From 48c463680b51fa767b4cd7bd62865f192d0354ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 18:30:32 +0100 Subject: Reintroduce interface to saemix Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. --- docs/dev/news/index.html | 211 ++++++++++++++++++++++++++--------------------- 1 file changed, 116 insertions(+), 95 deletions(-) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index c3597efe..998917f2 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 0.9.50.4 + 1.0.1.9000 @@ -141,13 +141,36 @@ Source: NEWS.md -
-

-mkin 0.9.50.4 (unreleased) Unreleased +
+

+mkin 1.0.1.9000 Unreleased

-
+
    +

  • Switch to a versioning scheme where the fourth version component indicates development versions

    • +

  • Reintroduce the interface to the current development version of saemix, in particular:

    • +

  • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

    • +

  • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

    • +
+
+
+

+mkin 1.0.1 Unreleased +

+
    +

  • ‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults

    • +

  • ‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax

    • +

  • ‘mkinresplot’: Re-add Katrin Lindenberger as coauthor who was accidentally removed long ago

    • +

  • Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset as this is platform dependent (revealed by the new additional tests on CRAN, thanks!)

    • +

  • Increase test tolerance for some parameter comparisons that also proved to be platform dependent

    • +
+
+
+

+mkin 1.0.0 2021-02-03 +

+

-General new features

+General

@@ -163,18 +188,14 @@ Mixed-effects models
-
+

-mkin 0.9.50.3 (2020-10-08) 2020-10-08 +mkin 0.9.50.3 (2020-10-08) 2020-10-08

  • ‘parms’: Add a method for mmkin objects

    • @@ -188,18 +209,18 @@

  • ‘endpoints’: Back-calculate DT50 value from DT90 also for the biphasic models DFOP, HS and SFORB

-
+

-mkin 0.9.50.2 (2020-05-12) 2020-05-12 +mkin 0.9.50.2 (2020-05-12) 2020-05-12

  • Increase tolerance for a platform specific test results on the Solaris test machine on CRAN

  • Updates and corrections (using the spelling package) to the documentation

-
+

-mkin 0.9.50.1 (2020-05-11) 2020-05-11 +mkin 0.9.50.1 (2020-05-11) 2020-05-11

  • Support SFORB with formation fractions

    • @@ -207,17 +228,17 @@

  • Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO

-
+

-mkin 0.9.49.11 (2020-04-20) 2020-04-20 +mkin 0.9.49.11 (2020-04-20) 2020-04-20

  • Increase a test tolerance to make it pass on all CRAN check machines
-
+

-mkin 0.9.49.10 (2020-04-18) 2020-04-18 +mkin 0.9.49.10 (2020-04-18) 2020-04-18

  • ‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods

    • @@ -228,18 +249,18 @@

  • ‘summary.mkinfit’: Add AIC, BIC and log likelihood to the summary

-
+

-mkin 0.9.49.9 (2020-03-31) 2020-03-31 +mkin 0.9.49.9 (2020-03-31) 2020-03-31

  • ‘mkinmod’: Use pkgbuild::has_compiler instead of Sys.which(‘gcc’), as the latter will often fail even if Rtools are installed

  • ‘mkinds’: Use roxygen for documenting fields and methods of this R6 class

-
+

-mkin 0.9.49.8 (2020-01-09) 2020-01-09 +mkin 0.9.49.8 (2020-01-09) 2020-01-09

  • ‘aw’: Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns

    • @@ -249,18 +270,18 @@

  • ‘confint.mkinfit’: Make the quadratic approximation the default, as the likelihood profiling takes a lot of time, especially if the fit has more than three parameters

-
+

-mkin 0.9.49.7 (2019-11-01) 2019-11-02 +mkin 0.9.49.7 (2019-11-01) 2019-11-02

  • Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation

  • Add a ‘nobs’ method for mkinfit objects, enabling the default ‘BIC’ method from the stats package. Also, add a ‘BIC’ method for mmkin column objects.

-
+

-mkin 0.9.49.6 (2019-10-31) 2019-10-31 +mkin 0.9.49.6 (2019-10-31) 2019-10-31

  • Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package

    • @@ -278,9 +299,9 @@

  • Support summarizing ‘mkinfit’ objects generated with versions < 0.9.49.5

-
+

-mkin 0.9.49.5 (2019-07-04) 2019-07-04 +mkin 0.9.49.5 (2019-07-04) 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.

