tls_bf() captures the per-sub-parameter formulas that define a freqTLS
model and returns them, unevaluated, as a tls_formula object. It is the
formula complement to the column interface of fit_tls(): instead of passing
bare column names, you write one response formula plus a formula per model
sub-parameter.
Value
A tls_formula object: a list with the captured response formula,
the named sub-parameter formulas, and the calling environment.
Details
The first argument must be the unnamed response-and-axes formula. Its
left-hand side names the survival counts, in either the brms idiom
successes | trials(total) or the glm idiom cbind(successes, failures).
Its right-hand side names the two thermal-load-sensitivity axes with the
tagged markers time(<duration>) and temp(<temperature>) (order does not
matter).
The remaining arguments are sub-parameter formulas keyed by their left-hand
side, one of low, up, log_k, CTmax, or log_z. Any sub-parameter you
omit defaults to ~ 1. Each of low, up, and log_k may carry its
own design independently — a grouping factor (low ~ group), a
continuous covariate (log_k ~ body_size), or an intercept — and need not
share one factor or match the headline-parameter grouping. CTmax and log_z
accept fixed-effect formulas but must produce the same model-matrix columns
(for example, use CTmax ~ group, log_z ~ group); their supported random-
intercept groupings may differ. A single random intercept,
<param> ~ <fixed> + (1 | group), is accepted on CTmax, log_z, low, and
log_k (one grouping factor each, intercept only) – but not on the upper
asymptote up, for which the compiled objective has no random-intercept term. Putting the same
grouping factor on two or more of them fits independent variances (no
correlation term) and warns. Phylogenetic covariance structures (for
example, gr(species, cov = tree)) are not implemented; use bayesTLS for
that model.
Parser provenance
The shape of the parser (variadic capture via substitute(), a per-entry
formula walk, and random-bar detection) is adapted from drmTMB's
drm_formula() / parse_drm_formula_entry() (GPL-3); see inst/COPYRIGHTS.
freqTLS writes its own grammar (the time() / temp() axis markers, the
five fixed sub-parameter handles, and the package's supported random-effect
grammar).
See also
fit_tls(), which accepts either a tls_formula or the column
interface.
Examples
tls_bf(
survived | trials(total) ~ time(duration) + temp(temp),
CTmax ~ population,
log_z ~ population
)
#> <tls_formula>
#> survived | trials(total) ~ time(duration) + temp(temp)
#> CTmax ~ population
#> log_z ~ population
# cbind() response idiom, ungrouped:
tls_bf(cbind(survived, died) ~ time(duration) + temp(temp))
#> <tls_formula>
#> cbind(survived, died) ~ time(duration) + temp(temp)