To install this github version type (in R):
#if devtools is not installed yet:
# install.packages("devtools")
library(devtools)
install_github("livioivil/flip")
library(flip)A univariate analysis
Testing the symmetry around 0 in a one sample (i.e. equivalent to one sample t-test)
set.seed(1)
y=rnorm(10)+.5
res=flip(y)
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
summary(res)
#> Call:
#> flip(Y = y)
#> 1023 permutations.
#> Test Stat tail p-value sig.
#> Y t 2.561 >< 0.0293 *and ploting
plot(res) # same ad hist(res)
A multivarite analysis
set.seed(1)
df=data.frame(y1=rnorm(10)+.5,y2=rnorm(10))
res=flip(~.,data=df)
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(c(rep(0, (2^p/2^n)), rep(1, (2^p/2^n))), length = 2^p):
#> partial argument match of 'length' to 'length.out'
#> Warning in rep(tail, len = ncol(permT)): partial argument match of 'len' to
#> 'length.out'
#> Warning in rep(tail, len = ncol(permT)): partial argument match of 'len' to
#> 'length.out'
summary(res)
#> Call:
#> flip(Y = ~., data = df)
#> 1023 permutations.
#> Test Stat tail p-value sig.
#> y1 t 2.5612 >< 0.0293 *
#> y2 t 0.7358 >< 0.4844
plot(res) 
Which is different from ploting
##set the following if you get an error (mostly using Rstudio)
#par(mar=c(1,1,1,1))
hist(res)
For the general framework of univariate and multivariate permutation tests see:
Pesarin, F. (2001) Multivariate Permutation Tests with Applications in Biostatistics. Wiley, New York.
For analysis of mixed-models see:
L. Finos and D. Basso (2014) Permutation Tests for Between-Unit Fixed Effectsin Multivariate Generalized Linear Mixed Models. Statistics and Computing. Volume 24, Issue 6, pp 941-952. DOI: 10.1007/s11222-013-9412-6
D. Basso, L. Finos (2011) Exact Multivariate Permutation Tests for Fixed Effects in Mixed-Models. Communications in Statistics - Theory and Methods. DOI 10.1080/03610926.2011.627103
For Rotation tests see:
Langsrud, O. (2005) Rotation tests, Statistics and Computing, 15, 1, 53-60
A. Solari, L. Finos, J.J. Goeman (2014) Rotation-based multiple testing in the multivariate linear model. Biometrics. Accepted
The colors of the plots of library flip are mostly taken from display.wes.palette(5, "Darjeeling") of library(wesanderson).
If you encounter a bug, please file a reprex (minimal reproducible example) on github.