    • @@ -297,9 +318,9 @@

  • Add example datasets obtained from risk assessment reports published by the European Food Safety Agency.

-
+

-mkin 0.9.48.1 (2019-03-04) 2019-03-04 +mkin 0.9.48.1 (2019-03-04) 2019-03-04

  • Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects

    • @@ -314,9 +335,9 @@

  • ‘nafta’: Add evaluations according to the NAFTA guidance

-
+

-mkin 0.9.47.5 (2018-09-14) 2018-09-14 +mkin 0.9.47.5 (2018-09-14) 2018-09-14

  • Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows

    • @@ -324,27 +345,27 @@

  • Exclude more example code from testing on CRAN to avoid NOTES from long execution times

-
+

-mkin 0.9.47.3 Unreleased +mkin 0.9.47.3 Unreleased

  • ‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’

  • Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’

-
+

-mkin 0.9.47.2 (2018-07-19) 2018-07-19 +mkin 0.9.47.2 (2018-07-19) 2018-07-19

  • ‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.

  • ‘mkinfit’: Use 1.1 as starting value for N parameter of IORE models to obtain convergence in more difficult cases. Show parameter names when ‘trace_parms’ is ‘TRUE’.

-
+

-mkin 0.9.47.1 (2018-02-06) 2018-02-06 +mkin 0.9.47.1 (2018-02-06) 2018-02-06

  • Skip some tests on CRAN and winbuilder to avoid timeouts

    • @@ -355,27 +376,27 @@

  • ‘summary.mkinfit’: Show versions of mkin and R used for fitting (not the ones used for the summary) if the fit was generated with mkin >= 0.9.47.1

-
+

-mkin 0.9.46.3 (2017-11-16) 2017-11-16 +mkin 0.9.46.3 (2017-11-16) 2017-11-16

  • README.md, vignettes/mkin.Rmd: URLs were updated

  • synthetic_data_for_UBA: Add the code used to generate the data in the interest of reproducibility

-
+

-mkin 0.9.46.2 (2017-10-10) 2017-10-10 +mkin 0.9.46.2 (2017-10-10) 2017-10-10

  • Converted the vignette FOCUS_Z from tex/pdf to markdown/html

  • DESCRIPTION: Add ORCID

-
+

-mkin 0.9.46.1 (2017-09-14) 2017-09-14 +mkin 0.9.46.1 (2017-09-14) 2017-09-14

  • plot.mkinfit: Fix scaling of residual plots for the case of separate plots for each observed variable

    • @@ -383,17 +404,17 @@

  • Documentation updates

-
+

-mkin 0.9.46 (2017-07-24) 2017-07-29 +mkin 0.9.46 (2017-07-24) 2017-07-29

  • Remove test_FOMC_ill-defined.R as it is too platform dependent
-
+

-mkin 0.9.45.2 (2017-07-24) 2017-07-22 +mkin 0.9.45.2 (2017-07-24) 2017-07-22

  • Rename twa to max_twa_parent to avoid conflict with twa from my pfm package

    • @@ -402,9 +423,9 @@

  • Switch from microbenchmark to rbenchmark as the former is not supported on all platforms

