From d2c1ab854491ff047135fa8377400a68499e72de Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Jul 2014 12:53:30 +0200 Subject: Handle non-convergence and maximum number of iterations For details see NEWS.md --- NEWS.md | 30 ++++++++++++++++++++++++++---- 1 file changed, 26 insertions(+), 4 deletions(-) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 3c0d72de..031ae954 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,11 +1,33 @@ +# CHANGES in mkin VERSION 0.9-32 + +## NEW FEATURES + +- 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. + +## BUG FIXES + +- Initial values for formation fractions were not set in all cases. + +- No warning was given when the fit did not converge when a method other than the default Levenberg-Marquardt method `Marq` was used. + +## MINOR CHANGES + +- Vignettes were rebuilt to reflect the changes in the summary method. + +- Algorithm `Pseudo` was excluded because it needs user-defined parameter limits which are not supported. + +- Algorithm `Newton` was excluded because of its different way to specify the maximum number of iterations and because it does not appear to provide additional benefits. + # CHANGES in mkin VERSION 0.9-31 ## BUG FIXES - The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in `mkinerrmin()` used by the summary function. -- Initial values for formation fractions were not set in all cases - # CHANGES in mkin VERSION 0.9-30 ## NEW FEATURES @@ -16,13 +38,13 @@ - 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 +- The order of some of the information blocks in `print.summary.mkinfit.R()` has been ordered in a more logical way. ## MINOR CHANGES - The vignette FOCUS_Z has been simplified to use formation fractions with turning off the sink, and slightly amended to use the new versions of DT50 values calculated since mkin 0.9-29. -- All vignettes have been rebuilt so they reflect all changes +- All vignettes have been rebuilt so they reflect all changes. - The ChangeLog was renamed to NEWS.md and the entries were converted to markdown syntax compatible with the `tools::news()` function built into R. -- cgit v1.2.1 From a1567638a3ba9f4d62fa199525097a94ddfd7912 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 21 Jul 2014 08:20:44 +0200 Subject: Bugfix, model shorthand, state.ini[[1]] from observed data - The bug occurred when using transform_rates=FALSE for FOMC, DFOP or HS - Make it possible to use mkinfit("SFO", ...) - Take initial mean value at time zero for the variable with the highest value in the observed data - Update of vignette/FOCUS_L - Improve the Makefile to build single vignettes --- NEWS.md | 6 ++++++ 1 file changed, 6 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 031ae954..c10a25b0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,10 @@ ## NEW FEATURES +- 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`. + - 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. @@ -10,6 +14,8 @@ ## BUG FIXES +- `transform_rates=FALSE` in `mkinfit` now also works for FOMC and HS models. + - Initial values for formation fractions were not set in all cases. - No warning was given when the fit did not converge when a method other than the default Levenberg-Marquardt method `Marq` was used. -- cgit v1.2.1 From 4c6f29fe2a3ece5a85160b891c89ce0f55299c11 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 23 Jul 2014 08:34:59 +0200 Subject: Parallel metabolite formation with formation fractions in mkinerrmin --- NEWS.md | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index c10a25b0..9d5129c9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,8 @@ ## NEW FEATURES +- 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`. @@ -14,6 +16,8 @@ ## BUG FIXES +- In the determination of the degrees of freedom in `mkinerrmin`, formation fractions were accounted for multiple times in the case of parallel formation of metabolites. See the new feature described above for the solution. + - `transform_rates=FALSE` in `mkinfit` now also works for FOMC and HS models. - Initial values for formation fractions were not set in all cases. -- cgit v1.2.1 From 8be01094ecbc65d4bdf1e7f819ef01b7a252b39d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 24 Jul 2014 09:58:55 +0200 Subject: Avoid artificial zero residual in mkinresplot --- NEWS.md | 2 ++ 1 file changed, 2 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 9d5129c9..02c7c661 100644 --- a/NEWS.md +++ b/NEWS.md @@ -16,6 +16,8 @@ ## BUG FIXES +- Avoid plotting an artifical 0 residual at time zero in `mkinresplot` + - In