vignettes/citing-permutation-test.Rmd
citing-permutation-test.Rmd
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 and Renaud
2021), the permutation methods and the multiple comparisons
procedure (when using the clusterlm(...)
):
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 and Lane (1983) | Default method in permuco
|
kennedy |
Kennedy (1995) | |
manly |
Manly (1991) | |
huh_jhun |
Huh and Jhun (2001) Kherad Pajouh and Renaud (2010) |
Huh and Jhun (2001) propose it for
factorial design Kherad Pajouh and Renaud (2010) generalized it to linear model |
terBraak |
ter Braak (1992) | |
dekker |
Dekker, Krackhardt, and Snijders (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 and Renaud (2015) | Default method in permuco
|
Rde_kheradPajouh_renaud |
Kherad-Pajouh and Renaud (2015) |
The clusterlm(...)
function has several multiple
comparisons procedures implemented. It can be chosen using the
multcomp
argument.
multcomp = |
Reference | Parameters | Comments |
---|---|---|---|
clustermass |
Maris and Oostenveld (2007) Bullmore et al. (1999) |
threshold , aggr_FUN
|
Default method in permuco . Maris and Oostenveld (2007) is used by the EEG community. |
troendle |
Troendle (1995) | ||
minP |
Westfall and Young (1993) |
H , E
|
The default parameters are suggested by Pernet et al. (2015). |
tfce |
Smith and Nichols (2009) | ||
bonferroni |
Dunn (1958) | ||
holm |
Holm (1979) | ||
benjamini_hochberg |
Benjamini and Hochberg (1995) | Control the FDR. | |
clusterdepth |
Frossard and Renaud (2022) | threshold |
For completeness and full reproducibility of the results, you can
also report the parameters used in the
clustermass
,tfce
or clusterdepth
methods.