NeuroDecodeR0.2.0 package

Decode Information from Neural Activity

aggregate_CV_split_results

A result metric (RM) method to aggregate results over cross-validation...

aggregate_CV_split_results.rm_confusion_matrix

A result metric (RM) method to aggregate results over cross-validation...

aggregate_CV_split_results.rm_main_results

A result metric (RM) method to aggregate results over cross-validation...

aggregate_resample_run_results

A result metric (RM) method to aggregate results over resample runs

aggregate_resample_run_results.rm_confusion_matrix

A result metric (RM) method to aggregate results over resample runs

aggregate_resample_run_results.rm_main_results

A result metric (RM) method to aggregate results over resample runs

cl_max_correlation

A maximum correlation coefficient classifier (CL)

cl_poisson_naive_bayes

A Poisson Naive Bayes classifier (CL)

cl_svm

A support vector machine classifier (CL)

convert_matlab_raster_data

Convert raster data in MATLAB to R

create_binned_data

Convert data from raster format to binned format

cv_standard

The standard cross-validator (CV)

ds_basic

A basic datasource (DS)

ds_generalization

A datasource (DS) that allows training and testing on different but re...

fp_select_k_features

A feature preprocessor (FP) that reduces data to the k most selective ...

fp_zscore

A feature preprocessor (FP) that z-score normalizes the data

get_data.ds_basic

A datasource (DS) method to generate training and test sets

get_data.ds_generalization

A datasource (DS) method to generate training and test sets

get_data

A datasource (DS) method to generate training and test sets

get_num_label_repetitions

Get the number of sites have at least k trials of each label level

get_num_label_repetitions_each_site

Get the number of trial repetitions for a given label for each site

get_parameters.cl_max_correlation

Get parameters of an NeuroDecodeR object

get_parameters.cl_poisson_naive_bayes

Get parameters of an NeuroDecodeR object

get_parameters.cl_svm

Get parameters of an NeuroDecodeR object

get_parameters.cv_standard

Get parameters of an NeuroDecodeR object

get_parameters.ds_basic

Get parameters of an NeuroDecodeR object

get_parameters.ds_generalization

Get parameters of an NeuroDecodeR object

get_parameters.fp_select_k_features

Get parameters of an NeuroDecodeR object

get_parameters.fp_zscore

Get parameters of an NeuroDecodeR object

get_parameters

Get parameters of an NeuroDecodeR object

get_parameters.rm_confusion_matrix

Get parameters of an NeuroDecodeR object

get_parameters.rm_main_results

Get parameters of an NeuroDecodeR object

get_predictions.cl_max_correlation

A classifier (CL) method to train the CL and return predictions

get_predictions.cl_poisson_naive_bayes

A classifier (CL) method to train the CL and return predictions

get_predictions.cl_svm

A classifier (CL) method to train the CL and return predictions

get_predictions

A classifier (CL) method to train the CL and return predictions

get_siteIDs_with_k_label_repetitions

Get the sitesIDs that have at least k trials for all label level

log_check_results_already_exist

A function that checks if a decoding analysis has already been run

log_load_results_from_params

A function that loads DECODING_RESULTS based on decoding_parameters

log_load_results_from_result_name

A function that loads DECODING_RESULTS based on the result_name

log_save_results

Saves the DECODING_RESULTS and logs the parameters used in the analysi...

NeuroDecodeR

NeuroDecodeR: A package for neural decoding analyses

plot.label_repetition

A plot function for label_repetition object

plot.raster_data

A plot function for data in raster format

plot.rm_confusion_matrix

A plot function for the rm_confusion_matrix object

plot.rm_main_results

A plot function for the rm_main_results object

plot_main_results

A plot function to plot multiple rm_main_results

preprocess_data.fp_select_k_features

A feature-preprocessor (FP) method to pre-process training and test da...

preprocess_data.fp_zscore

A feature-preprocessor (FP) method to pre-process training and test da...

preprocess_data

A feature-preprocessor (FP) method to pre-process training and test da...

read_matlab_raster_data

Reads MATLAB raster data

read_raster_data

Read a csv, rda, rds or mat file in raster format

rm_confusion_matrix

A result metric (RM) that calculates confusion matrices

rm_main_results

A result metric (RM) that calculates main decoding accuracy measures

run_decoding.cv_standard

A cross-validator (CV) method to run a decoding analysis

run_decoding

A cross-validator (CV) method to run a decoding analysis

test_valid_binned_format

Tests if a data frame is in valid binned format

test_valid_ndr_object

Tests if an object is a valid NDR object

test_valid_raster_format

Tests if a data frame is in valid raster format

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>.

  • Maintainer: Ethan Meyers
  • License: GPL-3
  • Last published: 2024-03-15