Changelog

Changes version 1.402023-11-27

  • compacted vignettes

Changes version 1.39

  • small documentation fix
  • printf fixes in forcings.c and rprintf.c

Changes version 1.372023-09-01

  • changed encoding of DESCIPTION to UTF-8
  • fixed also a NOTE about documentation,
  • format of citations

Changes version 1.372023-09-01

  • remove GNU extensions and improve compatibility by replacing KIND=8 with KIND=0.0d0 in Fortran code

Changes version 1.362023-07-01

  • remove GNU extensions to improve Fortran compatibility for complex numbers in file zvode.f

Changes version 1.352023-03-12

  • speedup of multiple lsoda solver calls with a pre-identified symbol table for compiled models. Feature request and idea from Johannes Ranke.
  • use new CITATION format
  • convert NEWS to NEWS.md in markdown format
  • documentation fixes

Changes version 1.342022-10-22

  • fix deprecated function declaration without prototype
  • fix LaTeX style issue
  • fix netlib.org URL

Changes version 1.332022-07-16

  • back-compatibility with R <= 3.6.2 (patch provided by Davis Vaughan)

Changes version 1.322022-04-14

  • USE_FC_LEN_T for Fortran BLAS/LAPACK routines to ensure compatibility with R > 4.2

Changes version 1.312022-03-30

  • replace deprecated S constant DOUBLE_XMAX with DBL_MAX

Changes version 1.302021-10-07

  • add doi to references

Changes version 1.292021-09-22

  • replace legacy S macros PROBLEM and ERROR in C code with Rf_error()
  • replace http:// with https:// if possible

Changes version 1.282020-03-08

  • minor: avoid an implicit type conversion at the C level

Changes version 1.27.12020-01-02

  • C level change to fix symbol clash on MacOS solution kindly provided by Brian Ripley

Changes version 1.272019-12-20

  • C level changes to ensure compatibility with gcc 10 solution kindly provided by Brian Ripley

Changes version 1.26

  • fix outdated class checks to ensure R 4.0.0 compatibility (Karline, Thomas)
  • Fortran modernization: initialization of variables (Karline)

Changes version 1.252019-11-19

  • add original authors of LINPACK, ODEPACK and SPARSKIT to (Thomas, Karline, Woody)

Changes version 1.242019-07-15

  • fix compiler warnings to improve Fortran compatibility (Thomas, Karline, Woody) thanks to Brian Ripley and Kurt Hornik
  • iteration: set attribute before calling diagnostics (Karline)
  • add open researcher id, ORCID (Thomas)

Changes version 1.232019-06-29

  • add FME to ‘Suggests’

Changes version 1.22

  • small updates of examples (Thomas)
  • improve Fortran compiler compatibility (Thomas)

Changes version 1.212018-05-09

  • change way how PROTECT/UNPROTECT is handled (Thomas) (suggested by Tomas Kalibera / R-Core)
  • fixed inconsistency in the aphid model example (suggested by Sarah Kintner)

Changes version 1.202017-07-14

  • register native routines (Thomas)
  • check if event data frame has ordered time (and if not, order)
  • change ‘event list’ to event matrix or data frame in docs
  • intentional version jump to indicate chances at the C level

Changes version 1.142016-09-05

  • matplot.deSolve is not anymore exported as matplot to avoid the respective startup message
  • please use matplot.deSolve or the alias matplot.0D instead (Thomas)
  • small fix that allows parameters in list format for DLLfunc and DLLres
  • a little bit Fortran modification (e.g. avoid real*8 and complex*16 types)

Changes version 1.132016-03-01

  • observed data and plot.deSolve / matplot for multiple outputs (Karline)
  • combining compiled code function with R code event function (Karline)
  • check sorting of event times (Karline)
  • fix bug related to negative event time (patch supplied by J. Stott)
  • relax setting of tcrit to make integration with events slightly faster (patch from J. Stott)
  • adapt maxstep calculation for rk methods, print a warning if maxsteps is exceeded, fix diagnostics (Thomas)
  • more argument checking for rk solvers (Thomas)
  • add reference to book of Soetaert, Cash and Mazzia (2012)

Changes version 1.122015-07-06

  • new functions matplot.deSolve and matplot.1D
  • fix valgrind issue (detected by new compilers)
  • small improvments of plotting functions
  • import standard packages as required by upcoming R versions

Changes version 1.112014-10-29

  • compiledCode vignette now with dede example
  • warning and error bug resolved
  • Time SEXP incompatibility with R 3.1.1 resolved
  • CFunc compatibility (compiled code)