-
+

-mkin 0.9.45.1 (2016-12-20) Unreleased +mkin 0.9.45.1 (2016-12-20) Unreleased

@@ -414,9 +435,9 @@

-
+

-mkin 0.9.45 (2016-12-08) 2016-12-08 +mkin 0.9.45 (2016-12-08) 2016-12-08

@@ -428,9 +449,9 @@

-
+

-mkin 0.9.44 (2016-06-29) 2016-06-29 +mkin 0.9.44 (2016-06-29) 2016-06-29

@@ -440,9 +461,9 @@

-
+

-mkin 0.9.43 (2016-06-28) 2016-06-28 +mkin 0.9.43 (2016-06-28) 2016-06-28

@@ -479,9 +500,9 @@

-
+

-mkin 0.9.42 (2016-03-25) 2016-03-25 +mkin 0.9.42 (2016-03-25) 2016-03-25

@@ -500,9 +521,9 @@

-
+

-mkin 0.9-41 (2015-11-09) 2015-11-09 +mkin 0.9-41 (2015-11-09) 2015-11-09

@@ -523,9 +544,9 @@

-
+

-mkin 0.9-40 (2015-07-21) 2015-07-21 +mkin 0.9-40 (2015-07-21) 2015-07-21

@@ -544,9 +565,9 @@

-
+

-mkin 0.9-39 (2015-06-26) 2015-06-26 +mkin 0.9-39 (2015-06-26) 2015-06-26

@@ -565,9 +586,9 @@

-
+

-mkin 0.9-38 (2015-06-24) 2015-06-23 +mkin 0.9-38 (2015-06-24) 2015-06-23

@@ -586,9 +607,9 @@

-
+

-mkin 0.9-36 (2015-06-21) 2015-06-21 +mkin 0.9-36 (2015-06-21) 2015-06-21

@@ -608,9 +629,9 @@

-
+

-mkin 0.9-35 (2015-05-15) 2015-05-15 +mkin 0.9-35 (2015-05-15) 2015-05-15

@@ -640,9 +661,9 @@

-
+

-mkin 0.9-34 (2014-11-22) 2014-11-22 +mkin 0.9-34 (2014-11-22) 2014-11-22

@@ -662,9 +683,9 @@

-
+

-mkin 0.9-33 (2014-10-22) 2014-10-12 +mkin 0.9-33 (2014-10-22) 2014-10-12

@@ -695,9 +716,9 @@

-
+

-mkin 0.9-32 (2014-07-24) 2014-07-24 +mkin 0.9-32 (2014-07-24) 2014-07-24

@@ -705,7 +726,7 @@

  • The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.

  • The default for the initial value for the first state value is now taken from the mean of the observations at time zero, if available.

    • -

  • The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. SFO, or DFOP.

    • +

  • The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. SFO, or DFOP.

  • Optimisation method, number of model evaluations and time elapsed during optimisation are given in the summary of mkinfit objects.

  • The maximum number of iterations in the optimisation algorithm can be specified using the argument maxit.modFit to the mkinfit function.

  • mkinfit gives a warning when the fit does not converge (does not apply to SANN method). This warning is included in the summary.

    • @@ -732,9 +753,9 @@

-
+

-mkin 0.9-31 (2014-07-14) 2014-07-14 +mkin 0.9-31 (2014-07-14) 2014-07-14

@@ -744,9 +765,9 @@

-
+

-mkin 0.9-30 (2014-07-11) 2014-07-11 +mkin 0.9-30 (2014-07-11) 2014-07-11

@@ -759,7 +780,7 @@

Major changes

    -

  • The original and the transformed parameters now have different names (e.g. k_parent and log_k_parent. They also differ in how many they are when we have formation fractions but no pathway to sink.

    • +

  • The original and the transformed parameters now have different names (e.g. k_parent and log_k_parent. They also differ in how many they are when we have formation fractions but no pathway to sink.

  • The order of some of the information blocks in print.summary.mkinfit.R() has been ordered in a more logical way.

@@ -776,9 +797,9 @@
-
+

-mkin 0.9-29 (2014-06-27) 2014-06-27 +mkin 0.9-29 (2014-06-27) 2014-06-27

  • R/mkinresplot.R: Make it possible to specify xlim

    • @@ -786,9 +807,9 @@

  • R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted

-
+

-mkin 0.9-28 (2014-05-20) 2014-05-20 +mkin 0.9-28 (2014-05-20) 2014-05-20

  • Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set

    • @@ -796,9 +817,9 @@

  • Correct ‘isotropic’ into ‘isometric’ for the ilr transformation

-
+

-mkin 0.9-27 (2014-05-10) 2014-05-10 +mkin 0.9-27 (2014-05-10) 2014-05-10

  • Fork the GUI into a separate package gmkin

    • @@ -820,9 +841,9 @@

  • Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin

-
+

-mkin 0.9-24 (2013-11-06) 2013-11-06 +mkin 0.9-24 (2013-11-06) 2013-11-06

  • Bugfix re-enabling the fixing of any combination of initial values for state variables

    • @@ -830,9 +851,9 @@

  • Backtransform fixed ODE parameters for the summary

-
+

-mkin 0.9-22 (2013-10-26) 2013-10-26 +mkin 0.9-22 (2013-10-26) 2013-10-26

  • Get rid of the optimisation step in mkinerrmin - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally

