Fix population scaling with other_keys + supporting fixes/changes
#422
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Recent/current epiprocess versions silently ignore `extra_keys =`. Pending epiprocess changes will soft-deprecate and route it to `other_keys =` instead, plus add some stricter checks on `other_keys =`.
- Rename `extra_keys` -> `other_keys` when we are going to feed it into `other_keys =`. - Remove some `<edf metadata>$other_keys %||% character()` hedges now that current epiprocess standardizes to character() not NULL and example `epi_df` objects have been updated to that standard.
- Roles should already factor in key_colnames.
dajmcdon
approved these changes
Nov 11, 2024
| @@ -112,7 +112,7 @@ make_quantile_reg <- function() { | |||
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| # can't make a method because object is second | |||
| out <- switch(type, | |||
| rq = dist_quantiles(unname(as.list(x)), object$quantile_levels), # one quantile | |||
| rq = dist_quantiles(unname(as.list(x)), object$tau), # one quantile | |||
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I'm surprised this didn't raise an error before...
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dajmcdon.
DESCRIPTIONandNEWS.md.Always increment the patch version number (the third number), unless you are
making a release PR from dev to main, in which case increment the minor
version number (the second number).
(backwards-incompatible changes to the documented interface) are noted.
Collect the changes under the next release number (e.g. if you are on
0.7.2, then write your changes under the 0.8 heading).
epiprocessversion in theDESCRIPTIONfile ifepiprocesssoonepipredictandepiprocessChange explanations for reviewer
extra_keys =withother_keys =, which is sometimes used in current epiprocess, and will consistently be used/checked in pending epiprocess versions.layer_population_scaling(by = NULL)when there areother_keys.step_population_scalingdefaultbysetting toprep; try to improve messaging.grab_forged_keysandkey_colnamesto try to be more self-consistent and consistent with pending epiprocesskey_colnamesupdates."geo_value","key", or"time_value"roles are present, use them to decide on key.epi_dfas training/test data, as this should set roles.c("geo_value", "time_value")and available columns. (Though population scaling attempts to deviate from this, instead using the intersection of all column names in the training/test data with non-population column names in the population data. It works for the step, but since postprocessing seems to require anepi_df, it doesn't effectively work on the layer.)step_population_scalingwork with non-epi_dfs.layer_population_scalingwork with non-epi_dfs it has both the"geo_value"and"time_value"columns, and, if other key columns are present, that all the epikeytime roles are manually set.quantile_regerrors producing just single predictions, to enable writing "simple" tests.Magic GitHub syntax to mark associated Issue(s) as resolved when this is merged into the default branch
layer_population_scalingwithby = NULLdoesn't work with anyother_keys#410key_colnames()is called with ignored argumentextra_keys =#412quantile_reg()with single level raises errors, at least withmethod = "fnc"#419