wald: Calculate Wald-Profiles

In mcprofile: Testing Generalized Linear Hypotheses for Generalized Linear Model Parameters by Profile Deviance

Description

Transforms a signed root deviance profile of a mcprofile object into a profile of Wald-type statistics

Usage

wald(object)

Arguments

object

An object of class mcprofile

Value

An object of class mcprofile with a wald profile in the srdp slot.

See Also

mcprofile

Examples

#######################################
## cell transformation assay example ##
#######################################

str(cta)
## change class of cta$conc into factor
cta$concf <- factor(cta$conc, levels=unique(cta$conc))

ggplot(cta, aes(y=foci, x=concf)) + 
  geom_boxplot() +
  geom_dotplot(binaxis = "y", stackdir = "center", binwidth = 0.2) + 
  xlab("concentration")
  
  
# glm fit assuming a Poisson distribution for foci counts
# parameter estimation on the log link
# removing the intercept
fm <- glm(foci ~ concf-1, data=cta, family=poisson(link="log"))

### Comparing each dose to the control by Dunnett-type comparisons
# Constructing contrast matrix
library(multcomp)
CM <- contrMat(table(cta$concf), type="Dunnett")

# calculating signed root deviance profiles
(dmcp <- mcprofile(fm, CM))
# computing profiles for the modified likelihood root
wp <- wald(dmcp)

plot(wp)

# comparing confidence intervals
confint(wp)
confint(dmcp)

Example output

Loading required package: ggplot2
'data.frame':	80 obs. of  2 variables:
 $ conc: num  0 0 0 0 0 0 0 0 0 0 ...
 $ foci: int  0 1 0 0 0 0 0 0 0 2 ...
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

The following object is masked from ‘package:MASS’:

    geyser


   Multiple Contrast Profiles

         Estimate Std.err
0.01 - 0    0.511   0.730
0.03 - 0   -0.405   0.913
0.1 - 0     1.386   0.645
0.3 - 0     2.159   0.610
1 - 0       2.730   0.596
3 - 0       2.813   0.594
10 - 0      2.979   0.592


   mcprofile - Confidence Intervals 

level: 		 0.95 
adjustment:	 single-step 

         Estimate  lower upper
0.01 - 0    0.511 -1.269  2.29
0.03 - 0   -0.405 -2.631  1.82
0.1 - 0     1.386 -0.187  2.96
0.3 - 0     2.159  0.673  3.65
1 - 0       2.730  1.278  4.18
3 - 0       2.813  1.365  4.26
10 - 0      2.979  1.536  4.42


   mcprofile - Confidence Intervals 

level: 		 0.95 
adjustment:	 single-step 

         Estimate  lower upper
0.01 - 0    0.511 -1.250  2.56
0.03 - 0   -0.405 -3.054  1.87
0.1 - 0     1.386 -0.018  3.31
0.3 - 0     2.159  0.895  4.04
1 - 0       2.730  1.519  4.59
3 - 0       2.813  1.608  4.67
10 - 0      2.979  1.783  4.83

mcprofile documentation built on April 20, 2021, 9:06 a.m.