    • -- cgit v1.2.1 From 3dde3b95f1db925c89cd04d19f95c6fc9f68f473 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 13 Feb 2021 12:40:44 +0100 Subject: Update docs --- docs/dev/news/index.html | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 998917f2..eab75984 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000
@@ -141,9 +141,9 @@ Source: NEWS.md
-
-

-mkin 1.0.1.9000 Unreleased +
+

+mkin 1.0.2.9000 Unreleased

  • Switch to a versioning scheme where the fourth version component indicates development versions

    • @@ -151,10 +151,18 @@

  • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

  • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

+
+
+

+mkin 1.0.2 Unreleased +

+
    +
  • ‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’
    • +

-mkin 1.0.1 Unreleased +mkin 1.0.1 2021-02-10

  • ‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults

    • -- cgit v1.2.1 From c4f327e62f19c0a3fc77a538f7cf0c2c619019d8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 13 Feb 2021 13:27:09 +0100 Subject: Update static docs --- docs/dev/news/index.html | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index eab75984..1421edf4 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -145,12 +145,22 @@

    mkin 1.0.2.9000 Unreleased

    +
    +

    +General

    +
      +
    • Switch to a versioning scheme where the fourth version component indicates development versions
      • +
    +
    +
    +

    +Mixed-effects models

      -

    • Switch to a versioning scheme where the fourth version component indicates development versions

    • Reintroduce the interface to the current development version of saemix, in particular:

    • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

    • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

    +

@@ -176,9 +186,9 @@

mkin 1.0.0 2021-02-03

-
+

-General

+General

  • ‘mkinmod’ models gain arguments ‘name’ and ‘dll_dir’ which, in conjunction with a current version of the ‘inline’ package, make it possible to still use the DLL used for fast ODE solutions with ‘deSolve’ after saving and restoring the ‘mkinmod’ object.

  • ‘mkindsg’ R6 class for groups of ‘mkinds’ datasets with metadata

    • @@ -191,9 +201,9 @@

  • ‘plot.mkinfit’: Change default ylab from “Observed” to “Residue”. Pass xlab to residual plot if show_residuals is TRUE.

-
+

-Mixed-effects models

+Mixed-effects models

  • ‘mixed.mmkin’ New container for mmkin objects for plotting with the ‘plot.mixed.mmkin’ method

  • ‘plot.mixed.mmkin’ method used for ‘nlme.mmkin’ inheriting from ‘mixed.mmkin’ (currently virtual)

    • -- cgit v1.2.1 From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 17:36:12 +0100 Subject: Fully rebuild docs, rerun tests and check --- docs/dev/news/index.html | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 1421edf4..31c392f7 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.2.9000 + 1.0.3.9000
@@ -141,9 +141,9 @@ Source: NEWS.md
-
-

-mkin 1.0.2.9000 Unreleased +
+

+mkin 1.0.3.9000 Unreleased

@@ -161,6 +161,14 @@

  • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

    • +
    +
    +

    +mkin 1.0.3 Unreleased +

    +
      +
    • Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages
      • +

    -- cgit v1.2.1 From c73b2f30ec836c949885784ab576e814eb8070a9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 9 Mar 2021 17:35:47 +0100 Subject: Some improvements for borderline cases - fit_with_errors for saem() - test_log_parms for mean_degparms() and saem() --- docs/dev/news/index.html | 161 ++++++++++++++++++----------------------------- 1 file changed, 62 insertions(+), 99 deletions(-) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 31c392f7..10585403 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.3.9000 + 1.0.4.9000

    @@ -141,10 +141,9 @@ Source: NEWS.md

    -
    -

    -mkin 1.0.3.9000 Unreleased -

    +
    +

    +mkin 1.0.4.9000

    General

    @@ -159,29 +158,35 @@

  • Reintroduce the interface to the current development version of saemix, in particular:

  • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

  • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

    • +

  • ‘mean_degparms’: New argument ‘test_log_parms’ that makes the function only consider log-transformed parameters where the untransformed parameters pass the t-test for a certain confidence level. This can be used to check more plausible parameters for ‘saem’

    • -
    +
    +

    +mkin 1.0.4 (Unreleased)

