I am running a multinomial analysis with vglm(). It all works, but then I try to follow the instructions from the following website (https://rcompanion.org/handbook/H_08.html) to do a pairwise test, because emmeans cannot handle pairwise for vglm models. The lrtest() part gives me the following error: Error in lrtest.default(model) : 'list' object cannot be coerced to type 'double'
I cannot figure out what is wrong, I even copy and pasted the exact code that the website used (see below) and get the same error with their own code and dataset. Any ideas?
Their code and suggestion for doing pairwise testing with vglm() is the only pairwise testing option I found for vglm() anywhere on the web.
Here is the code along with all the expected output and extra details from their website (it is simpler than mine but gets same error anyways).
Input = ("
County Sex Result Count
Bloom Female Pass 9
Bloom Female Fail 5
Bloom Male Pass 7
Bloom Male Fail 17
Cobblestone Female Pass 11
Cobblestone Female Fail 4
Cobblestone Male Pass 9
Cobblestone Male Fail 21
Dougal Female Pass 9
Dougal Female Fail 7
Dougal Male Pass 19
Dougal Male Fail 9
Heimlich Female Pass 15
Heimlich Female Fail 8
Heimlich Male Pass 14
Heimlich Male Fail 17
")
Data = read.table(textConnection(Input),header=TRUE)
### Order factors otherwise R will alphabetize them
Data$County = factor(Data$County,
levels=unique(Data$County))
Data$Sex = factor(Data$Sex,
levels=unique(Data$Sex))
Data$Result = factor(Data$Result,
levels=unique(Data$Result))
### Check the data frame
library(psych)
headTail(Data)
str(Data)
summary(Data)
### Remove unnecessary objects
rm(Input)
Multinomial regression
library(VGAM)
model = vglm(Result ~ Sex + County + Sex:County,
family=multinomial(refLevel=1),
weights = Count,
data = Data)
summary(model)
library(car)
Anova(model,
type="II",
test="Chisq")```
Analysis of Deviance Table (Type II tests)
Response: Result
Df Chisq Pr(>Chisq)
Sex 1 6.7132 0.00957 **
County 3 4.1947 0.24120
Sex:County 3 7.1376 0.06764 .
library(rcompanion)
nagelkerke(model)
$Pseudo.R.squared.for.model.vs.null Pseudo.R.squared McFadden 0.0797857 Cox and Snell (ML) 0.7136520 Nagelkerke (Cragg and Uhler) 0.7136520
$Likelihood.ratio.test Df.diff LogLik.diff Chisq p.value 7 -10.004 20.009 0.0055508
library(lmtest)
lrtest(model)
Likelihood ratio test
Model 1: Result ~ Sex + County + Sex:County Model 2: Result ~ 1
#Df LogLik Df Chisq Pr(>Chisq)
1 8 -115.39
2 15 -125.39 7 20.009 0.005551 **
Post-hoc analysis
At the time of writing, the lsmeans package cannot be used with vglm models.
One option for post-hoc analysis would be to conduct analyses on reduced models, including only two levels of a factor. For example, if the variable County x Sex term had been significant, the following code could be used to create a reduced dataset with only Bloom–Female and Bloom–Male, and analyze this data with vglm.
Data.b = Data[Data$County=="Bloom" &
(Data$Sex=="Female"| Data$Sex=="Male") , ]
Data.b$County = factor(Data.b$County)
Data.b$Sex = factor(Data.b$Sex)
summary(Data.b)
County Sex Result Count
Bloom:4 Female:2 Pass:2 Min. : 5.0
Male :2 Fail:2 1st Qu.: 6.5
Median : 8.0
Mean : 9.5
3rd Qu.:11.0
Max. :17.0
library(VGAM)
model.b = vglm(Result ~ Sex,
family=multinomial(refLevel=1),
weights = Count,
data = Data.b)
lrtest(model.b)
Likelihood ratio test
#Df LogLik Df Chisq Pr(>Chisq)
1 2 -23.612
2 3 -25.864 1 4.5041 0.03381 *
Summary table of results
Comparison p-value Bloom–Female - Bloom–Male 0.034 Cobblestone–Female - Cobblestone–Male 0.0052 Dougal–Female - Dougal–Male 0.44 Heimlich–Female - Heimlich–Male 0.14
p.value = c(0.034, 0.0052, 0.44, 0.14)
p.adj = p.adjust(p.value,
method = "fdr")
p.adj = signif(p.adj,
2)
p.adj
[1] 0.068 0.021 0.440 0.190
Comparison p-value p.adj Bloom–Female - Bloom–Male 0.034 0.068 Cobblestone–Female - Cobblestone–Male 0.0052 0.021 Dougal–Female - Dougal–Male 0.44 0.44 Heimlich–Female - Heimlich–Male 0.14 0.19
