Checks that the given MizerParams object is valid and upgrades it if necessary.
validParams(params, info_level = default_info_level())A valid MizerParams object
The MizerParams object to validate
Controls the amount of information messages and warnings
that are shown. Higher levels lead to more messages, info_level = 0
gives silence. The default is taken from the mizer_info_level option,
see default_info_level().
Because validParams() returns an already-valid object unchanged, it is
safe to call it at the start of any function that takes a MizerParams
object. To make that cheap, the repair work (rebuilding the species
parameter tables and the w_min_idx and ft_mask slots, and checking the
structural validity of the object) is skipped for an object that has already
been through it. Mizer recognises such an object by a fingerprint calculated
from the contents of the slots that the repair and the validity checks
depend on. The fingerprint is recalculated on every call, so it cannot become
stale: any change to any of those slots, made by any route, gives a new
fingerprint and triggers the full validation.
The checks for non-finite values in the rate arrays are always performed, because the fingerprint does not cover the values in those arrays.
Occasionally, during the development of new features for mizer, the
MizerParams object gains extra slots. MizerParams objects
created in older versions of mizer are then no longer valid in the new
version because of the missing slots. You need to upgrade them with this
function. It adds the missing slots and fills them with default values. Any
object from version 0.4 onwards can be upgraded. Any old
MizerSim objects should be similarly updated with
validSim().
This function uses newMultispeciesParams() to create a new
MizerParams object using the parameters extracted from the old MizerParams
object.
The internal numerics in mizer have changed over time, so there may be small discrepancies between the results obtained with the upgraded object in the new version and the original object in the old version. If it is important for you to reproduce the exact results then you should install the version of mizer with which you obtained the results. You can do this with
remotes::install_github("sizespectrum/mizer", ref = "v0.2")
where you should replace "v0.2" with the version number you require. You can see the list of available releases at https://github.com/sizespectrum/mizer/tags.
If you only have a serialised version of the old object, for example
created via saveRDS(), and you get an error when trying to read it in
with readRDS() then unfortunately you will need to install the old version
of mizer first to read the params object into your workspace, then switch
to the current version and then call validParams(). You can then save
the new version again with saveParams().
It is possible to render a MizerParams object invalid by manually changing its slots. This function checks that the object is valid and if not it attempts to upgrade it to a valid object or gives an error message. If the object is valid then it is returned unchanged. The function reports an error if any of the rate arrays contain any non-finite numbers (except for the maximum intake rate that is allowed to be infinite).