    +
      +

    • ‘plot.mixed.mmkin’: Reset graphical parameters on exit

      • +

    • All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters

      • +
    +
    +

    -mkin 1.0.3 Unreleased -

    +mkin 1.0.3 (2021-02-15)
    • Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages
    -
    +

    -mkin 1.0.2 Unreleased -

    +mkin 1.0.2 (Unreleased)
    • ‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’
    -
    +

    -mkin 1.0.1 2021-02-10 -

    +mkin 1.0.1 (2021-02-10)

    • ‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults

    • ‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax

      • @@ -190,10 +195,9 @@

    • Increase test tolerance for some parameter comparisons that also proved to be platform dependent

    -
    +

    -mkin 1.0.0 2021-02-03 -

    +mkin 1.0.0 (2021-02-03)

    General

    @@ -221,8 +225,7 @@

    -mkin 0.9.50.3 (2020-10-08) 2020-10-08 -

    +mkin 0.9.50.3 (2020-10-08)

    • ‘parms’: Add a method for mmkin objects

    • ‘mmkin’ and ‘confint(method = ’profile’): Use all cores detected by parallel::detectCores() per default

      • @@ -237,8 +240,7 @@

    -mkin 0.9.50.2 (2020-05-12) 2020-05-12 -

    +mkin 0.9.50.2 (2020-05-12)

    • Increase tolerance for a platform specific test results on the Solaris test machine on CRAN

    • Updates and corrections (using the spelling package) to the documentation

      • @@ -246,8 +248,7 @@

    -mkin 0.9.50.1 (2020-05-11) 2020-05-11 -

    +mkin 0.9.50.1 (2020-05-11)

    • Support SFORB with formation fractions

    • ‘mkinmod’: Make ‘use_of_ff’ = “max” the default

      • @@ -256,16 +257,14 @@

    -mkin 0.9.49.11 (2020-04-20) 2020-04-20 -

    +mkin 0.9.49.11 (2020-04-20)
    • Increase a test tolerance to make it pass on all CRAN check machines

    -mkin 0.9.49.10 (2020-04-18) 2020-04-18 -

    +mkin 0.9.49.10 (2020-04-18)

    • ‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods

    • ‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects

      • @@ -277,8 +276,7 @@

    -mkin 0.9.49.9 (2020-03-31) 2020-03-31 -

    +mkin 0.9.49.9 (2020-03-31)

    • ‘mkinmod’: Use pkgbuild::has_compiler instead of Sys.which(‘gcc’), as the latter will often fail even if Rtools are installed

    • ‘mkinds’: Use roxygen for documenting fields and methods of this R6 class

      • @@ -286,8 +284,7 @@

    -mkin 0.9.49.8 (2020-01-09) 2020-01-09 -

    +mkin 0.9.49.8 (2020-01-09)

    • ‘aw’: Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns

    • ‘loftest’: Add a lack-of-fit test

      • @@ -298,8 +295,7 @@

    -mkin 0.9.49.7 (2019-11-01) 2019-11-02 -

    +mkin 0.9.49.7 (2019-11-01)

    • Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation

    • Add a ‘nobs’ method for mkinfit objects, enabling the default ‘BIC’ method from the stats package. Also, add a ‘BIC’ method for mmkin column objects.

      • @@ -307,8 +303,7 @@

    -mkin 0.9.49.6 (2019-10-31) 2019-10-31 -

    +mkin 0.9.49.6 (2019-10-31)

    • Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package

    • Add an ‘update’ method for mkinfit objects which remembers fitted parameters if appropriate

      • @@ -327,8 +322,7 @@

    -mkin 0.9.49.5 (2019-07-04) 2019-07-04 -

    +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.

    • The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ and ‘error_model_algorithm’ instead

      • @@ -346,8 +340,7 @@

    -mkin 0.9.48.1 (2019-03-04) 2019-03-04 -

    +mkin 0.9.48.1 (2019-03-04)

    • Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects

    • Add the function ‘AIC.mmkin’ to make it easy to compare columns of mmkin objects

      • @@ -363,8 +356,7 @@

    -mkin 0.9.47.5 (2018-09-14) 2018-09-14 -

    +mkin 0.9.47.5 (2018-09-14)

    • Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows

    • Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)

      • @@ -373,8 +365,7 @@

    -mkin 0.9.47.3 Unreleased -

    +mkin 0.9.47.3

    • ‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’

    • Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’

      • @@ -382,8 +373,7 @@

    -mkin 0.9.47.2 (2018-07-19) 2018-07-19 -

    +mkin 0.9.47.2 (2018-07-19)

    • ‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.

