Adjust a layer in an epi_workflow or frosting

Make a parameter adjustment to a layer in either an epi_workflow or frosting object.

Usage

adjust_frosting(x, which_layer, ...)

# S3 method for class 'epi_workflow'
adjust_frosting(x, which_layer, ...)

# S3 method for class 'frosting'
adjust_frosting(x, which_layer, ...)

Arguments

x

An epi_workflow or frosting object

which_layer

the number or name of the layer to adjust

...

Used to input a parameter adjustment

Value

x, updated with the adjustment to the specified frosting layer.

Details

This function can either adjust a layer in a frosting object or a layer from a frosting object in an epi_workflow. The layer to be adjusted is indicated by either the layer number or name (if a name is used, it must be unique). In either case, the argument name and update value must be inputted as .... See the examples below for brief illustrations of the different types of updates.

Examples

library(dplyr)
jhu <- covid_case_death_rates %>%
  filter(time_value > "2021-11-01", geo_value %in% c("ak", "ca", "ny"))
r <- epi_recipe(jhu) %>%
  step_epi_lag(death_rate, lag = c(0, 7, 14)) %>%
  step_epi_ahead(death_rate, ahead = 7) %>%
  step_epi_naomit()

wf <- epi_workflow(r, linear_reg()) %>% fit(jhu)

# in the frosting from the workflow
f1 <- frosting() %>%
  layer_predict() %>%
  layer_threshold(.pred)

wf2 <- wf %>% add_frosting(f1)

# Adjust `layer_threshold` to have an upper bound of 1
# in the `epi_workflow`
# Option 1. Using the layer number:
wf2 <- wf2 %>% adjust_frosting(which_layer = 2, upper = 1)
extract_frosting(wf2)
#> 
#> ── Frosting ────────────────────────────────────────────────────────────────────
#> 
#> ── Layers 
#> 1. Creating predictions: "<calculated>"
#> 2. Thresholding predictions: .pred to [0, 1]
# Option 2. Using the layer name:
wf3 <- wf2 %>% adjust_frosting(which_layer = "layer_threshold", upper = 1)
extract_frosting(wf3)
#> 
#> ── Frosting ────────────────────────────────────────────────────────────────────
#> 
#> ── Layers 
#> 1. Creating predictions: "<calculated>"
#> 2. Thresholding predictions: .pred to [0, 1]

# Adjust `layer_threshold` to have an upper bound of 5
# in the `frosting` object
# Option 1. Using the layer number:
f2 <- f1 %>% adjust_frosting(which_layer = 2, upper = 5)
f2
#> 
#> ── Frosting ────────────────────────────────────────────────────────────────────
#> 
#> ── Layers 
#> 1. Creating predictions: "<calculated>"
#> 2. Thresholding predictions: .pred to [0, 5]
# Option 2. Using the layer name
f3 <- f1 %>% adjust_frosting(which_layer = "layer_threshold", upper = 5)
f3
#> 
#> ── Frosting ────────────────────────────────────────────────────────────────────
#> 
#> ── Layers 
#> 1. Creating predictions: "<calculated>"
#> 2. Thresholding predictions: .pred to [0, 5]