Direct error model fitting works

- No IRLS required
- Removed optimization algorithms other than Port
- Removed the dependency on FME
- Fitting the error model 'obs' is much faster for the FOCUS_2006_D
  dataset and the FOMC_SFO model (1 second versus 3.4 seconds)
- Vignettes build slower. Compiled models needs 3 minutes instead of 1.5
- For other vignettes, the trend is less clear. Some fits are faster,
  even for error_model = "const". FOCUS_Z is faster (34.9 s versus
  44.1 s)
- Standard errors and confidence intervals are slightly smaller
- Removed code for plotting during the fit, as I hardly ever used it
- Merged the two cost functions (using transformed and untransformed
  parameters) into one log-likelihood function

1 files changed, 4 insertions, 4 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index c6746eb7..527d79d1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 0.9.48.1
-Date: 2019-03-04
+Version: 0.9.49.1
+Date: 2019-04-04
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
                     email = "jranke@uni-bremen.de",
                     comment = c(ORCID = "0000-0003-4371-6538")),
@@ -17,8 +17,8 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006,
   equation models are solved using compiled C functions.  Please note that no
   warranty is implied for correctness of results or fitness for a particular
   purpose.
-Imports: stats, graphics, methods, FME, deSolve, R6, minpack.lm, rootSolve,
-  inline, parallel, plyr
+Imports: stats, graphics, methods, deSolve, R6, inline, parallel, plyr,
+  numDeriv
 Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr
 License: GPL
 LazyLoad: yes