    • ‘mkinfit’: Use 1.1 as starting value for N parameter of IORE models to obtain convergence in more difficult cases. Show parameter names when ‘trace_parms’ is ‘TRUE’.

      • @@ -391,8 +381,7 @@

    -mkin 0.9.47.1 (2018-02-06) 2018-02-06 -

    +mkin 0.9.47.1 (2018-02-06)

    • Skip some tests on CRAN and winbuilder to avoid timeouts

    • ‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014

      • @@ -404,8 +393,7 @@

    -mkin 0.9.46.3 (2017-11-16) 2017-11-16 -

    +mkin 0.9.46.3 (2017-11-16)

    • README.md, vignettes/mkin.Rmd: URLs were updated

    • synthetic_data_for_UBA: Add the code used to generate the data in the interest of reproducibility

      • @@ -413,8 +401,7 @@

    -mkin 0.9.46.2 (2017-10-10) 2017-10-10 -

    +mkin 0.9.46.2 (2017-10-10)

    • Converted the vignette FOCUS_Z from tex/pdf to markdown/html

    • DESCRIPTION: Add ORCID

      • @@ -422,8 +409,7 @@

    -mkin 0.9.46.1 (2017-09-14) 2017-09-14 -

    +mkin 0.9.46.1 (2017-09-14)

    • plot.mkinfit: Fix scaling of residual plots for the case of separate plots for each observed variable

    • plot.mkinfit: Use all data points of the fitted curve for y axis scaling for the case of separate plots for each observed variable

      • @@ -432,16 +418,14 @@

    -mkin 0.9.46 (2017-07-24) 2017-07-29 -

    +mkin 0.9.46 (2017-07-24)
    • Remove test_FOMC_ill-defined.R as it is too platform dependent

    -mkin 0.9.45.2 (2017-07-24) 2017-07-22 -

    +mkin 0.9.45.2 (2017-07-24)

    • Rename twa to max_twa_parent to avoid conflict with twa from my pfm package

    • Update URLs in documentation

      • @@ -451,8 +435,7 @@

    -mkin 0.9.45.1 (2016-12-20) Unreleased -

    +mkin 0.9.45.1 (2016-12-20)

    New features

    @@ -463,8 +446,7 @@

    -mkin 0.9.45 (2016-12-08) 2016-12-08 -

    +mkin 0.9.45 (2016-12-08)

    Minor changes

    @@ -477,8 +459,7 @@

    -mkin 0.9.44 (2016-06-29) 2016-06-29 -

    +mkin 0.9.44 (2016-06-29)

    Bug fixes

    @@ -489,8 +470,7 @@

    -mkin 0.9.43 (2016-06-28) 2016-06-28 -

    +mkin 0.9.43 (2016-06-28)

    Major changes

    @@ -528,8 +508,7 @@

    -mkin 0.9.42 (2016-03-25) 2016-03-25 -

    +mkin 0.9.42 (2016-03-25)

    Major changes

    @@ -549,8 +528,7 @@

    -mkin 0.9-41 (2015-11-09) 2015-11-09 -

    +mkin 0.9-41 (2015-11-09)

    Minor changes

    @@ -572,8 +550,7 @@

    -mkin 0.9-40 (2015-07-21) 2015-07-21 -

    +mkin 0.9-40 (2015-07-21)

    Bug fixes

    @@ -593,8 +570,7 @@

    -mkin 0.9-39 (2015-06-26) 2015-06-26 -

    +mkin 0.9-39 (2015-06-26)

    Major changes

    @@ -614,8 +590,7 @@

    -mkin 0.9-38 (2015-06-24) 2015-06-23 -

    +mkin 0.9-38 (2015-06-24)

    Minor changes

    @@ -635,8 +610,7 @@

    -mkin 0.9-36 (2015-06-21) 2015-06-21 -

    +mkin 0.9-36 (2015-06-21)

    Major changes

    @@ -657,8 +631,7 @@

    -mkin 0.9-35 (2015-05-15) 2015-05-15 -

    +mkin 0.9-35 (2015-05-15)

