print.factorplot.Rd
Prints the output from an object of class factorplot
. By
default, the function prints all pairwise differences along with standard
errors and p-values (optionally adjusted for multiple testing). Optionally,
it can print only significant differences.
# S3 method for factorplot print(x, ..., digits = 3, sig = FALSE, trans = NULL)
x | An object of class |
---|---|
... | Other arguments passed to print, currently not implemented |
digits | The number of digits to print in each column |
sig | Logical indicating whether only significant differences should be printed. |
trans | A character string representing the post-hypothesis-testing
transformation to be performed on the estimates. For example, if the
estimates provided to the |
est1 <- log(c(1.00,2.12,1.44,1.31,1.44, 1.46,0.90)) var1 <- c(0.242,0.096,0.156,0.140, 0.380,0.484,0.375)^2 names(est1) <- c( "Normal & superficial gastritis", "Chronic gastritis", "Chronic atrophic gastritits", "Intestinal metaplasia I", "Intestinal metaplasia II", "Intestinal metaplasia III", "Dysplasia") plummer_fp1 <- factorplot(est1, var=var1, resdf=Inf) print(plummer_fp1, trans="exp")#> Difference #> Normal_&_superficial_gastritis - Chronic_gastritis 0.472 #> Normal_&_superficial_gastritis - Chronic_atrophic_gastritits 0.694 #> Chronic_gastritis - Chronic_atrophic_gastritits 1.472 #> Normal_&_superficial_gastritis - Intestinal_metaplasia_I 0.763 #> Chronic_gastritis - Intestinal_metaplasia_I 1.618 #> Chronic_atrophic_gastritits - Intestinal_metaplasia_I 1.099 #> Normal_&_superficial_gastritis - Intestinal_metaplasia_II 0.694 #> Chronic_gastritis - Intestinal_metaplasia_II 1.472 #> Chronic_atrophic_gastritits - Intestinal_metaplasia_II 1.000 #> Intestinal_metaplasia_I - Intestinal_metaplasia_II 0.910 #> Normal_&_superficial_gastritis - Intestinal_metaplasia_III 0.685 #> Chronic_gastritis - Intestinal_metaplasia_III 1.452 #> Chronic_atrophic_gastritits - Intestinal_metaplasia_III 0.986 #> Intestinal_metaplasia_I - Intestinal_metaplasia_III 0.897 #> Intestinal_metaplasia_II - Intestinal_metaplasia_III 0.986 #> Normal_&_superficial_gastritis - Dysplasia 1.111 #> Chronic_gastritis - Dysplasia 2.356 #> Chronic_atrophic_gastritits - Dysplasia 1.600 #> Intestinal_metaplasia_I - Dysplasia 1.456 #> Intestinal_metaplasia_II - Dysplasia 1.600 #> Intestinal_metaplasia_III - Dysplasia 1.622 #> SE p.val #> Normal_&_superficial_gastritis - Chronic_gastritis 0.260 0.004 #> Normal_&_superficial_gastritis - Chronic_atrophic_gastritits 0.288 0.205 #> Chronic_gastritis - Chronic_atrophic_gastritits 0.183 0.035 #> Normal_&_superficial_gastritis - Intestinal_metaplasia_I 0.280 0.334 #> Chronic_gastritis - Intestinal_metaplasia_I 0.170 0.005 #> Chronic_atrophic_gastritits - Intestinal_metaplasia_I 0.210 0.652 #> Normal_&_superficial_gastritis - Intestinal_metaplasia_II 0.451 0.418 #> Chronic_gastritis - Intestinal_metaplasia_II 0.392 0.324 #> Chronic_atrophic_gastritits - Intestinal_metaplasia_II 0.411 1.000 #> Intestinal_metaplasia_I - Intestinal_metaplasia_II 0.405 0.815 #> Normal_&_superficial_gastritis - Intestinal_metaplasia_III 0.541 0.484 #> Chronic_gastritis - Intestinal_metaplasia_III 0.493 0.450 #> Chronic_atrophic_gastritits - Intestinal_metaplasia_III 0.509 0.978 #> Intestinal_metaplasia_I - Intestinal_metaplasia_III 0.504 0.830 #> Intestinal_metaplasia_II - Intestinal_metaplasia_III 0.615 0.982 #> Normal_&_superficial_gastritis - Dysplasia 0.446 0.813 #> Chronic_gastritis - Dysplasia 0.387 0.027 #> Chronic_atrophic_gastritits - Dysplasia 0.406 0.247 #> Intestinal_metaplasia_I - Dysplasia 0.400 0.348 #> Intestinal_metaplasia_II - Dysplasia 0.534 0.379 #> Intestinal_metaplasia_III - Dysplasia 0.612 0.429