EmpiricalDynamics

lm and glm equations are now evaluated through their own predict()

machinery (on the response scale for glm), so the coefficients enter

exactly as fitted -- I() terms, factors and link functions included, and

no name collision is possible. The nls and symbolic_equation paths,

whose coefficient names are genuine symbols of their expressions, were

correct and are unchanged.

A name that binds nothing is now reported instead of ignored

Every name the equation consults must now be accounted for -- the search

variable, a fitted coefficient, or a declared exogenous value. Previously,

each of the following was silent: an unnamed exogenous_values entry (bound

nothing -- for (nm in names(x)) over a NULL runs zero times); declaring

the search variable (overwritten at every grid point); declaring a name the

equation never uses (no effect); declaring a name that collides with a

fitted coefficient (silently *overwrote the fit*); and a free symbol with no

declared value (evaluation failed point by point into NAs, or worse,

picked up whatever the name meant in the enclosing environment). The first

two and the last two are errors now; the never-consulted name is a warning.

A new coefficient_values argument takes the deliberate case the collision

error forbids: overriding a fitted coefficient by name, validated against

the coefficients that exist.

A root the grid landed on exactly was reported twice

Fixed points were detected as diff(sign(f)) != 0 over the grid. A grid

point falling exactly on a root has sign 0, which that test counts as two

changes -- one into the zero and one out of it -- so uniroot() refined the

same root from both adjacent brackets and the point appeared twice in the

output. An exact zero is now taken as a root in its own right, a crossing

requires a strict sign flip, and two detections closer than half a grid step

-- the instrument's own resolution -- are merged.

analyze_bifurcations() swept parameters that were not there

The parameter was injected as a binding under its name and handed down as an

exogenous value; if that name appeared nowhere in the equation, the binding

was never consulted and the sweep returned n_param identical copies of the

same fixed points, each labelled with the absent parameter's name. The

parameter is now validated before the sweep: a fitted coefficient is varied

as a coefficient (which also makes coefficients of lm equations, like

I(Z), valid bifurcation parameters -- previously impossible), a variable

of the equation is varied as an exogenous value, anything else is an error,

as is parameter == variable.

Two more silences in the same loop: a parameter value whose analysis found

no fixed points was dropped from the output entirely, so the requested grid

could not be reconstructed from the result; and any error was caught and

converted into the same empty frame, so a failure was indistinguishable from

an absence. The returned object now carries $status, one row per requested

parameter value -- ok, no_fixed_points, or error with the error's

message -- plus $mode, and a print() method states the accounting.