    Major changes

    @@ -689,8 +662,7 @@

    -mkin 0.9-34 (2014-11-22) 2014-11-22 -

    +mkin 0.9-34 (2014-11-22)

    New features

    @@ -711,8 +683,7 @@

    -mkin 0.9-33 (2014-10-22) 2014-10-12 -

    +mkin 0.9-33 (2014-10-22)

    New features

    @@ -744,8 +715,7 @@

    -mkin 0.9-32 (2014-07-24) 2014-07-24 -

    +mkin 0.9-32 (2014-07-24)

    New features

    @@ -781,8 +751,7 @@

    -mkin 0.9-31 (2014-07-14) 2014-07-14 -

    +mkin 0.9-31 (2014-07-14)

    Bug fixes

    @@ -793,8 +762,7 @@

    -mkin 0.9-30 (2014-07-11) 2014-07-11 -

    +mkin 0.9-30 (2014-07-11)

    New features

    @@ -825,8 +793,7 @@

    -mkin 0.9-29 (2014-06-27) 2014-06-27 -

    +mkin 0.9-29 (2014-06-27)

    • R/mkinresplot.R: Make it possible to specify xlim

    • R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function

      • @@ -835,8 +802,7 @@

    -mkin 0.9-28 (2014-05-20) 2014-05-20 -

    +mkin 0.9-28 (2014-05-20)

    • Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set

    • Add historical remarks and some background to the main package vignette

      • @@ -845,8 +811,7 @@

    -mkin 0.9-27 (2014-05-10) 2014-05-10 -

    +mkin 0.9-27 (2014-05-10)

    • Fork the GUI into a separate package gmkin

    • DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information

      • @@ -869,8 +834,7 @@

    -mkin 0.9-24 (2013-11-06) 2013-11-06 -

    +mkin 0.9-24 (2013-11-06)

    • Bugfix re-enabling the fixing of any combination of initial values for state variables

    • Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions

      • @@ -879,8 +843,7 @@

    -mkin 0.9-22 (2013-10-26) 2013-10-26 -

    +mkin 0.9-22 (2013-10-26)

    • Get rid of the optimisation step in mkinerrmin - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally

    • Fix plot.mkinfit as it passed graphical arguments like main to the solver

      • -- cgit v1.2.1 From 0c9b2f0e3c8ce65cb790c9e048476784cbbea070 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Jun 2021 11:14:45 +0200 Subject: Finished 'summary.nlmixr.mmkin', checks, docs --- docs/dev/news/index.html | 34 ++++++++++++++-------------------- 1 file changed, 14 insertions(+), 20 deletions(-) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 10585403..234ba02f 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.4.9000 + 1.0.5
    @@ -141,33 +141,27 @@ Source: NEWS.md
    -
    -

    -mkin 1.0.4.9000

    -
    -

    -General

    -
      -
    • Switch to a versioning scheme where the fourth version component indicates development versions
      • -
    -
    +
    +

    +mkin 1.0.5 (unreleased)

    Mixed-effects models

      -

    • Reintroduce the interface to the current development version of saemix, in particular:

      • -

    • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

      • -

    • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

      • -

    • ‘mean_degparms’: New argument ‘test_log_parms’ that makes the function only consider log-transformed parameters where the untransformed parameters pass the t-test for a certain confidence level. This can be used to check more plausible parameters for ‘saem’

      • +

    • Introduce an interface to nlmixr, supporting estimation methods ‘saem’ and ‘focei’: S3 method ‘nlmixr.mmkin’ using the helper functions ‘nlmixr_model’ and ‘nlmixr_data’ to set up nlmixr models for mmkin row objects, with summary and plot methods.

