Package: NeuroDecodeR 0.2.0

NeuroDecodeR: Decode Information from Neural Activity

Neural decoding is method of analyzing neural data that uses a pattern classifiers to predict experimental conditions based on neural activity. 'NeuroDecodeR' is a system of objects that makes it easy to run neural decoding analyses. For more information on neural decoding see Meyers & Kreiman (2011) <doi:10.7551/mitpress/8404.003.0024>.

Authors:Ethan Meyers [aut, cre]

NeuroDecodeR_0.2.0.tar.gz
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NeuroDecodeR.pdf |NeuroDecodeR.html✨
NeuroDecodeR/json (API)

# Install 'NeuroDecodeR' in R:
install.packages('NeuroDecodeR', repos = c('https://emeyers.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/emeyers/neurodecoder/issues

On CRAN:

6.94 score 12 stars 16 scripts 149 downloads 30 exports 51 dependencies

Last updated 8 months agofrom:826e2119a6. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 10 2024
R-4.5-winOKNov 10 2024
R-4.5-linuxOKNov 10 2024
R-4.4-winOKNov 10 2024
R-4.4-macOKNov 10 2024
R-4.3-winOKNov 10 2024
R-4.3-macOKNov 10 2024

Exports:aggregate_CV_split_resultsaggregate_resample_run_resultscl_max_correlationcl_poisson_naive_bayescl_svmconvert_matlab_raster_datacreate_binned_datacv_standardds_basicds_generalizationfp_select_k_featuresfp_zscoreget_dataget_num_label_repetitionsget_parametersget_predictionsget_siteIDs_with_k_label_repetitionslog_check_results_already_existlog_load_results_from_paramslog_load_results_from_result_namelog_save_resultsplot_main_resultspreprocess_dataread_matlab_raster_dataread_raster_datarm_confusion_matrixrm_main_resultsrun_decodingtest_valid_ndr_objecttest_valid_raster_format

Dependencies:classclicodetoolscolorspacecpp11doSNOWdplyre1071fansifarverforcatsforeachgenericsggplot2gluegridExtragtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigproxypurrrR.matlabR.methodsS3R.ooR.utilsR6RColorBrewerrlangscalessnowstringistringrtibbletictoctidyrtidyselectutf8vctrsviridisLitewithr

Data formats

Rendered fromdata_formats.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2021-07-09
Started: 2020-07-08

Datasets

Rendered fromdatasets.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2022-09-19
Started: 2020-07-08

Generalization analysis tutorial

Rendered fromgeneralization_tutorial.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2022-09-27
Started: 2020-06-17

Introductory tutorial

Rendered fromintroduction_tutorial.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2022-09-30
Started: 2019-07-26

NeuroDecodeR object specification

Rendered fromNDR_object_specification.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2022-09-30
Started: 2020-08-11

Readme and manuals

Help Manual

Help pageTopics
A maximum correlation coefficient classifier (CL)cl_max_correlation
A Poisson Naive Bayes classifier (CL)cl_poisson_naive_bayes
A support vector machine classifier (CL)cl_svm
Convert raster data in MATLAB to Rconvert_matlab_raster_data
Convert data from raster format to binned formatcreate_binned_data
The standard cross-validator (CV)cv_standard
A basic datasource (DS)ds_basic
A datasource (DS) that allows training and testing on different but related labelsds_generalization
A feature preprocessor (FP) that reduces data to the k most selective featuresfp_select_k_features
A feature preprocessor (FP) that z-score normalizes the datafp_zscore
Get the number of sites have at least k trials of each label levelget_num_label_repetitions
Get the number of trial repetitions for a given label for each siteget_num_label_repetitions_each_site
Get parameters of an NeuroDecodeR objectget_parameters.cv_standard
Get the sitesIDs that have at least k trials for all label levelget_siteIDs_with_k_label_repetitions
A function that checks if a decoding analysis has already been runlog_check_results_already_exist
A function that loads DECODING_RESULTS based on decoding_parameterslog_load_results_from_params
A function that loads DECODING_RESULTS based on the result_namelog_load_results_from_result_name
Saves the DECODING_RESULTS and logs the parameters used in the analysislog_save_results
A plot function to plot multiple rm_main_resultsplot_main_results
A plot function for label_repetition objectplot.label_repetition
A plot function for data in raster formatplot.raster_data
A plot function for the rm_confusion_matrix objectplot.rm_confusion_matrix
A plot function for the rm_main_results objectplot.rm_main_results
Read a csv, rda, rds or mat file in raster formatread_raster_data
A result metric (RM) that calculates confusion matricesrm_confusion_matrix
A result metric (RM) that calculates main decoding accuracy measuresrm_main_results
A cross-validator (CV) method to run a decoding analysisrun_decoding.cv_standard
Tests if a data frame is in valid raster formattest_valid_raster_format