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-rw-r--r--NEWS.md4
-rw-r--r--R/mkinfit.R18
-rw-r--r--inst/testdata/fit_old_FOCUS_D.rdabin0 -> 21174 bytes
-rw-r--r--test.log15
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/test_summary_old_objects.R29
6 files changed, 51 insertions, 17 deletions
diff --git a/NEWS.md b/NEWS.md
index d517f0e4..949776ca 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -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
new file mode 100644
index 00000000..b60faa96
--- /dev/null
+++ b/inst/testdata/fit_old_FOCUS_D.rda
Binary files differ
diff --git a/test.log b/test.log
index cf24608c..361359cf 100644
--- a/test.log
+++ b/test.log
@@ -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)
+})

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