Likelihood ratio test for mkinfit models

@@ -155,115 +94,112 @@ 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.

# S3 method for mkinfit
-lrtest(object, object_2 = NULL, ...)
-
-# S3 method for 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.

# S3 method for mkinfit
+lrtest(object, object_2 = NULL, ...)
 
-    Details
+# S3 method for 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 +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
# }
-

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
+# }
+