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-rw-r--r--NEWS.md4
-rw-r--r--R/mkinfit.R46
-rw-r--r--R/mmkin.R5
-rw-r--r--check.log12
-rw-r--r--test.log10
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
6 files changed, 48 insertions, 31 deletions
diff --git a/NEWS.md b/NEWS.md
index 4a923f09..25fe7f14 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -12,6 +12,10 @@
- 'mkinfit': Run 'stats::shapiro.test()' on standardized residuals and warn if p < 0.05
+- 'mkinfit': 'error_model_algorithm' = 'd_3' does not fail if direct fitting fails, but reports that the results for the threestep algorithm are returned
+
+- 'mmkin': Do not fail any more if one of the fits fails, but assign the try-error to the respective position in the mmkin object
+
# mkin 0.9.50.2 (2020-05-12)
- Increase tolerance for a platform specific test results on the Solaris test machine on CRAN
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 154c2a18..73fe43e0 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -712,17 +712,17 @@ mkinfit <- function(mkinmod, observed,
if (error_model_algorithm == "d_3") {
if (!quiet) message("Directly optimising the complete model")
parms.start <- c(degparms, errparms)
- fit_direct <- nlminb(parms.start, cost_function,
+ fit_direct <- try(nlminb(parms.start, cost_function,
lower = lower[names(parms.start)],
upper = upper[names(parms.start)],
- control = control, ...)
- fit_direct$logLik <- - cost.current
- if (error_model_algorithm == "direct") {
- degparms <- fit_direct$par[degparms_index]
- errparms <- fit_direct$par[errparms_index]
- } else {
+ control = control, ...))
+ if (!inherits(fit_direct, "try-error")) {
+ fit_direct$logLik <- - cost.current
cost.current <- Inf # reset to avoid conflict with the OLS step
data_direct <- current_data # We need this later if it was better
+ direct_failed = FALSE
+ } else {
+ direct_failed = TRUE
}
}
if (error_model_algorithm != "direct") {
@@ -775,24 +775,30 @@ mkinfit <- function(mkinmod, observed,
if (error_model_algorithm == "d_3") {
d_3_messages = c(
+ direct_failed = "Direct fitting failed, results of three-step fitting are returned",
same = "Direct fitting and three-step fitting yield approximately the same likelihood",
threestep = "Three-step fitting yielded a higher likelihood than direct fitting",
direct = "Direct fitting yielded a higher likelihood than three-step fitting")
- rel_diff <- abs((fit_direct$logLik - fit$logLik))/-mean(c(fit_direct$logLik, fit$logLik))
- if (rel_diff < 0.0001) {
- if (!quiet) message(d_3_messages["same"])
- fit$d_3_message <- d_3_messages["same"]
+ if (direct_failed) {
+ if (!quiet) message(d_3_messages["direct_failed"])
+ fit$d_3_message <- d_3_messages["direct_failed"]
} else {
- if (fit$logLik > fit_direct$logLik) {
- if (!quiet) message(d_3_messages["threestep"])
- fit$d_3_message <- d_3_messages["threestep"]
+ rel_diff <- abs((fit_direct$logLik - fit$logLik))/-mean(c(fit_direct$logLik, fit$logLik))
+ if (rel_diff < 0.0001) {
+ if (!quiet) message(d_3_messages["same"])
+ fit$d_3_message <- d_3_messages["same"]
} else {
- if (!quiet) message(d_3_messages["direct"])
- fit <- fit_direct
- fit$d_3_message <- d_3_messages["direct"]
- degparms <- fit$par[degparms_index]
- errparms <- fit$par[errparms_index]
- current_data <- data_direct
+ if (fit$logLik > fit_direct$logLik) {
+ if (!quiet) message(d_3_messages["threestep"])
+ fit$d_3_message <- d_3_messages["threestep"]
+ } else {
+ if (!quiet) message(d_3_messages["direct"])
+ fit <- fit_direct
+ fit$d_3_message <- d_3_messages["direct"]
+ degparms <- fit$par[degparms_index]
+ errparms <- fit$par[errparms_index]
+ current_data <- data_direct
+ }
}
}
}
diff --git a/R/mmkin.R b/R/mmkin.R
index adb9f4d0..d879fec4 100644
--- a/R/mmkin.R
+++ b/R/mmkin.R
@@ -19,8 +19,9 @@
#' @param \dots Further arguments that will be passed to \code{\link{mkinfit}}.
#' @importFrom parallel mclapply parLapply detectCores
#' @return A two-dimensional \code{\link{array}} of \code{\link{mkinfit}}
-#' objects that can be indexed using the model names for the first index (row index)
-#' and the dataset names for the second index (column index).
+#' objects and/or try-errors that can be indexed using the model names for the
+#' first index (row index) and the dataset names for the second index (column
+#' index).
#' @author Johannes Ranke
#' @seealso \code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for
#' plotting.
diff --git a/check.log b/check.log
index cae31a24..b9a17217 100644
--- a/check.log
+++ b/check.log
@@ -1,5 +1,5 @@
* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.0.0 (2020-04-24)
+* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-tests --as-cran’
@@ -7,8 +7,10 @@
* checking extension type ... Package
* this is package ‘mkin’ version ‘0.9.50.3’
* package encoding: UTF-8
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
+
+The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
@@ -67,5 +69,9 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
* checking for detritus in the temp directory ... OK
* DONE
-Status: OK
+Status: 1 NOTE
+See
+ ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
+for details.
+
diff --git a/test.log b/test.log
index 3f217296..e96960ef 100644
--- a/test.log
+++ b/test.log
@@ -9,7 +9,7 @@ Testing mkin
✔ | 5 | Analytical solutions for coupled models [3.2 s]
✔ | 5 | Calculation of Akaike weights
✔ | 10 | Confidence intervals and p-values [1.1 s]
-✔ | 14 | Error model fitting [3.8 s]
+✔ | 14 | Error model fitting [3.7 s]
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s]
✔ | 1 | Fitting the logistic model [0.2 s]
✔ | 1 | Test dataset class mkinds used in gmkin
@@ -24,22 +24,22 @@ Reason: getRversion() < "4.1.0" is TRUE
test_nafta.R:53: skip: Test data from Appendix D are correctly evaluated
Reason: getRversion() < "4.1.0" is TRUE
────────────────────────────────────────────────────────────────────────────────
-✔ | 9 | Nonlinear mixed-effects models [7.8 s]
+✔ | 9 | Nonlinear mixed-effects models [7.7 s]
✔ | 0 1 | Plotting [0.7 s]
────────────────────────────────────────────────────────────────────────────────
test_plot.R:24: skip: Plotting mkinfit and mmkin objects is reproducible
Reason: getRversion() < "4.1.0" is TRUE
────────────────────────────────────────────────────────────────────────────────
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
✔ | 4 | Summary [0.1 s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s]
✔ | 9 | Hypothesis tests [6.8 s]
-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.5 s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 37.2 s
+Duration: 36.8 s
OK: 145
Failed: 0
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index aa9fc233..232d7dad 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
MeasurementUnits: % AR
TimeUnits: days
Comments: Created using mkin::CAKE_export
-Date: 2020-06-15
+Date: 2020-07-15
Optimiser: IRLS
[Data]

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