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README.Rmd
View file @ 0361d845
...@@ -25,7 +25,7 @@ knitr::opts_chunk$set( ...@@ -25,7 +25,7 @@ knitr::opts_chunk$set(
## Installation ## Installation
Install via cran or if you have access to Install via cran or if you have access to
[https://gitlab.ai-env.de/use-case-luft/ubair](https://gitlab.ai-env.de/use-case-luft/ubair) [https://gitlab.opencode.de/uba-ki-lab/ubair](https://gitlab.opencode.de/uba-ki-lab/ubair)
you can use one of the following options: you can use one of the following options:
#### Using an archive file #### Using an archive file
...@@ -41,7 +41,7 @@ Recommended if you do not have git installed. ...@@ -41,7 +41,7 @@ Recommended if you do not have git installed.
- 'Install' - 'Install'
- alternatively, type in console: - alternatively, type in console:
```{r install_package_local} ```{r install_package_local}
install.packages("<path-to-zip>/ubair-master.zip", repos = NULL, type = "source") remotes::install_local("<path-to-zip>/ubair-main.zip")
``` ```
#### Using remote package #### Using remote package
...@@ -49,9 +49,9 @@ Git needs to be installed. ...@@ -49,9 +49,9 @@ Git needs to be installed.
```{r install_package_remote} ```{r install_package_remote}
install.packages("remotes") install.packages("remotes")
# requires a configures ssh-key # requires a configures ssh-key
remotes::install_git("git@gitlab.ai-env.de:use-case-luft/ubair.git") remotes::install_git("git@gitlab.opencode.de:uba-ki-lab/ubair.git")
# alternative via password # alternative via password
remotes::install_git("https://gitlab.ai-env.de/use-case-luft/ubair.git") remotes::install_git("https://gitlab.opencode.de/uba-ki-lab/ubair.git")
``` ```
## Sample Usage of package ## Sample Usage of package
......
README.md
View file @ 0361d845
<!-- README.md is generated from README.Rmd. Please edit that file --> <!-- README.md is generated from README.Rmd. Please edit that file -->
# ubair <img src="inst/sticker/stickers-ubair-1.png" align="right" width="20%"/> # ubair <img src="inst/sticker/stickers-ubair-1.png" align="right" width="20%"/>
**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. **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 ## Installation
Install via cran or if you have access to <https://gitlab.ai-env.de/use-case-luft/ubair> you can use one of the following options: Install via cran or if you have access to
<https://gitlab.opencode.de/uba-ki-lab/ubair> you can use one of the
following options:
#### Using an archive file #### Using an archive file
Recommended if you do not have git installed. Recommended if you do not have git installed.
- Download zip/tar.gz from GitLab - Download zip/tar.gz from GitLab
- Start a new R-Project or open an existing one - Start a new R-Project or open an existing one
- in R-Studio: - in R-Studio:
- go to ‘Packages’-Tab (next to Help/Plots/Files) - go to ‘Packages’-Tab (next to Help/Plots/Files)
- Click on ‘Install’ (left upper corner) - Click on ‘Install’ (left upper corner)
- Install from: choose “Package Archive File” - Install from: choose “Package Archive File”
- Browse to zip-file - Browse to zip-file
- ‘Install’ - ‘Install’
- alternatively, type in console: - alternatively, type in console:
``` r ``` r
install.packages("<path-to-zip>/ubair-master.zip", repos = NULL, type = "source") remotes::install_local("<path-to-zip>/ubair-main.zip")
``` ```
#### Using remote package #### Using remote package
...@@ -33,17 +41,21 @@ Git needs to be installed. ...@@ -33,17 +41,21 @@ Git needs to be installed.
``` r ``` r
install.packages("remotes") install.packages("remotes")
# requires a configures ssh-key # requires a configures ssh-key
remotes::install_git("git@gitlab.ai-env.de:use-case-luft/ubair.git") remotes::install_git("git@gitlab.opencode.de:uba-ki-lab/ubair.git")
# alternative via password # alternative via password
remotes::install_git("https://gitlab.ai-env.de/use-case-luft/ubair.git") remotes::install_git("https://gitlab.opencode.de/uba-ki-lab/ubair.git")
``` ```
## Sample Usage of package ## Sample Usage of package
For a more detailed explanation of the package, you can access the vignettes: For a more detailed explanation of the package, you can access the
vignettes:
- View user_sample source code directly in the [vignettes/](vignettes/) folder. - View user_sample source code directly in the [vignettes/](vignettes/)
- Open vignette by function `vignette("user_sample_1", package = "ubair")`, if the package was installed with vignettes folder.
