Package index • rTFT

Fitting

Building the table of intervals at risk from the failure times and the temperature of each trial, and fitting the model.

build_hazard_data(): Build the row-per-interval table a failure-rate model is fitted to
ramp_path(): Build a linear ramp temperature trajectory
assess_ramp_linearity(): Assess how linear a logged temperature trace is
fit_hazard(): Fit a failure-rate hazard model with brms
costressor(): Declare a co-stressor for a failure-rate hazard model
build_hazard_prior(): Weakly-informative default priors for a failure-rate hazard model
M_catalogue: Failure rate functions M(T)
h0_catalogue: Baseline hazard functions h0(tau)

check_survival(): Check a fitted model against the survival observed in each group
plot_check(): Plot the check of a fitted model against observed survival
hazard_residuals(): Residuals of a fitted model, one per individual
plot_residuals(): Plot the residuals of a fitted model

Critical thermal maxima, thermal death time curves and thermal tolerance landscapes, each with its posterior uncertainty.

derive_tdt_ttl(): Thermal tolerance derived from a fitted failure-rate model
derive_dctmax(): Dynamic critical thermal maximum under a ramp, from a fitted model
plot_tdt(): Plot the thermal death time curves
plot_ttl(): Plot the thermal tolerance landscape
plot_ttl_3d(): Plot the thermal tolerance landscape as a surface to rotate
M_draws(): The fitted failure rate over temperature, for each posterior draw

loo_hazard(): Leave-one-out cross-validation that leaves out whole individuals or groups
kfold_hazard(): Cross-validation by refitting, leaving out whole individuals or groups
hazard_weights(): Weights for averaging failure-rate models
average_tdt_ttl(): Thermal tolerance averaged over several fitted models
average_dctmax(): Dynamic critical thermal maximum averaged over several fitted models
average_survival(): Survival along a record of temperature, averaged over several fitted models

predict_survival(): Survival along a record of temperature, from a fitted failure-rate model
plot_survival(): Plot survival along a record of temperature
plot_risk(): Plot each period's share of the risk along a record

Simulated datasets used in the help pages and the vignettes.

static_assay: A simulated static assay of thermal tolerance
ramp_assay: A simulated ramping assay of thermal tolerance, with two levels of oxygen
stream_record: A simulated record of stream temperature

The pieces that fit_hazard() and the derived quantities are assembled from. Most analyses do not call them directly.

build_hazard_spec(): Assemble the brms formula and family for a failure-rate hazard model
brms_log_M: log M(T) for each failure rate function, as a brms expression string
brms_log_h0: log h0(tau) for each baseline function, as a brms expression string
H0_of(): The cumulative baseline hazard of a given baseline function
H0inv_of(): The inverse of the cumulative baseline hazard
cloglog_bern_family(): Complementary log-log Bernoulli response, on the identity link
hazard_mixed_family(): Response distribution for a table mixing interval-censored and known-time failures