Changes version 1.10.9

  • documentation updates, hyperlinks to examples and vignettes
  • moved example directories

Changes version 1.10.8

  • remove redundant .R files from inst/doc
  • fixed bug in event code (patch contributed by Jonathan Stott)

Changes version 1.10.7

  • Fortran examples of compiled dede models (Woody)
  • vignettes moved to /vignettes
  • roles of authors ()
  • function timestep is now internal
  • small documentation updates

Changes version 1.10.6 (Thomas)

  • change declaration of variable dimensions from (1) to (*) in legacy Fortran code to pass automatic bounds check
  • remove the Jacobian examples from ?ode because banddown=0 can lead to problems on some systems; examples will come back in a next release
  • fixed bug in the iteration solver
  • small documentation updates

Changes version 1.10.5 (Karline, Thomas)

  • extended subset.deSolve with argument arr, when TRUE returns an array for >2-D output
  • fixed the R compiler notes
  • plot.ode.2D now has an mtext argument, via the ..., to label multiple figures in margin… CHECK - see ode.2D
  • subset can also be a vector with indices in addition to logical
  • image with legend = TRUE changed size of plot in different layouts - now solved (by adding par(mar = par("mar")))
  • new method to output warnings and error messages
  • add data type check for external outputs in rk_util.c
  • add interface for compiled dede models
  • emphasize consistent order of states in y and return value of func
  • changes of Fortran error messages (to be continued)

Changes version 1.10-4 (Thomas, Karline)2012-07-27

  • allow reverted time vector for fixed step solvers
    • todo: find solution for dense output methods, and Livermore solvers
  • all solvers now have default atol = 1e-6; before this daspk and vode had 1e-8.
  • multiple warnings from daspk if num steps = 500 toggled off.
  • added input argument nind to daspk, to make it compatible with radau. this also changes the way the variables are weighed, hence this differs from the original daspk 2.0 code.
  • improved warning printing in daspk and vode
  • extended sparse Jacobian input in lsodes. (2-D and 3-D sparsity with mapping var and arbitrary sparsity in ian/jan format).

Changes version 1.10-3 (Karline)2011-08-10

  • rwork and iwork in lsodes from Fortran -> C (to remove compiler warnings)
  • roots + events: now certain roots can stop simulation + fixed bug in radau root
  • improved eventshelp file
  • diagnostics(out) gave error in case method=iteration (no rstate) now fixed
  • the package authors agreed to assign the maintainer role to T.P., but the order of authorship and credits remain unchanged.

Changes version 1.10-2 (Karline)2011-06-01

  • remove NAs from forcing functions - when used in DLL (file forcings.R)
  • new argument restructure in ode.1D, for use with implicit solvers not in deSolve
  • removed requirement to have eventfunc in compiled code when func is in compiled code
  • subsetting on summary.deSolve

Changes version 1.10-1 (Thomas)

  • remove several redundant variables from C code
  • add NEWS file

Changes version 1.10 (Karline, Thomas)2011-05-10

  • compiled code using mass in daspk
  • cleanEventTimes

Changes version 1.9+ (Karline)2011-01-10

  • roots, events, lags in radau
  • roots in lsodes
  • lags in daspk
  • ode (method = “iteration”)

Changes version 1.9 (Karline, Thomas)2011-01-10

  • summary.deSolve
  • subset.deSolve
  • plotting deSolve objects improved:
    • plot more than one output in same figures (scenarios),
    • add observations
  • vignette improved
  • fixed bug in ‘timesteps’

Changes version 1.8.1 (Thomas, Woody, Karline)2010-10-02

  • fixed compiler warnings using valgrind
  • fixed compiler warning C-code

Changes version 1.8 (Thomas)2010-09-11

  • Dormand-Prince 8(7) coefficients use now common instead of decimal fractions

Changes version 1.8 (Karline)2010-09-11

  • Runge-Kuttas:
    • extra output: number of failed steps (see also 2)
    • number of function evaluations + 1 for initial condition
    • dense output for cash-karp
    • dopri8(7) added
    • radau added!! implicit runge kutta, solves also DAE up to index 3!
  • other:
    • image function for ode.2-D added.
    • changed warning printing in FORTRAN code
    • common interface for radau and daspk: both can solve systems written as M*dy = f(x,y). daspk can also solve systems written as 0 = g(x,y,dy) (=default for daspk)