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ubair

ubair is an R package for Statistical Investigation of the Impact of External Conditions on Air Quality: it uses the statistical software R to analyze and visualize the impact of external factors, such as traffic restrictions, hazards, and political measures, on air quality. It aims to provide experts with a transparent comparison of modeling approaches and to support data-driven evaluations for policy advisory purposes.

Installation

install.packages("remotes")
remotes::install_local()

Using remote package

Git needs to be installed.

install.packages("remotes")
remotes::install_git("git@gitlab.opencode.de:uba-ki-lab/ubair.git")
# alternative via https
remotes::install_git("https://gitlab.opencode.de/uba-ki-lab/ubair.git")

Sample Usage of package

For a more detailed explanation of the package, you can access the vignettes:

library(ubair)
params <- load_params()
env_data <- sample_data_DESN025
# Plot meteo data
plot_station_measurements(env_data, params$meteo_variables)

application_start <- lubridate::ymd("20191201") # This coincides with the start of the reference window
date_effect_start <- lubridate::ymd_hm("20200323 00:00") # This splits the forecast into reference and effect
application_end <- lubridate::ymd("20200504") # This coincides with the end of the effect window

buffer <- 24 * 14 # 14 days buffer

dt_prepared <- prepare_data_for_modelling(env_data, params)
dt_prepared <- dt_prepared[complete.cases(dt_prepared)]
split_data <- split_data_counterfactual(
  dt_prepared, application_start,
  application_end
)
res <- run_counterfactual(split_data,
  params,
  detrending_function = "linear",
  model_type = "lightgbm",
  alpha = 0.9,
  log_transform = TRUE,
  calc_shaps = TRUE
)
#> [LightGBM] [Info] Auto-choosing col-wise multi-threading, the overhead of testing was 0.023641 seconds.
#> You can set `force_col_wise=true` to remove the overhead.
#> [LightGBM] [Info] Total Bins 1557
#> [LightGBM] [Info] Number of data points in the train set: 104486, number of used features: 9
#> [LightGBM] [Info] Start training from score -0.000000
predictions <- res$prediction

plot_counterfactual(predictions, params,
  window_size = 14,
  date_effect_start,
  buffer = buffer,
  plot_pred_interval = TRUE
)

round(calc_performance_metrics(predictions, date_effect_start, buffer = buffer), 2)
#>           RMSE            MSE            MAE           MAPE           Bias 
#>           7.38          54.48           5.38           0.18          -2.73 
#>             R2 Coverage lower Coverage upper       Coverage    Correlation 
#>           0.74           0.97           0.95           0.92           0.89 
#>            MFB            FGE 
#>          -0.05           0.19
round(calc_summary_statistics(predictions, date_effect_start, buffer = buffer), 2)
true prediction
min 3.36 5.58
max 111.90 59.71
var 212.96 128.16
mean 30.80 28.07
5-percentile 9.29 10.73
25-percentile 19.85 19.40
median/50-percentile 29.60 27.09
75-percentile 40.54 36.27
95-percentile 56.80 47.69 
estimate_effect_size(predictions, date_effect_start, buffer = buffer, verbose = TRUE)
#> The external effect changed the target value on average by -6.294 compared to the reference time window. This is a -26.37% relative change.

#> $absolute_effect
#> [1] -6.294028
#> 
#> $relative_effect
#> [1] -0.2637

SHAP feature importances

shapviz::sv_importance(res$importance, kind = "bee")

xvars <- c("TMP", "WIG", "GLO", "WIR")
shapviz::sv_dependence(res$importance, v = xvars)

Development

Prerequisites

  1. R: Make sure you have R installed (recommended version 4.4.1). You can download it from CRAN.
  2. RStudio (optional but recommended): Download from RStudio.

Setting Up the Environment

Install the development version of ubair:

install.packages("renv")
renv::restore()
devtools::build()
devtools::load_all()

Development

Install pre-commit hook (required to ensure tidyverse code formatting)

pip install pre-commit

Add new requirements

If you add new dependencies to ubair package, make sure to update the renv.lock file:

renv::snapshot()

style and documentation

Before you commit your changes update documentation, ensure style complies with tidyverse styleguide and all tests run without error

# update documentation and check package integrity
devtools::check()
# apply tidyverse style (also applied as precommit hook)
usethis::use_tidy_style()
# you can check for existing lintr warnings by
devtools::lint()
# run tests
devtools::test()
# build README.md if any changes have been made to README.Rmd
devtools::build_readme()

Pre-commit hook

in .pre-commit-hook.yaml pre-commit rules are defined and applied before each commmit. This includes: split - run styler to format code in tidyverse style - run roxygen to update doc - check if readme is up to date - run lintr to finally check code style format

If precommit fails, check the automatically applied changes, stage them and retry to commit.

Test Coverage

Install covr to run this.

cov <- covr::package_coverage(type = "all")
cov_list <- covr::coverage_to_list(cov)
data.table::data.table(
  part = c("Total", names(cov_list$filecoverage)),
  coverage = c(cov_list$totalcoverage, as.vector(cov_list$filecoverage))
)
covr::report(cov)

Contacts

Jore Noa Averbeck JoreNoa.Averbeck@uba.de

Raphael Franke Raphael.Franke@uba.de

Imke Voß imke.voss@uba.de

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.