Running ‘anova.R’ [2s/3s]
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Running the tests in ‘tests/clmm.methods.R’ failed.
Complete output:
  > library(ordinal)
  > data(wine)
  > 
  > #################################
  > ## model.matrix method for clmm-objects:
  > fmm1 <- clmm(rating ~ contact + temp + (1|judge), data=wine)
  > mm <- model.matrix(fmm1)
  > stopifnot(inherits(mm, "matrix"),
  +           dim(mm) == c(72, 3))
  > 
  > #################################
  > ## anova.clmm works even if formula does not have an environment:
  > fmm1 <- clmm(rating ~ temp * contact + (1|judge), data = wine)
  > fmm2 <- clmm(rating ~ temp + contact + (1|judge), data = wine)
  > environment(fmm1$formula) <- NULL
  > environment(fmm2$formula) <- NULL
  > anova(fmm1, fmm2)
  Likelihood ratio tests of cumulative link models:
   
       formula:                              link: threshold:
  fmm2 rating ~ temp + contact + (1 | judge) logit flexible  
  fmm1 rating ~ temp * contact + (1 | judge) logit flexible  
  
       no.par    AIC  logLik LR.stat df Pr(>Chisq)
  fmm2      7 177.13 -81.565                      
  fmm1      8 179.07 -81.536  0.0589  1     0.8082
  > 
  > 
  > #################################
  > ## Test that ranef, condVar and VarCorr work as they are supposed to whether or
  > ## not nlme and lme4 are loaded:
  > 
  > fm <- clmm(rating ~ temp + contact + (1|judge), data = wine)
  > fm
  Cumulative Link Mixed Model fitted with the Laplace approximation
  
  formula: rating ~ temp + contact + (1 | judge)
  data:    wine
  
   link  threshold nobs logLik AIC    niter    max.grad
   logit flexible  72   -81.57 177.13 332(999) 1.03e-05
  
  Random effects:
   Groups Name        Variance Std.Dev.
   judge  (Intercept) 1.279    1.131   
  Number of groups:  judge 9 
  
  Coefficients:
    tempwarm contactyes 
       3.063      1.835 
  
  Thresholds:
     1|2    2|3    3|4    4|5 
  -1.624  1.513  4.229  6.089 
  > ranef(fm)
  $judge
    (Intercept)
  1  1.69617818
  2 -0.56578308
  3  0.96880828
  4 -0.05954989
  5  0.23051011
  6  0.47703864
  7 -1.91097339
  8 -0.27294385
  9 -0.55467576
  
  > VarCorr(fm)
  $judge
              (Intercept)
  (Intercept)    1.279461
  attr(,"stddev")
  (Intercept) 
     1.131133 
  
  > condVar(fm)
  $judge
    (Intercept)
  1   0.3067453
  2   0.3779358
  3   0.3545529
  4   0.3651870
  5   0.3566066
  6   0.3485475
  7   0.3435693
  8   0.3050453
  9   0.3183194
  
  > summary(fm)
  Cumulative Link Mixed Model fitted with the Laplace approximation
  
  formula: rating ~ temp + contact + (1 | judge)
  data:    wine
  
   link  threshold nobs logLik AIC    niter    max.grad cond.H 
   logit flexible  72   -81.57 177.13 332(999) 1.03e-05 2.8e+01
  
  Random effects:
   Groups Name        Variance Std.Dev.
   judge  (Intercept) 1.279    1.131   
  Number of groups:  judge 9 
  
  Coefficients:
             Estimate Std. Error z value Pr(>|z|)    
  tempwarm     3.0630     0.5954   5.145 2.68e-07 ***
  contactyes   1.8349     0.5125   3.580 0.000344 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  Threshold coefficients:
      Estimate Std. Error z value
  1|2  -1.6237     0.6824  -2.379
  2|3   1.5134     0.6038   2.507
  3|4   4.2285     0.8090   5.227
  4|5   6.0888     0.9725   6.261
  > 
  > library(nlme)
  > ranef(fm)
  $judge
    (Intercept)
  1  1.69617818
  2 -0.56578308
  3  0.96880828
  4 -0.05954989
  5  0.23051011
  6  0.47703864
  7 -1.91097339
  8 -0.27294385
  9 -0.55467576
  
  > VarCorr(fm)
  $judge
              (Intercept)
  (Intercept)    1.279461
  attr(,"stddev")
  (Intercept) 
     1.131133 
  
  > condVar(fm)
  $judge
    (Intercept)
  1   0.3067453
  2   0.3779358
  3   0.3545529
  4   0.3651870
  5   0.3566066
  6   0.3485475
  7   0.3435693
  8   0.3050453
  9   0.3183194
  
  > library(lme4)
  Error in library(lme4) : there is no package called 'lme4'
  Execution halted
Running the tests in ‘tests/ranef.loading.R’ failed.
Complete output:
  > # check that ranef and VarCorr work even after loading ordinal: 
  > library(lme4)
  Error in library(lme4) : there is no package called 'lme4'
  Execution halted