diff options
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | NEWS.md | 4 | ||||
| -rw-r--r-- | R/mkinfit.R | 1 | ||||
| -rw-r--r-- | build.log | 9 | ||||
| -rw-r--r-- | tests/testthat/test_FOCUS_chi2_error_level.R | 45 |
5 files changed, 32 insertions, 29 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 0fcc052c..66d22a95 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.49.4 -Date: 2019-05-07 +Date: 2019-05-23 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), @@ -1,4 +1,4 @@ -# mkin 0.9.49.4 (2019-05-08) +# mkin 0.9.49.4 (2019-05-23) - Direct minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable @@ -18,6 +18,8 @@ - Adapt tests +- Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting via mmkin this could easily go unnoticed. + # mkin 0.9.48.1 (2019-03-04) - Add the function 'logLik.mkinfit' which makes it possible to calculate an AIC for mkinfit objects diff --git a/R/mkinfit.R b/R/mkinfit.R index 5e7b5bd3..bc8b9d11 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -91,6 +91,7 @@ mkinfit <- function(mkinmod, observed, if (length(wrongpar.names) > 0) {
warning("Initial parameter(s) ", paste(wrongpar.names, collapse = ", "),
" not used in the model")
+ parms.ini <- parms.ini[setdiff(names(parms.ini), wrongpar.names)]
}
# Warn that the sum of formation fractions may exceed one if they are not
@@ -1,10 +1 @@ * checking for file ‘./DESCRIPTION’ ... OK -* preparing ‘mkin’: -* checking DESCRIPTION meta-information ... OK -* installing the package to build vignettes -* creating vignettes ... OK -* checking for LF line-endings in source and make files and shell scripts -* checking for empty or unneeded directories -* looking to see if a ‘data/datalist’ file should be added -* building ‘mkin_0.9.49.4.tar.gz’ - diff --git a/tests/testthat/test_FOCUS_chi2_error_level.R b/tests/testthat/test_FOCUS_chi2_error_level.R index 69a8c2ad..d7f8d9e7 100644 --- a/tests/testthat/test_FOCUS_chi2_error_level.R +++ b/tests/testthat/test_FOCUS_chi2_error_level.R @@ -1,4 +1,4 @@ -# Copyright (C) 2014,2015,2018 Johannes Ranke +# Copyright (C) 2014,2015,2018,2019 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package mkin @@ -16,40 +16,49 @@ # You should have received a copy of the GNU General Public License along with # this program. If not, see <http://www.gnu.org/licenses/> -# These tests were migrated from inst/unitTests/runit.mkinerrmin.R - context("Calculation of FOCUS chi2 error levels") SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), + m1 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE) +errmin.FOCUS_2006_D_rounded = data.frame( + err.min = c(0.0640, 0.0646, 0.0469), + n.optim = c(4, 2, 2), + df = c(15, 7, 8), + row.names = c("All data", "parent", "m1")) + +errmin.FOCUS_2006_E_rounded = data.frame( + err.min = c(0.1544, 0.1659, 0.1095), + n.optim = c(4, 2, 2), + df = c(13, 7, 6), + row.names = c("All data", "parent", "m1")) + test_that("Chi2 error levels for FOCUS D are as in mkin 0.9-33", { - fit <- expect_warning(mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE), + fit <- expect_warning(mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE), "Observations with value of zero") - errmin.FOCUS_2006_D_rounded = data.frame( - err.min = c(0.0640, 0.0646, 0.0469), - n.optim = c(4, 2, 2), - df = c(15, 7, 8), - row.names = c("All data", "parent", "m1")) expect_equal(round(mkinerrmin(fit), 4), errmin.FOCUS_2006_D_rounded) }) +test_that("Chi2 error levels are independent of setting parms.ini that are not in the model", { + + fit.2 <- expect_warning(mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE, + parms.ini = c(tb = 5)), + "Observations with value of zero") + + expect_equal(round(mkinerrmin(fit.2), 4), + errmin.FOCUS_2006_D_rounded) +}) + test_that("Chi2 error levels for FOCUS E are as in mkin 0.9-33", { skip_on_cran() - fit <- mkinfit(SFO_SFO.ff, FOCUS_2006_E, quiet = TRUE) + fit.3 <- mkinfit(SFO_SFO.ff, FOCUS_2006_E, quiet = TRUE) - errmin.FOCUS_2006_E_rounded = data.frame( - err.min = c(0.1544, 0.1659, 0.1095), - n.optim = c(4, 2, 2), - df = c(13, 7, 6), - row.names = c("All data", "parent", "m1")) - - expect_equal(round(mkinerrmin(fit), 4), + expect_equal(round(mkinerrmin(fit.3), 4), errmin.FOCUS_2006_E_rounded) }) |