NEWS.md

In deSolve: Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE')

Changes version 1.40

• compacted vignettes

Changes version 1.39

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

Changes version 1.37

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

Changes version 1.37

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

Changes version 1.36

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

Changes version 1.35

• 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 1.34

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

Changes version 1.33

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

Changes version 1.32

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

Changes version 1.31

• replace deprecated S constant DOUBLE_XMAX with DBL_MAX

Changes version 1.30

• add doi to references

Changes version 1.29

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

Changes version 1.28

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

Changes version 1.27.1

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

Changes version 1.27

• 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• fix outdated class checks to ensure R 4.0.0 compatibility (Karline, Thomas)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 1.25

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

Changes version 1.24

• 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 1.23

• add FME to 'Suggests'

Changes version 1.22

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

Changes version 1.21

• 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 1.20

• 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 1.14

• 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 1.13

• 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 1.12

• 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 1.11

• 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 (Authors@R)
• 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)

• 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)

• 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 events\roots help 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)

• 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)

• compiled code using mass in daspk
• cleanEventTimes

Changes version 1.9+ (Karline)

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

Changes version 1.9 (Karline, Thomas)

• 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)

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

Changes version 1.8 (Thomas)

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

Changes version 1.8 (Karline)

• 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)

deSolve documentation built on Nov. 28, 2023, 1:11 a.m.