- Open vignette by function
`vignette("user_sample_1", package = "ubair")`, if the package was
installed with vignettes
``` r ``` r
library(ubair) library(ubair)
...@@ -56,9 +68,10 @@ env_data <- sample_data_DESN025 ...@@ -56,9 +68,10 @@ env_data <- sample_data_DESN025
plot_station_measurements(env_data, params$meteo_variables) plot_station_measurements(env_data, params$meteo_variables)
``` ```
<img src="man/figures/README-plot-meteo-data-1.png" width="100%"/> <img src="man/figures/README-plot-meteo-data-1.png" width="100%" />
- split data into training, reference and effect time intervals <img src="man/figures/time_split_overview.png" width="100%"/> - split data into training, reference and effect time intervals
<img src="man/figures/time_split_overview.png" width="100%"/>
``` r ``` r
application_start <- lubridate::ymd("20191201") # This coincides with the start of the reference window application_start <- lubridate::ymd("20191201") # This coincides with the start of the reference window
...@@ -83,13 +96,12 @@ res <- run_counterfactual(split_data, ...@@ -83,13 +96,12 @@ res <- run_counterfactual(split_data,
) )
``` ```
``` #> [LightGBM] [Info] Auto-choosing row-wise multi-threading, the overhead of testing was 0.000597 seconds.
#> [LightGBM] [Info] Auto-choosing col-wise multi-threading, the overhead of testing was 0.028078 seconds. #> You can set `force_row_wise=true` to remove the overhead.
#> You can set `force_col_wise=true` to remove the overhead. #> And if memory is not enough, you can set `force_col_wise=true`.
#> [LightGBM] [Info] Total Bins 1557 #> [LightGBM] [Info] Total Bins 1557
#> [LightGBM] [Info] Number of data points in the train set: 104486, number of used features: 9 #> [LightGBM] [Info] Number of data points in the train set: 104486, number of used features: 9
#> [LightGBM] [Info] Start training from score -0.000000 #> [LightGBM] [Info] Start training from score -0.000000
```
``` r ``` r
predictions <- res$prediction predictions <- res$prediction
...@@ -102,26 +114,25 @@ plot_counterfactual(predictions, params, ...@@ -102,26 +114,25 @@ plot_counterfactual(predictions, params,
) )
``` ```
<img src="man/figures/README-counterfactual-scenario-1.png" width="100%"/> <img src="man/figures/README-counterfactual-scenario-1.png" width="100%" />
``` r ``` r
round(calc_performance_metrics(predictions, date_effect_start, buffer = buffer), 2) round(calc_performance_metrics(predictions, date_effect_start, buffer = buffer), 2)
``` ```
``` #> RMSE MSE MAE MAPE Bias
#> RMSE MSE MAE MAPE Bias #> 7.38 54.48 5.38 0.18 -2.73
#> 7.38 54.48 5.38 0.18 -2.73 #> R2 Coverage lower Coverage upper Coverage Correlation
#> R2 Coverage lower Coverage upper Coverage Correlation #> 0.74 0.97 0.95 0.92 0.89
#> 0.74 0.97 0.95 0.92 0.89 #> MFB FGE
#> MFB FGE #> -0.05 0.19
#> -0.05 0.19
```
``` r ``` r
round(calc_summary_statistics(predictions, date_effect_start, buffer = buffer), 2) round(calc_summary_statistics(predictions, date_effect_start, buffer = buffer), 2)
``` ```
::: kable-table <div class="kable-table">
| | true | prediction | | | true | prediction |
|:---------------------|-------:|-----------:| |:---------------------|-------:|-----------:|
| min | 3.36 | 5.58 | | min | 3.36 | 5.58 |
...@@ -133,21 +144,20 @@ round(calc_summary_statistics(predictions, date_effect_start, buffer = buffer), ...@@ -133,21 +144,20 @@ round(calc_summary_statistics(predictions, date_effect_start, buffer = buffer),
| median/50-percentile | 29.60 | 27.09 | | median/50-percentile | 29.60 | 27.09 |
| 75-percentile | 40.54 | 36.27 | | 75-percentile | 40.54 | 36.27 |
| 95-percentile | 56.80 | 47.69 | | 95-percentile | 56.80 | 47.69 |
:::
</div>
``` r ``` r
estimate_effect_size(predictions, date_effect_start, buffer = buffer, verbose = TRUE) 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.
