diff options
-rw-r--r-- | NEWS.md | 4 | ||||
-rw-r--r-- | R/mkinfit.R | 18 | ||||
-rw-r--r-- | inst/testdata/fit_old_FOCUS_D.rda | bin | 0 -> 21174 bytes | |||
-rw-r--r-- | test.log | 15 | ||||
-rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 | ||||
-rw-r--r-- | tests/testthat/test_summary_old_objects.R | 29 |
6 files changed, 51 insertions, 17 deletions
@@ -1,9 +1,11 @@ -# mkin 0.9.49.6 (2019-07-05) +# mkin 0.9.49.6 (2019-07-08) - Update README and the introductory vignette - Report 'OLS' as error_model_algorithm in the summary in the case that the default error_model ('const') is used +- Support summarizing 'mkinfit' objects generated with versions < 0.9.49.5 + # mkin 0.9.49.5 (2019-07-04) - Several algorithms for 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. The default algorithm 'd_3' tries direct minimization and a three-step procedure, and returns the model with the highest likelihood. diff --git a/R/mkinfit.R b/R/mkinfit.R index 6606ec7a..c14c1cea 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -803,14 +803,16 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), . cat("\nFitted using", x$calls, "model solutions performed in", x$time[["elapsed"]], "s\n")
- cat("\nError model: ")
- cat(switch(x$err_mod,
- const = "Constant variance",
- obs = "Variance unique to each observed variable",
- tc = "Two-component variance function"), "\n")
-
- cat("\nError model algorithm:", x$error_model_algorithm, "\n")
- if (!is.null(x$d_3_message)) cat(x$d_3_message, "\n")
+ if (!is.null(x$err_mod)) {
+ cat("\nError model: ")
+ cat(switch(x$err_mod,
+ const = "Constant variance",
+ obs = "Variance unique to each observed variable",
+ tc = "Two-component variance function"), "\n")
+
+ cat("\nError model algorithm:", x$error_model_algorithm, "\n")
+ if (!is.null(x$d_3_message)) cat(x$d_3_message, "\n")
+ }
cat("\nStarting values for parameters to be optimised:\n")
print(x$start)
diff --git a/inst/testdata/fit_old_FOCUS_D.rda b/inst/testdata/fit_old_FOCUS_D.rda Binary files differnew file mode 100644 index 00000000..b60faa96 --- /dev/null +++ b/inst/testdata/fit_old_FOCUS_D.rda @@ -2,7 +2,7 @@ Loading mkin Testing mkin ✔ | OK F W S | Context
⠏ | 0 | Export dataset for reading into CAKE
✔ | 1 | Export dataset for reading into CAKE -
⠏ | 0 | Error model fitting
⠋ | 1 | Error model fitting
⠹ | 3 | Error model fitting
⠸ | 4 | Error model fitting
⠼ | 5 | Error model fitting
⠴ | 6 | Error model fitting
⠧ | 8 | Error model fitting
⠏ | 10 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 11 | Error model fitting
⠹ | 13 | Error model fitting
⠸ | 14 | Error model fitting
⠼ | 15 | Error model fitting
⠴ | 16 | Error model fitting
⠦ | 17 | Error model fitting
⠧ | 18 | Error model fitting
⠇ | 19 | Error model fitting
⠏ | 20 | Error model fitting
✔ | 20 | Error model fitting [415.0 s] +
⠏ | 0 | Error model fitting
⠋ | 1 | Error model fitting
⠹ | 3 | Error model fitting
⠸ | 4 | Error model fitting
⠼ | 5 | Error model fitting
⠴ | 6 | Error model fitting
⠧ | 8 | Error model fitting
⠏ | 10 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 10 1 | Error model fitting
⠋ | 11 | Error model fitting
⠹ | 13 | Error model fitting
⠸ | 14 | Error model fitting
⠼ | 15 | Error model fitting
⠴ | 16 | Error model fitting
⠦ | 17 | Error model fitting
⠧ | 18 | Error model fitting
⠇ | 19 | Error model fitting
⠏ | 20 | Error model fitting
✔ | 20 | Error model fitting [413.8 s]
⠏ | 0 | Calculation of FOCUS chi2 error levels
⠋ | 1 | Calculation of FOCUS chi2 error levels
⠹ | 3 | Calculation of FOCUS chi2 error levels
⠼ | 5 | Calculation of FOCUS chi2 error levels
✔ | 5 | Calculation of FOCUS chi2 error levels [3.5 s]
⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.7 s]
⠏ | 0 | Test fitting the decline of metabolites from their maximum
⠋ | 1 | Test fitting the decline of metabolites from their maximum
⠹ | 3 | Test fitting the decline of metabolites from their maximum
⠼ | 5 | Test fitting the decline of metabolites from their maximum
✔ | 6 | Test fitting the decline of metabolites from their maximum [0.9 s] @@ -11,19 +11,20 @@ Testing mkin
⠏ | 0 | Special cases of mkinfit calls
⠋ | 1 | Special cases of mkinfit calls
⠇ | 9 | Special cases of mkinfit calls
⠏ | 10 | Special cases of mkinfit calls
⠋ | 11 | Special cases of mkinfit calls
⠙ | 12 | Special cases of mkinfit calls
✔ | 12 | Special cases of mkinfit calls [2.7 s]