the determination of the degrees of freedom in `mkinerrmin`, formation fractions were accounted for multiple times in the case of parallel formation of metabolites. See the new feature described above for the solution. - `transform_rates=FALSE` in `mkinfit` now also works for FOMC and HS models. -- cgit v1.2.1 From 9b947f0358d3a1b1fc922bfd0187ca444ce5811d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 24 Jul 2014 14:42:59 +0200 Subject: Bump version, better default for state.ini --- NEWS.md | 6 ++++++ 1 file changed, 6 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 02c7c661..4c45a0d1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# CHANGES in mkin VERSION 0.9-33 + +## NEW FEATURES + +- The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and `state.ini = "auto"` + # CHANGES in mkin VERSION 0.9-32 ## NEW FEATURES -- cgit v1.2.1 From e5c955f82adf6139d76f842a0b85e5d383685793 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 25 Jul 2014 09:36:15 +0200 Subject: Fix internal naming of g for transform_fractions=FALSE --- NEWS.md | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 4c45a0d1..d3c43d60 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,10 @@ - The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and `state.ini = "auto"` +## BUG FIXES + +- `mkinfit()`: The internally fitted parameter for `g` was named `g_ilr` even when `transform_fractions=FALSE` + # CHANGES in mkin VERSION 0.9-32 ## NEW FEATURES -- cgit v1.2.1 From 6794ef94a860b5e88b7c1dec06b29d071a25b95a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 20 Aug 2014 07:20:59 +0200 Subject: Update NEWS with change from yesterday --- NEWS.md | 6 ++++++ 1 file changed, 6 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index d3c43d60..a24c31bc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -8,6 +8,12 @@ - `mkinfit()`: The internally fitted parameter for `g` was named `g_ilr` even when `transform_fractions=FALSE` +## MINOR CHANGES + +- The formatting of differential equations in the summary was improved by wrapping overly long lines + +- The FOCUS_Z vignette was rebuilt with the above improvement and using a width of 70 to avoid output outside of the grey area + # CHANGES in mkin VERSION 0.9-32 ## NEW FEATURES -- cgit v1.2.1 From 81dc12a8c149e11d57190ebf59f3f7e9c7b99af7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 20 Aug 2014 14:42:20 +0200 Subject: Fix mkinfit for a special situation See NEWS.md: When the parent was not the (only) variable with the highest value out of all variables in the observed data, it could happen that the initial value (state.ini) was not initialised. --- NEWS.md | 2 ++ 1 file changed, 2 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index a24c31bc..d05c2095 100644 --- a/NEWS.md +++ b/NEWS.md @@ -8,6 +8,8 @@ - `mkinfit()`: The internally fitted parameter for `g` was named `g_ilr` even when `transform_fractions=FALSE` +- `mkinfit()`: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data. + ## MINOR CHANGES - The formatting of differential equations in the summary was improved by wrapping overly long lines -- cgit v1.2.1 From f30472ecd2afea6bd2153b8ad2bb2f663f3a2742 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 25 Aug 2014 10:39:40 +0200 Subject: Bug fix and unit tests for mkinerrmin See NEWS.md for details --- NEWS.md | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index d05c2095..1ed94c97 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,12 +4,19 @@ - The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and `state.ini = "auto"` +- A basic unit test for `mkinerrmin()` was written + ## BUG FIXES - `mkinfit()`: The internally fitted parameter for `g` was named `g_ilr` even when `transform_fractions=FALSE` - `mkinfit()`: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data. +- `mkinerrmin()`: When checking for degrees of freedom for metabolites, check + if their time zero value is fixed instead of checking if the observed value + is zero. This ensures correct calculation of degrees of freedom also in cases + where the metabolite residue at time zero is greater zero. + ## MINOR CHANGES - The formatting of differential equations in the summary was improved by wrapping overly long lines -- cgit v1.2.1 From 2dc4f2f87048c28252992fe70055e0d7652a61ef Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 29 Aug 2014 12:33:26 +0200 Subject: Avoid an unnecessary warning --- NEWS.