From 31fd7412f46c9715962763d435cb0060ea420752 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 4 Nov 2019 17:21:04 +0100 Subject: Include fixed parameters in model names in lrtest --- NEWS.md | 4 +++- R/confint.mkinfit.R | 8 ++++---- R/lrtest.mkinfit.R | 18 ++++++++++++++---- docs/news/index.html | 5 +++-- docs/reference/confint.mkinfit.html | 20 ++++++++++---------- docs/reference/lrtest.mkinfit.html | 30 ++++++++++++++++++++++++------ man/confint.mkinfit.Rd | 8 ++++---- man/lrtest.mkinfit.Rd | 8 ++++++-- 8 files changed, 68 insertions(+), 33 deletions(-) diff --git a/NEWS.md b/NEWS.md index b9d58a27..cfb9fa96 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,8 @@ # mkin 0.9.49.8 (unreleased) -- 'confint.mkinfit': Make the quadratic approximation the default, as the likelihood profiling takes too much time for any with more than three parameters +- 'lrtest.mkinfit': Improve naming of the compared fits in the case of fixed parameters + +- 'confint.mkinfit': Make the quadratic approximation the default, as the likelihood profiling takes a lot of time, especially if the fit has more than three parameters # mkin 0.9.49.7 (2019-11-01) diff --git a/R/confint.mkinfit.R b/R/confint.mkinfit.R index 84183808..78dda95d 100644 --- a/R/confint.mkinfit.R +++ b/R/confint.mkinfit.R @@ -4,10 +4,10 @@ #' the curvature of the likelihood function at the maximum likelihood parameter #' estimates. #' The alternative method 'profile' is based on the profile likelihood for each -#' parameter. The method uses two nested optimisations and can take a very long -#' time, even if parallelized by specifying 'cores' on unixoid platforms. The -#' speed of the method could likely be improved by using the method of Venzon -#' and Moolgavkar (1988). +#' parameter. The 'profile' method uses two nested optimisations and can take a +#' very long time, even if parallelized by specifying 'cores' on unixoid +#' platforms. The speed of the method could likely be improved by using the +#' method of Venzon and Moolgavkar (1988). #' #' @param object An \code{\link{mkinfit}} object #' @param parm A vector of names of the parameters which are to be given diff --git a/R/lrtest.mkinfit.R b/R/lrtest.mkinfit.R index 60b6c46a..a5689830 100644 --- a/R/lrtest.mkinfit.R +++ b/R/lrtest.mkinfit.R @@ -30,17 +30,27 @@ lmtest::lrtest #' dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE) #' lrtest(dfop_fit, sfo_fit) #' lrtest(sfo_fit, dfop_fit) -#' +#' #' # 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)) +#' #lrtest(dfop_fit, error_model = "tc") +#' #lrtest(dfop_fit, fixed_parms = c(k2 = 0)) +#' +#' # However, this equivalent syntax works for static help pages +#' lrtest(dfop_fit, update(dfop_fit, error_model = "tc")) +#' lrtest(dfop_fit, update(dfop_fit, fixed_parms = c(k2 = 0))) #' } #' @export lrtest.mkinfit <- function(object, object_2 = NULL, ...) { name_function <- function(x) { - paste(x$mkinmod$name, "with error model", x$err_mod) + object_name <- paste(x$mkinmod$name, "with error model", x$err_mod) + if (length(x$bparms.fixed) > 0) { + object_name <- paste(object_name, + "and fixed parameter(s)", + paste(names(x$bparms.fixed), collapse = ", ")) + } + return(object_name) } if (is.null(object_2)) { diff --git a/docs/news/index.html b/docs/news/index.html index baddfc96..5aef06f9 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -134,12 +134,13 @@ mkin 0.9.49.8 (unreleased) Unreleased

-mkin 0.9.49.7 (2019-11-01) Unreleased +mkin 0.9.49.7 (2019-11-01) 2019-11-02 

# S3 method for mkinfit
@@ -254,13 +254,13 @@ On Windows machines, cores > 1 is currently not supported.

   use_of_ff = "max", quiet = TRUE)
 f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE)
 system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
#>        User      System verstrichen 
-#>      51.341       0.000      51.370 
# Using more cores does not save much time here, as parent_0 takes up most of the time
+#>      51.058       0.000      51.088 
# Using more cores does not save much time here, as parent_0 takes up most of the time
 # If we additionally exclude parent_0 (the confidence of which is often of
 # minor interest), we get a nice performance improvement from about 50
 # seconds to about 12 seconds if we use at least four cores
 system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile",
   c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#>        User      System verstrichen 
-#>       0.001       0.007      11.432 
ci_profile
#>                       2.5%        97.5%
+#>       0.005       0.004      11.349 
ci_profile
#>                       2.5%        97.5%
 #> parent_0      96.456003650 1.027703e+02
 #> k_parent_sink  0.040762501 5.549764e-02
 #> k_parent_m1    0.046786482 5.500879e-02
diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html
index fae471fc..1d82eb74 100644
--- a/docs/reference/lrtest.mkinfit.html
+++ b/docs/reference/lrtest.mkinfit.html
@@ -73,7 +73,7 @@ and can be expressed by fixing the parameters of the other." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.8
       
     

 
@@ -196,11 +196,29 @@ lower number of fitted parameters (null hypothesis).

 #> 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))
-# }
+# 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 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
# }