Likelihood ratio test for mkinfit models

+ +

Compare two mkinfit models based on their likelihood. If two fitted +mkinfit objects are given as arguments, it is checked if they have been +fitted to the same data. It is the responsibility of the user to make sure +that the models are nested, i.e. one of them has less degrees of freedom +and can be expressed by fixing the parameters of the other.

+ +

Usage

# S3 method for class 'mkinfit'
+lrtest(object, object_2 = NULL, ...)
+
+# S3 method for class 'mmkin'
+lrtest(object, ...)

+ +

Arguments

+ + +

object: An mkinfit object, or an mmkin column +object containing two fits to the same data.
object_2: Optionally, another mkinfit object fitted to the same data.
...: Argument to mkinfit, passed to +update.mkinfit for creating the alternative fitted object.

Details

Alternatively, an argument to mkinfit can be given which is then passed +to update.mkinfit to obtain the alternative model.

The comparison is then made by the lrtest.default +method from the lmtest package. The model with the higher number of fitted +parameters (alternative hypothesis) is listed first, then the model with the +lower number of fitted parameters (null hypothesis).

+ +

Examples

# \dontrun{
+test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")
+sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)
+dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE)
+lrtest(dfop_fit, sfo_fit)
+#> Likelihood ratio test
+#> 
+#> Model 1: DFOP with error model const
+#> Model 2: SFO with error model const
+#>   #Df  LogLik Df  Chisq Pr(>Chisq)    
+#> 1   5 -42.453                         
+#> 2   3 -63.954 -2 43.002  4.594e-10 ***
+#> ---
+#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
+lrtest(sfo_fit, dfop_fit)
+#> Likelihood ratio test
+#> 
+#> Model 1: DFOP with error model const
+#> Model 2: SFO with error model const
+#>   #Df  LogLik Df  Chisq Pr(>Chisq)    
+#> 1   5 -42.453                         
+#> 2   3 -63.954 -2 43.002  4.594e-10 ***
+#> ---
+#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
+
+# The following two examples are commented out as they fail during
+# generation of the static help pages by pkgdown
+#lrtest(dfop_fit, error_model = "tc")
+#lrtest(dfop_fit, fixed_parms = c(k2 = 0))
+
+# However, this equivalent syntax also works for static help pages
+lrtest(dfop_fit, update(dfop_fit, error_model = "tc"))
+#> Likelihood ratio test
+#> 
+#> Model 1: DFOP with error model tc
+#> Model 2: DFOP with error model const
+#>   #Df  LogLik Df  Chisq Pr(>Chisq)    
+#> 1   6 -34.587                         
+#> 2   5 -42.453 -1 15.731  7.302e-05 ***
+#> ---
+#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
+lrtest(dfop_fit, update(dfop_fit, fixed_parms = c(k2 = 0)))
+#> Likelihood ratio test
+#> 
+#> Model 1: DFOP with error model const
+#> Model 2: DFOP with error model const and fixed parameter(s) k2
+#>   #Df  LogLik Df  Chisq Pr(>Chisq)    
+#> 1   5 -42.453                         
+#> 2   4 -57.340 -1 29.776  4.851e-08 ***
+#> ---
+#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
+# }
+