Retained photosystem-II function for snow gum (Eucalyptus pauciflora)
leaf sections after a temperature x duration heat dose and either Dark or
Light recovery. fvfm_prop is post-exposure Fv/Fm divided by the
pre-exposure value. It is a continuous proportion, so the canonical model
uses the experimental Beta family rather than a count likelihood.
Format
A data frame with 394 rows and 8 variables:
- Temp
Assay temperature (degrees C).
- Time
Exposure duration (minutes).
- recovery
Recovery condition:
DarkorLight.- plant
Plant identifier for the CTmax random intercept.
- meas_day
Measurement-day identifier.
- initial_fvfm
Pre-exposure Fv/Fm.
- final_fvfm
Post-exposure Fv/Fm.
- fvfm_prop
Retained PSII proportion.
Source
Arnold et al. (2026), doi:10.64898/2026.04.09.717599
. The
development copy is redistributed under CC BY-NC 4.0 with attribution.
Pieter A. Arnold, the data holder, authorised package use on 2026-07-16.
The dataset remains separately licensed CC BY-NC 4.0; retain its
attribution and source URL when reusing it. See inst/COPYRIGHTS.
Examples
# \donttest{
std <- standardize_data(snowgum_psii, temp = "Temp", duration = "Time",
proportion = "fvfm_prop", duration_unit = "minutes")
#> Warning: standardize_data() clamped 90 of 394 finite proportion values into [0.001, 0.999] for the Beta likelihood. Check whether boundary values and this epsilon are scientifically appropriate.
wf <- fit_4pl(std, ctmax = ~ 0 + recovery + (1 | plant),
z = ~ 0 + recovery, low = ~ 1, up = ~ 1, k = ~ 1,
family = "beta", t_ref = 60, method = "wald", quiet = TRUE)
tls(wf, by = "recovery", lethal = FALSE, method = "wald")
#> <tls> relative threshold; quantities: z, CTmax (wald intervals)
#> # A tibble: 4 × 5
#> recovery quantity median lower upper
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 Dark CTmax 45.7 45.2 46.3
#> 2 Light CTmax 44.1 43.6 44.6
#> 3 Dark z 4.71 4.29 5.16
#> 4 Light z 3.64 3.20 4.14
# }