Skip to contents

Extracts p-values

extract_p.Rd

For a given object it will look for the column named "p adj" or "difference" and extract its value keeping its names

Usage

extract_p(x)

# Default S3 method
extract_p(x)

# S3 method for class 'TukeyHSD'
extract_p(x)

# S3 method for class 'mc'
extract_p(x)

Arguments

x

A object that has p-values or logical values.

Value

A named vector with p-values or logical values.

Methods (by class)

  • extract_p(default):

  • extract_p(TukeyHSD): extract p values from a TukeyHSD object

  • extract_p(mc):

See also

multcompLetters multcompTs

Author

Luciano Selzer

Examples


experiment <- data.frame(treatments = gl(11, 20, labels = c("dtl", "ctrl", "treat1", 
              "treat2", "treatA2", "treatB", "treatB2",
              "treatC", "treatD", "treatA1", "treatX")),
              y = c(rnorm(20, 10, 5), rnorm(20, 20, 5), rnorm(20, 22, 5), rnorm(20, 24, 5),
               rnorm(20, 35, 5), rnorm(20, 37, 5), rnorm(20, 40, 5), rnorm(20, 43, 5),
               rnorm(20, 45, 5), rnorm(20, 60, 5), rnorm(20, 60, 5)))
exp_tukey <- TukeyHSD(exp_aov <- aov(y  ~ treatments, data = experiment))

extract_p(exp_tukey)
#> $treatments
#>        ctrl-dtl      treat1-dtl      treat2-dtl     treatA2-dtl      treatB-dtl 
#>    1.181586e-08    4.181100e-13    9.414691e-14    0.000000e+00    0.000000e+00 
#>     treatB2-dtl      treatC-dtl      treatD-dtl     treatA1-dtl      treatX-dtl 
#>    0.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00 
#>     treat1-ctrl     treat2-ctrl    treatA2-ctrl     treatB-ctrl    treatB2-ctrl 
#>    8.108838e-01    1.466757e-01    8.948398e-14    9.481305e-14    0.000000e+00 
#>     treatC-ctrl     treatD-ctrl    treatA1-ctrl     treatX-ctrl   treat2-treat1 
#>    0.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00    9.901471e-01 
#>  treatA2-treat1   treatB-treat1  treatB2-treat1   treatC-treat1   treatD-treat1 
#>    8.544276e-13    1.108336e-12    8.526513e-14    0.000000e+00    0.000000e+00 
#>  treatA1-treat1   treatX-treat1  treatA2-treat2   treatB-treat2  treatB2-treat2 
#>    0.000000e+00    0.000000e+00    6.511587e-10    8.485427e-10    9.392487e-14 
#>   treatC-treat2   treatD-treat2  treatA1-treat2   treatX-treat2  treatB-treatA2 
#>    7.993606e-15    0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00 
#> treatB2-treatA2  treatC-treatA2  treatD-treatA2 treatA1-treatA2  treatX-treatA2 
#>    5.993468e-01    8.528938e-04    4.826761e-05    0.000000e+00    0.000000e+00 
#>  treatB2-treatB   treatC-treatB   treatD-treatB  treatA1-treatB   treatX-treatB 
#>    5.671536e-01    7.079746e-04    3.913932e-05    0.000000e+00    0.000000e+00 
#>  treatC-treatB2  treatD-treatB2 treatA1-treatB2  treatX-treatB2   treatD-treatC 
#>    4.161509e-01    1.037188e-01    0.000000e+00    1.354472e-14    9.998833e-01 
#>  treatA1-treatC   treatX-treatC  treatA1-treatD   treatX-treatD  treatX-treatA1 
#>    2.731149e-14    8.903989e-14    7.926992e-14    2.726708e-13    5.929523e-01 
#> 

if(require(pgirmess)){
extract_p(kruskalmc(y ~ treatments, data = experiment))
}
#> Loading required package: pgirmess
#>        dtl-ctrl      dtl-treat1      dtl-treat2     dtl-treatA2      dtl-treatB 
#>           FALSE           FALSE           FALSE            TRUE            TRUE 
#>     dtl-treatB2      dtl-treatC      dtl-treatD     dtl-treatA1      dtl-treatX 
#>            TRUE            TRUE            TRUE            TRUE            TRUE 
#>     ctrl-treat1     ctrl-treat2    ctrl-treatA2     ctrl-treatB    ctrl-treatB2 
#>           FALSE           FALSE            TRUE            TRUE            TRUE 
#>     ctrl-treatC     ctrl-treatD    ctrl-treatA1     ctrl-treatX   treat1-treat2 
#>            TRUE            TRUE            TRUE            TRUE           FALSE 
#>  treat1-treatA2   treat1-treatB  treat1-treatB2   treat1-treatC   treat1-treatD 
#>           FALSE           FALSE            TRUE            TRUE            TRUE 
#>  treat1-treatA1   treat1-treatX  treat2-treatA2   treat2-treatB  treat2-treatB2 
#>            TRUE            TRUE           FALSE           FALSE            TRUE 
#>   treat2-treatC   treat2-treatD  treat2-treatA1   treat2-treatX  treatA2-treatB 
#>            TRUE            TRUE            TRUE            TRUE           FALSE 
#> treatA2-treatB2  treatA2-treatC  treatA2-treatD treatA2-treatA1  treatA2-treatX 
#>           FALSE           FALSE           FALSE            TRUE            TRUE 
#>  treatB-treatB2   treatB-treatC   treatB-treatD  treatB-treatA1   treatB-treatX 
#>           FALSE           FALSE           FALSE            TRUE            TRUE 
#>  treatB2-treatC  treatB2-treatD treatB2-treatA1  treatB2-treatX   treatC-treatD 
#>           FALSE           FALSE            TRUE            TRUE           FALSE 
#>  treatC-treatA1   treatC-treatX  treatD-treatA1   treatD-treatX  treatA1-treatX 
#>           FALSE           FALSE           FALSE           FALSE           FALSE