Support summarizing older fits

generated with mkin < 0.9.49.5

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
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)
+})