      • +

    • Reintroduce the interface to current development versions (not on CRAN) of saemix, in particular the generic function ‘saem’ with a generator ‘saem.mmkin’, currently using ‘saemix_model’ and ‘saemix_data’, summary and plot methods

      • +

    • ‘mean_degparms’: New argument ‘test_log_parms’ that makes the function only consider log-transformed parameters where the untransformed parameters pass the t-test for a certain confidence level. This can be used to obtain more plausible starting parameters for the different mixed-effects model backends

      • +

    • ‘plot.mixed.mmkin’: Gains arguments ‘test_log_parms’ and ‘conf.level’

    -
    +

    -mkin 1.0.4 (Unreleased)

    +mkin 1.0.4 (2021-04-20)
      -

    • ‘plot.mixed.mmkin’: Reset graphical parameters on exit

    • All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters

      • +

    • ‘plot.mkinfit’: Use xlab and xlim for the residual plot if show_residuals is TRUE

      • +

    • ‘mmkin’: Use cores = 1 per default on Windows to make it easier for first time users

    @@ -198,9 +192,9 @@

    mkin 1.0.0 (2021-02-03)

    -
    +

    -General

    +General

    • ‘mkinmod’ models gain arguments ‘name’ and ‘dll_dir’ which, in conjunction with a current version of the ‘inline’ package, make it possible to still use the DLL used for fast ODE solutions with ‘deSolve’ after saving and restoring the ‘mkinmod’ object.

    • ‘mkindsg’ R6 class for groups of ‘mkinds’ datasets with metadata

      • -- cgit v1.2.1 From 0b754ffa91b9496bdd2f892cf3ca2bd887028dea Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 27 Jul 2021 18:22:01 +0200 Subject: Fix dimethenamid vignette problems and update docs --- docs/dev/news/index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 234ba02f..cfe577cf 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.5 + 1.1.0
    -- cgit v1.2.1 From 137612045c23198f10d6e8612c32e266c2a6c00e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 29 Jul 2021 12:17:56 +0200 Subject: Go back to 1.0.x version, update docs --- docs/dev/news/index.html | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index cfe577cf..5b153f37 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.1.0 + 1.0.5
    @@ -152,6 +152,7 @@

  • Reintroduce the interface to current development versions (not on CRAN) of saemix, in particular the generic function ‘saem’ with a generator ‘saem.mmkin’, currently using ‘saemix_model’ and ‘saemix_data’, summary and plot methods

  • ‘mean_degparms’: New argument ‘test_log_parms’ that makes the function only consider log-transformed parameters where the untransformed parameters pass the t-test for a certain confidence level. This can be used to obtain more plausible starting parameters for the different mixed-effects model backends

  • ‘plot.mixed.mmkin’: Gains arguments ‘test_log_parms’ and ‘conf.level’

    • +

  • ‘vignettes/web_only/dimethenamid_2018.rmd’: Example evaluations of the dimethenamid data.

    • -- cgit v1.2.1 From c41381a961263c28d60976e68923157916c78b15 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Sep 2021 15:31:13 +0200 Subject: Adapt and improve the dimethenamid vignette Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs --- docs/dev/news/index.html | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 5b153f37..f3cc89d9 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.5 + 1.1.0
    @@ -141,9 +141,9 @@ Source: NEWS.md
    -
    -

    -mkin 1.0.5 (unreleased)

    +
    +

    +mkin 1.1.0 (unreleased)

    Mixed-effects models

    @@ -155,6 +155,13 @@

  • ‘vignettes/web_only/dimethenamid_2018.rmd’: Example evaluations of the dimethenamid data.

    • +
    +
    +

    +mkin 1.0.5 (2021-09-15)

    +
      +
    • ‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”
      • +

    -- cgit v1.2.1 From 5c15ef747568b3a9a9c094b6aa546dc80e3aa87a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 27 Sep 2021 20:10:01 +0200 Subject: intervals() methods, more DFOP/tc variants --- docs/dev/news/index.html | 1 + 1 file changed, 1 insertion(+) (limited to 'docs/dev/news') diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index f3cc89d9..2a6b3d9d 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -153,6 +153,7 @@

  • ‘mean_degparms’: New argument ‘test_log_parms’ that makes the function only consider log-transformed parameters where the untransformed parameters pass the t-test for a certain confidence level. This can be used to obtain more plausible starting parameters for the different mixed-effects model backends

  • ‘plot.mixed.mmkin’: Gains arguments ‘test_log_parms’ and ‘conf.level’

  • ‘vignettes/web_only/dimethenamid_2018.rmd’: Example evaluations of the dimethenamid data.

    • +

  • ‘intervals’: Provide methods of this nlme function for ‘nlmixr.mmkin’ and ‘saem.mmkin’ objects.

    • -- cgit v1.2.1