diff --git a/README.Rmd b/README.Rmd
index ba5f0cc42e023486ce5653ad0be8fd37e7257ae1..78ea7e08411dba0b1cf82a102a83b9b65adb1172 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -25,7 +25,7 @@ knitr::opts_chunk$set(
## Installation
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:
#### Using an archive file
@@ -41,7 +41,7 @@ Recommended if you do not have git installed.
- 'Install'
- alternatively, type in console:
```{r install_package_local}
-install.packages("<path-to-zip>/ubair-master.zip", repos = NULL, type = "source")
+install.packages("<path-to-zip>/ubair-main.zip", repos = NULL, type = "source")
```
#### Using remote package
@@ -49,9 +49,9 @@ Git needs to be installed.
```{r install_package_remote}
install.packages("remotes")
# 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
-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
diff --git a/README.md b/README.md
index 67b106df9bfc8ab2b78a5a94b49ed5296e954b99..517c8ce237b689ce9442ec052c9f4592f2a52354 100644
--- a/README.md
+++ b/README.md
@@ -1,29 +1,37 @@
+
<!-- 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** 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
-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
Recommended if you do not have git installed.
-- Download zip/tar.gz from GitLab
-- Start a new R-Project or open an existing one
-- in R-Studio:
- - go to ‘Packages’-Tab (next to Help/Plots/Files)
- - Click on ‘Install’ (left upper corner)
- - Install from: choose “Package Archive Fileâ€
- - Browse to zip-file
- - ‘Install’
-- alternatively, type in console:
+- Download zip/tar.gz from GitLab
+- Start a new R-Project or open an existing one
+- in R-Studio:
+ - go to ‘Packages’-Tab (next to Help/Plots/Files)
+ - Click on ‘Install’ (left upper corner)
+ - Install from: choose “Package Archive Fileâ€
+ - Browse to zip-file
+ - ‘Install’
+- alternatively, type in console:
``` r
-install.packages("<path-to-zip>/ubair-master.zip", repos = NULL, type = "source")
+install.packages("<path-to-zip>/ubair-main.zip", repos = NULL, type = "source")
```
#### Using remote package
@@ -33,17 +41,21 @@ Git needs to be installed.
``` r
install.packages("remotes")
# 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
-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
-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.
-- Open vignette by function `vignette("user_sample_1", package = "ubair")`, if the package was installed with vignettes
+- View user_sample source code directly in the [vignettes/](vignettes/)
+ folder.
+- Open vignette by function
+ `vignette("user_sample_1", package = "ubair")`, if the package was
+ installed with vignettes
``` r
library(ubair)
@@ -56,9 +68,10 @@ env_data <- sample_data_DESN025
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
application_start <- lubridate::ymd("20191201") # This coincides with the start of the reference window
@@ -83,13 +96,12 @@ res <- run_counterfactual(split_data,
)
```
-```
-#> [LightGBM] [Info] Auto-choosing col-wise multi-threading, the overhead of testing was 0.028078 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
-```
+ #> [LightGBM] [Info] Auto-choosing row-wise multi-threading, the overhead of testing was 0.000509 seconds.
+ #> You can set `force_row_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] Number of data points in the train set: 104486, number of used features: 9
+ #> [LightGBM] [Info] Start training from score -0.000000
``` r
predictions <- res$prediction
@@ -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
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
-```
+ #> 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
``` r
round(calc_summary_statistics(predictions, date_effect_start, buffer = buffer), 2)
```
-::: kable-table
+<div class="kable-table">
+
| | true | prediction |
|:---------------------|-------:|-----------:|
| min | 3.36 | 5.58 |
@@ -133,21 +144,20 @@ round(calc_summary_statistics(predictions, date_effect_start, buffer = buffer),
| median/50-percentile | 29.60 | 27.09 |
| 75-percentile | 40.54 | 36.27 |
| 95-percentile | 56.80 | 47.69 |
-:::
+
+</div>
``` r
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
-#> [1] -6.294028
-#>
-#> $relative_effect
-#> [1] -0.2637
-```
+ #> $absolute_effect
+ #> [1] -6.294028
+ #>
+ #> $relative_effect
+ #> [1] -0.2637
### SHAP feature importances
@@ -155,21 +165,23 @@ estimate_effect_size(predictions, date_effect_start, buffer = buffer, verbose =
shapviz::sv_importance(res$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
xvars <- c("TMP", "WIG", "GLO", "WIR")
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
### 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/).
-2. **RStudio** (optional but recommended): Download from [RStudio](https://www.rstudio.com/).
+1. **R**: Make sure you have R installed (recommended version 4.4.1).
+ 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
@@ -186,13 +198,12 @@ devtools::load_all()
#### Install pre-commit hook (required to ensure tidyverse code formatting)
-```
-pip install pre-commit
-```
+ pip install pre-commit
#### 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
renv::snapshot()
@@ -200,7 +211,8 @@ renv::snapshot()
#### 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
# update documentation and check package integrity
@@ -217,9 +229,13 @@ 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
+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
@@ -240,8 +256,8 @@ covr::report(cov)
## 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>