Function that shifts a value by some offset and then applies the natural logarithm to it.
Usage
log_shift(x, offset = 0, base = exp(1))Arguments
- x
vector of input values to be transformed
- offset
number to add to the input value before taking the natural logarithm
- base
a positive or complex number: the base with respect to which logarithms are computed. Defaults to e = exp(1).
References
Transformation of forecasts for evaluating predictive performance in an epidemiological context Nikos I. Bosse, Sam Abbott, Anne Cori, Edwin van Leeuwen, Johannes Bracher, Sebastian Funk medRxiv 2023.01.23.23284722 doi:10.1101/2023.01.23.23284722 https://www.medrxiv.org/content/10.1101/2023.01.23.23284722v1 # nolint
Examples
log_shift(1:10)
#> [1] 0.0000000 0.6931472 1.0986123 1.3862944 1.6094379 1.7917595 1.9459101
#> [8] 2.0794415 2.1972246 2.3025851
log_shift(0:9, offset = 1)
#> [1] 0.0000000 0.6931472 1.0986123 1.3862944 1.6094379 1.7917595 1.9459101
#> [8] 2.0794415 2.1972246 2.3025851
transform_forecasts(
example_quantile[true_value > 0, ],
fun = log_shift,
offset = 1
)
#> location target_end_date target_type true_value location_name
#> 1: DE 2021-01-02 Cases 1.273000e+05 Germany
#> 2: DE 2021-01-02 Deaths 4.534000e+03 Germany
#> 3: DE 2021-01-09 Cases 1.549220e+05 Germany
#> 4: DE 2021-01-09 Deaths 6.117000e+03 Germany
#> 5: DE 2021-01-16 Cases 1.101830e+05 Germany
#> ---
#> 40672: IT 2021-07-24 Deaths 4.369448e+00 Italy
#> 40673: IT 2021-07-24 Deaths 4.369448e+00 Italy
#> 40674: IT 2021-07-24 Deaths 4.369448e+00 Italy
#> 40675: IT 2021-07-24 Deaths 4.369448e+00 Italy
#> 40676: IT 2021-07-24 Deaths 4.369448e+00 Italy
#> forecast_date quantile prediction model horizon scale
#> 1: <NA> NA NA <NA> NA natural
#> 2: <NA> NA NA <NA> NA natural
#> 3: <NA> NA NA <NA> NA natural
#> 4: <NA> NA NA <NA> NA natural
#> 5: <NA> NA NA <NA> NA natural
#> ---
#> 40672: 2021-07-12 0.850 5.866468 epiforecasts-EpiNow2 2 log
#> 40673: 2021-07-12 0.900 5.986452 epiforecasts-EpiNow2 2 log
#> 40674: 2021-07-12 0.950 6.214608 epiforecasts-EpiNow2 2 log
#> 40675: 2021-07-12 0.975 6.416732 epiforecasts-EpiNow2 2 log
#> 40676: 2021-07-12 0.990 6.579251 epiforecasts-EpiNow2 2 log