-method show,CalmrFit-method |
| S4 class for calmr Models | CalmrModel-class |
| CalmrModel methods | CalmrModel-methods graph,CalmrModel-method parameters,CalmrModel-method parameters<-,CalmrModel-method parse,CalmrModel-method parsed_results,CalmrModel-method plot,CalmrModel-method raw_results,CalmrModel-method run run,ANCCR-method run,CalmrModel-method run,HD2022-method run,HDI2020-method run,MAC1975-method run,PKH1982-method run,RAND-method run,RW1972-method run,SM2007-method run,TD-method show,CalmrModel-method |
| S4 class for calmr representational similarity analysis | CalmrRSA-class |
| CalmrRSA methods | CalmrRSA-methods plot,CalmrRSA-method show,CalmrRSA-method test test,CalmrRSA-method |
| Run models given a set of parameters | compare_models |
| Fit model to data | fit_model |
| Get basic designs | get_design |
| Get optimizer options | get_optimizer_opts |
| Get model parameters | get_parameters |
| Get timing design parameters | get_timings |
| Make CalmrExperiment | make_experiment |
| Model information functions | get_model model_information model_outputs model_parameters supported_families supported_models supported_optimizers supported_plots supported_timed_models |
| Parse design data.frame | parse_design |
| Rat responses from Patittucci et al. 2016 | pati |
| Parses a phase string | phase_parser |
| General plotting functions | plotting_functions plot_targeted_complex_trials plot_targeted_tbins plot_targeted_trials plot_targeted_typed_trials plot_tbins plot_trials |
| General plotting options | get_plot_opts patch_plots plotting_options plot_common_scale |
| Perform representational similarity analysis | rsa |
| Run experiment | run_experiment |
| Get/set the colour/fill palette for plots | set_calmr_palette |
| Set reward parameters for ANCCR model | set_reward_parameters |
