Changes to version 1.1.105
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- The two vignettes that were available in previous versions were removed because
they are now obsolete given the recent changes in model constructure functions.
These vignettes will be re-written and will be available in future versions.
- Funtions to compute information theory metrics (entropy) were added for models
in equilibrium.
Changes to version 1.1.103
==============================================================================================
- This is an intermediate release in response to requests from users who have
trouble to install from github. The version has many new features but needs
more refactoring to integrate the existing codebase with the new concepts.
Everything that used to work still does but behind the scenes a lot of
changes are in progress.
- A new way of describing models entirely by fluxes has been experimentally
included. This additional way is independent of the order of the state
variables and requires much less effort in describing huge models.
Instead of the $n^2$ matrix entries for a n-pool system only the usually far fewer
existing fluxes have to be provided. Furthermore these can be formulated as
functions of only those state-variables they depend on. This information is
sufficient to compute the matrices automatically and produce graphs showing
the connections between the pools, something that could not be inferred from
the previously exclusively used matrix valued functions. The new formulation
incorporates nonlinear models and even state dependent inputs by default.
- A new solution method is implemented which speeds up computations that can be expressed
by automatically extending the ODE system and solving it immediately for derived properties.
- While all this is possible, most of the front end models internally still use the old interface
and some of the functionality of the old models has not been implemented for the new ones, let
alone factored out.
- The documentation is still incomplete since we changed to roxygen and have to rewrite
many S4-generic, class and method descriptions as comments.
- With the generalization of most of the functionality for linear to nonlinear models
some of the old classes themselves become obsolete and will have to be removed
when the internal clients will have been converted to the new internal infrastructure.
Changes to version 1.1-29
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- Two new functions were added to compute transit time and age densities for linear models.
These functions are systemAge and transitTime.
- Package expm is now required. It is used to calculate the matrix exponential in the
computation of system age and transit time distributions.
- The Century model was added.
- Nonlinear microbial models were implemented. These include: AWBmodel, ThreepairMMmodel,
TwopMMmodel, and bacwaveModel.
Changes to version 1.1.
==============================================================================================
- The name structure of the SoilR internal classes has been changed.
There are two new main virtual super classes, DecompOp and InFlux.
DecompOp includes the subclasses ConstLinDecompOp and BoundLinDecompOp.
ConstLinDecompOp implements time-invariant decomposition operators, while
BoundLinDecompOp implements time-dependent decomposition operators with time bounds.
At the moment, InFlux only includes the subclass BoundInFlux, which is a time-bounded
input flux.
- The TimeMap class is now deprecated. It is replaced by the classes DecompOp and InFlux.
- The radiocarbon component of SoilR is now fully implemented.
The function GeneralModel_14 is the constructor of linear models
that track the radiocarbon fraction in different pools.
- Two new classes were created for radiocarbon-related objects, ConstFc and BoundFc.
ConstFc takes a numeric argument and a unit argument specifying the units of radiocarbon
reporting. BoundFc also takes these arguments plus two others specifying the time range
for which the values are valid. See help files of these classes for additional details.
- New datasets were added with the concentration of radiocarbon in the atmosphere. These are
IntCal13 and Hua2013.
- SoilR now requires package parallel in addition to deSolve.