tests/testthat/test-lrf_1991.R

In padpadpadpad/rTPC: Fitting and Analysing Thermal Performance Curves

context("test-lrf_1991.R")

# do not run the test on CRAN as they take too long
testthat::skip_on_cran()

# method: fit model and get predictions. Check these are consistent.

# load in ggplot
library(ggplot2)

# laod in data
data('chlorella_tpc')
d <- subset(chlorella_tpc, curve_id == 1)

# get start values and fit model
start_vals <- get_start_vals(d$temp, d$rate, model_name = 'lrf_1991')

# fit model
mod <- suppressWarnings(mod <- nls.multstart::nls_multstart(rate~lrf_1991(temp = temp, rmax, topt, tmin, tmax),
                                             data = d,
                                             iter = c(3,3,3,3),
                                             start_lower = start_vals - 10,
                                             start_upper = start_vals + 10,
                                             lower = get_lower_lims(d$temp, d$rate, model_name = 'lrf_1991'),
                                             upper = get_upper_lims(d$temp, d$rate, model_name = 'lrf_1991'),
                                             supp_errors = 'Y',
                                             convergence_count = FALSE))

# get predictions
preds <- broom::augment(mod)

# plot
ggplot(preds) +
  geom_point(aes(temp, rate)) +
  geom_line(aes(temp, .fitted)) +
  theme_bw()

# run test
testthat::test_that("lrf_1991 function works", {
  testthat::expect_equal(
    round(preds$.fitted, 1),
    c(0.0, 0.1, 0.3, 0.6, 0.9, 1.1, 1.3, 1.4, 1.4, 1.1, 0.7, -0.1))
})