#> 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 #> $absolute_effect
#> [1] -6.294028 #> [1] -6.294028
#> #>
#> $relative_effect #> $relative_effect
#> [1] -0.2637 #> [1] -0.2637
```
### SHAP feature importances ### SHAP feature importances
...@@ -155,21 +165,23 @@ estimate_effect_size(predictions, date_effect_start, buffer = buffer, verbose = ...@@ -155,21 +165,23 @@ estimate_effect_size(predictions, date_effect_start, buffer = buffer, verbose =
shapviz::sv_importance(res$importance, kind = "bee") shapviz::sv_importance(res$importance, kind = "bee")
``` ```
<img src="man/figures/README-feature_importance-1.png" width="100%"/> <img src="man/figures/README-feature_importance-1.png" width="100%" />
``` r ``` r
xvars <- c("TMP", "WIG", "GLO", "WIR") xvars <- c("TMP", "WIG", "GLO", "WIR")
shapviz::sv_dependence(res$importance, v = xvars) shapviz::sv_dependence(res$importance, v = xvars)
``` ```
<img src="man/figures/README-feature_importance-2.png" width="100%"/> <img src="man/figures/README-feature_importance-2.png" width="100%" />
## Development ## Development
### Prerequisites ### Prerequisites
1. **R**: Make sure you have R installed (recommended version 4.4.1). You can download it from [CRAN](https://cran.r-project.org/). 1. **R**: Make sure you have R installed (recommended version 4.4.1).
2. **RStudio** (optional but recommended): Download from [RStudio](https://www.rstudio.com/). You can download it from [CRAN](https://cran.r-project.org/).
2. **RStudio** (optional but recommended): Download from
[RStudio](https://www.rstudio.com/).
### Setting Up the Environment ### Setting Up the Environment
...@@ -186,13 +198,12 @@ devtools::load_all() ...@@ -186,13 +198,12 @@ devtools::load_all()
#### Install pre-commit hook (required to ensure tidyverse code formatting) #### Install pre-commit hook (required to ensure tidyverse code formatting)
``` pip install pre-commit
pip install pre-commit
```
#### Add new requirements #### Add new requirements
If you add new dependencies to *ubair* package, make sure to update the renv.lock file: If you add new dependencies to *ubair* package, make sure to update the
renv.lock file:
``` r ``` r
renv::snapshot() renv::snapshot()
...@@ -200,7 +211,8 @@ renv::snapshot() ...@@ -200,7 +211,8 @@ renv::snapshot()
#### style and documentation #### style and documentation
Before you commit your changes update documentation, ensure style complies with tidyverse styleguide and all tests run without error Before you commit your changes update documentation, ensure style
complies with tidyverse styleguide and all tests run without error
``` r ``` r
# update documentation and check package integrity # update documentation and check package integrity
...@@ -217,9 +229,13 @@ devtools::build_readme() ...@@ -217,9 +229,13 @@ devtools::build_readme()
#### Pre-commit hook #### 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 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. If precommit fails, check the automatically applied changes, stage them
and retry to commit.
#### Test Coverage #### Test Coverage
...@@ -240,8 +256,8 @@ covr::report(cov) ...@@ -240,8 +256,8 @@ covr::report(cov)
## Contacts ## Contacts
**Jore Noa Averbeck** [JoreNoa.Averbeck\@uba.de](mailto:JoreNoa.Averbeck@uba.de){.email} **Jore Noa Averbeck** <JoreNoa.Averbeck@uba.de>
**Raphael Franke** [Raphael.Franke\@uba.de](mailto:Raphael.Franke@uba.de){.email} **Raphael Franke** <Raphael.Franke@uba.de>
**Imke Voß** [imke.voss\@uba.de](mailto:imke.voss@uba.de){.email} **Imke Voß** <imke.voss@uba.de>

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