In jaromilfrossard/permuco: Permutation Tests for Regression, (Repeated Measures) ANOVA/ANCOVA and Comparison of Signals

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How to cite results using permuco

The permuco package includes several permutation methods as well as several multiple comparisons procedures. We propose here the citation commonly used in the literature to cite these methods. When reporting a results using permuco, we suggest to cite the permuco package [@frossard_permuco], the permutation methods and the multiple comparisons procedure (when using the clusterlm(...)):

Citing the permutation method

The method argument set the permutation method for the aovperm(...), lmperm(...) and clusterlm(...) functions. If you are using a fixed effect linear model (without + Error(...) in the formula) you can use the following references:

method = | Reference | Comments ----------------|-----------------------------------------|---------------------------------------------------- freedmand_lane| @freedman_nonstochastic_1983 | Default method in permuco kennedy | @kennedy_randomization_1995 | manly | @manly_randomization_1991 | huh_jhun | @huh_random_2001
@kheradpajouh_exact_2010 | @huh_random_2001 propose it for factorial design
@kheradpajouh_exact_2010 generalized it to linear model terBraak | @terbraak_permutation_1992 | dekker | @dekker_sensitivity_2007 |

For repeated measures ANOVA/ANCOVA using aovperm(...) and clusterlm(...) (when the formula contains + Error(...)), the methods are:

method = | Reference | Comments --------------------------|------------------------------|---------------------------------- Rd_kheradPajouh_renaud | @kherad-pajouh_general_2015 | Default method in permuco Rde_kheradPajouh_renaud | @kherad-pajouh_general_2015 |

Citing the multiple comparisons procedure

The clusterlm(...) function has several multiple comparisons procedures implemented. It can be chosen using the multcomp argument.

multcomp = | Reference |Parameters | Comments -----------------------|--------------------------------|---------------|------------------------------------- clustermass | @maris_nonparametric_2007
@bullmore_global_1999 | threshold, aggr_FUN | Default method in permuco.
@maris_nonparametric_2007 is used by the EEG community. troendle | @troendle_stepwise_1995 | | minP | @westfall_resamplingbased_1993 | H, E | The default parameters are suggested by @pernet_clusterbased_2015. tfce | @smith_thresholdfree_2009 | | bonferroni | @dunn_estimation_1958 | | holm | @holm_simple_1979 | | benjamini_hochberg | @benjamini_controlling_1995 | | Control the FDR. clusterdepth | @frossard_cluster_2022 |threshold|

For completeness and full reproducibility of the results, you can also report the parameters used in the clustermass,tfce or clusterdepth methods.

Citing the dataset

The permuco package offers 3 data-sets as example. You will find the reference of the data below:

data-set | Reference -----------------------------|---------------------------------- attentionshifting_signal
attentionshifting_design | @tipura_attention_2019 emergencycost | @heritier_robust_2009 jpah2016 | @cheval_effect_2016

Reference

jaromilfrossard/permuco documentation built on July 2, 2022, 10:34 p.m.