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 1ed94c97..0d690b37 100644 --- a/NEWS.md +++ b/NEWS.md @@ -12,10 +12,10 @@ - `mkinfit()`: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data. -- `mkinerrmin()`: When checking for degrees of freedom for metabolites, check - if their time zero value is fixed instead of checking if the observed value - is zero. This ensures correct calculation of degrees of freedom also in cases - where the metabolite residue at time zero is greater zero. +- `mkinerrmin()`: When checking for degrees of freedom for metabolites, check if their time zero value is fixed instead of checking if the observed value is zero. This ensures correct calculation of degrees of freedom also in cases where the metabolite residue at time zero is greater zero. + +- `plot.mkinfit()`: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly + ## MINOR CHANGES -- cgit v1.2.1 From 45942cc099c258fa07f42691cf2e2ee163f3b6d6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 6 Oct 2014 20:17:17 +0200 Subject: Avoid a warning produced by initial fits in gmkin --- NEWS.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 0d690b37..19745300 100644 --- a/NEWS.md +++ b/NEWS.md @@ -16,13 +16,14 @@ - `plot.mkinfit()`: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly - ## MINOR CHANGES - The formatting of differential equations in the summary was improved by wrapping overly long lines - The FOCUS_Z vignette was rebuilt with the above improvement and using a width of 70 to avoid output outside of the grey area +- `print.summary.mkinfit()`: Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations + # CHANGES in mkin VERSION 0.9-32 ## NEW FEATURES -- cgit v1.2.1 From 8ec5b635e104b94a1a5bb1614e97fdc2ce6e6f7b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 11 Oct 2014 09:56:17 +0200 Subject: Updates intended for releasing mkin 0.9-33 --- NEWS.md | 2 ++ 1 file changed, 2 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 19745300..453d7d4e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -24,6 +24,8 @@ - `print.summary.mkinfit()`: Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations +- `mkinfit()`: Avoid a warning that occurred when summarising a fit that was performed with maxitmodFit = 0 as done in gmkin for configuring new fits. + # CHANGES in mkin VERSION 0.9-32 ## NEW FEATURES -- cgit v1.2.1 From 2635402fbc6400b8418a6b4eddaf0c91cc65a102 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 11 Oct 2014 11:19:03 +0200 Subject: Start new development version --- NEWS.md | 2 ++ 1 file changed, 2 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 453d7d4e..55a11818 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# CHANGES in mkin VERSION 0.9-34 + # CHANGES in mkin VERSION 0.9-33 ## NEW FEATURES -- cgit v1.2.1 From 4510a609159216041f10a33146534f5a8366ac76 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 14 Oct 2014 22:04:54 +0200 Subject: Further formatting improvement for differential equations --- NEWS.md | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 55a11818..4478be6b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # CHANGES in mkin VERSION 0.9-34 +## MINOR CHANGES + +- The formatting of differential equations in the summary was further improved + # CHANGES in mkin VERSION 0.9-33 ## NEW FEATURES -- cgit v1.2.1 From 65d31e345f9e61e9d05584b24df6a01c6c6ed18d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 15 Oct 2014 01:13:48 +0200 Subject: Switch to using the Port algorithm per default --- NEWS.md | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 4478be6b..60974b14 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # CHANGES in mkin VERSION 0.9-34 +## NEW FEATURES + +- Switch to using the Port algorithm (using a model/trust region approach) per default. While needing more iterations than the Levenberg-Marquardt algorithm previously used per default, it is less sensitive to starting parameters. + ## MINOR CHANGES - The formatting of differential equations in the summary was further improved -- cgit v1.2.1 From c0803a4e6660a6ad3a3a219476b6269bab528bfe Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 22 Oct 2014 09:18:41 +0200 Subject: Always include 0 on y axis when plotting during the fit --- NEWS.md | 2 ++ 1 file changed, 2 insertions(+) (limited to 'NEWS.md') diff --git a/NEWS.md b/NEWS.md index 60974b14..837293bb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -8,6 +8,8 @@ - The formatting of differential equations in the summary was further improved +- Always include 0 on y axis when plotting during the fit + # CHANGES in mkin VERSION 0.9-33 ## NEW FEATURES -- cgit v1.2.1