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add docs and newa
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seabbs committed Aug 15, 2024
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2 changes: 1 addition & 1 deletion NEWS.md
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- The interface for defining delay distributions has been generalised to also cater for continuous distributions
- When defining probability distributions these can now be truncated using the `tolerance` argument
- Ornstein-Uhlenbeck and 5 / 2 Matérn kernels have been added. By @sbfnk in #741 and reviewed by @seabbs.
- Gaussian processes have been vectorised and the `gp_opts()` function has been updated to allow for the specification of a periodic kernel. By @seabbs in #742 and reviewed by @jamesmbaazam.
- Gaussian processes have been vectorised and the `gp_opts()` function has been updated to allow for the specification of periodic and linear kernels. By @seabbs in #742 and reviewed by @jamesmbaazam.
- Prior predictive checks have been used to update the following priors: the prior on the magnitude of the Gaussian process (from HalfNormal(0, 1) to HalfNormal(0, 0.1)), and the prior on the overdispersion (from 1 / HalfNormal(0, 1)^2 to 1 / HalfNormal(0, 0.25)). By @seabbs in #742 and reviewed by @jamesmbaazam.
- The default stan control options have been updated from `list(adapt_delta = 0.95, max_treedepth = 15)` to `list(adapt_delta = 0.9, max_treedepth = 12)` due to improved performance and to reduce the runtime of the default parameterisations. By @seabbs in #742 and reviewed by @jamesmbaazam.
- Initialisation has been simplified by sampling directly from the priors, where possible, rather than from a constrained space. By @seabbs in #742 and reviewed by @jamesmbaazam.
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17 changes: 11 additions & 6 deletions man/gp_opts.Rd

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2 changes: 0 additions & 2 deletions tests/testthat/test-create_gp_data.R
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Expand Up @@ -54,7 +54,5 @@ test_that("create_gp_data correctly handles linear kernel", {
data <- list(t = 30, seeding_time = 7, horizon = 7, future_fixed = 0, fixed_from = 0, stationary = 0)
linear_gp_opts <- gp_opts(kernel = "linear")
gp_data <- create_gp_data(linear_gp_opts, data)

# Check that gp_type is set to 3 for linear kernel
expect_equal(gp_data$gp_type, 3)
})

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