⠏ | 0 | mkinmod model generation and printing
⠇ | 9 | mkinmod model generation and printing
✔ | 9 | mkinmod model generation and printing [0.2 s]
⠏ | 0 | Model predictions with mkinpredict
⠋ | 1 | Model predictions with mkinpredict
✔ | 3 | Model predictions with mkinpredict [0.3 s] -
⠏ | 0 | Evaluations according to 2015 NAFTA guidance
⠙ | 2 | Evaluations according to 2015 NAFTA guidance
⠇ | 9 | Evaluations according to 2015 NAFTA guidance
⠏ | 10 | Evaluations according to 2015 NAFTA guidance
⠴ | 16 | Evaluations according to 2015 NAFTA guidance
✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.1 s] -
⠏ | 0 | Fitting of parent only models
⠋ | 1 | Fitting of parent only models
⠙ | 2 | Fitting of parent only models
⠹ | 3 | Fitting of parent only models
⠸ | 4 | Fitting of parent only models
⠼ | 5 | Fitting of parent only models
⠴ | 6 | Fitting of parent only models
⠦ | 7 | Fitting of parent only models
⠧ | 8 | Fitting of parent only models
⠇ | 9 | Fitting of parent only models
⠏ | 10 | Fitting of parent only models
⠋ | 11 | Fitting of parent only models
⠙ | 12 | Fitting of parent only models
⠹ | 13 | Fitting of parent only models
⠴ | 16 | Fitting of parent only models
⠧ | 18 | Fitting of parent only models
⠏ | 20 | Fitting of parent only models
✔ | 21 | Fitting of parent only models [40.7 s] +
⠏ | 0 | Evaluations according to 2015 NAFTA guidance
⠙ | 2 | Evaluations according to 2015 NAFTA guidance
⠇ | 9 | Evaluations according to 2015 NAFTA guidance
⠏ | 10 | Evaluations according to 2015 NAFTA guidance
⠴ | 16 | Evaluations according to 2015 NAFTA guidance
✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.0 s] +
⠏ | 0 | Fitting of parent only models
⠋ | 1 | Fitting of parent only models
⠙ | 2 | Fitting of parent only models
⠹ | 3 | Fitting of parent only models
⠸ | 4 | Fitting of parent only models
⠼ | 5 | Fitting of parent only models
⠴ | 6 | Fitting of parent only models
⠦ | 7 | Fitting of parent only models
⠧ | 8 | Fitting of parent only models
⠇ | 9 | Fitting of parent only models
⠏ | 10 | Fitting of parent only models
⠋ | 11 | Fitting of parent only models
⠙ | 12 | Fitting of parent only models
⠹ | 13 | Fitting of parent only models
⠴ | 16 | Fitting of parent only models
⠧ | 18 | Fitting of parent only models
⠏ | 20 | Fitting of parent only models
✔ | 21 | Fitting of parent only models [40.6 s]
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs)
⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs)
⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs)
⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs)
⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs)
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
⠏ | 0 | Summary
✔ | 1 | Summary
⠏ | 0 | Plotting
⠹ | 3 | Plotting
✔ | 4 | Plotting [0.3 s]
⠏ | 0 | AIC calculation
✔ | 2 | AIC calculation -
⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.4 s] -
⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.0 s] +
⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.2 s] +
⠏ | 0 | Summaries of old mkinfit objects
✔ | 1 | Summaries of old mkinfit objects +
⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 492.4 s +Duration: 491.0 s -OK: 125 +OK: 126 Failed: 0 Warnings: 0 Skipped: 0 diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index 0869672b..f9233770 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: 2019-07-05 +Date: 2019-07-08 Optimiser: IRLS [Data] diff --git a/tests/testthat/test_summary_old_objects.R b/tests/testthat/test_summary_old_objects.R new file mode 100644 index 00000000..11e63553 --- /dev/null +++ b/tests/testthat/test_summary_old_objects.R @@ -0,0 +1,29 @@ +# Copyright (C) 2019 Johannes Ranke +# Contact: jranke@uni-bremen.de + +# This file is part of the R package mkin + +# mkin is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see <http://www.gnu.org/licenses/> + +context("Summaries of old mkinfit objects") + +test_that("A fit generated with mkin 0.9.48.1 can be summarised", { + # Generated with mkin 0.9.48.1 + # SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"), + # m1 = list(type = "SFO"), quiet = TRUE) + # fit_old <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) + # save(fit_old, file = "~/git/mkin/inst/testdata/fit_old_FOCUS_D.rda", version = 2 ) + load(system.file("testdata/fit_old_FOCUS_D.rda", package = "mkin")) + expect_true(length(summary(fit_old)) > 0) +}) |