Guillaume Cinkus, Naomi Mazzilli and Hervé Jourde
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KarstID is an R Package devoted to the analysis of karst systems hydrological functioning. The package consists in an interactive application that can be loaded through a web browser or the RStudio viewer. The application is developed in the R Shiny framework.
The goal of KarstID is to facilitate the completion of common analyses of karst spring hydrographs such as:
- Statistical analyses
- Recession curves analysis
- Simple correlational and spectral analyses
- Analyses of classified discharges
The equations behind the analyses and the calculation of the indicators are detailed in Cinkus et al. (2021) (https://doi.org/10.1016/j.jhydrol.2021.127006). The application also provides the classification of karst systems hydrological functioning based on the proposal of Cinkus et al. (2021) and offers to compare the results with a database of 78 karst systems located worldwide (Olarinoye et al., 2020, https://doi.org/10.1038/s41597-019-0346-5).
The KarstID package is open source, actively developed and available on Github (https://github.com/busemorose/KarstID). We will try to address user requests (new features or bug report). We also consider future developments such as different recession models, or adding other hydrodynamic analyses.
KarstID requires an installation of R. It is recommended to use at
least R 4.0.0. Note that it is possible to install the package with
an R version prior to 4.0.0 but some conflicts may exist. The
instruction for the installation and the download of R can be found on
the CRAN website.
Once R is installed, KarstID can be installed from GitHub.
if (!require("remotes")) install.packages("remotes") # install remotes package if needed
remotes::install_github("busemorose/KarstID") # install KarstID packageOnce the package is installed, the application can be loaded with the
KarstID() function.
library(KarstID)
KarstID()The data import tab allows to load a spring discharge time series:
- The data must be a plain text or Excel file
- The file must have two columns representing date and discharge, respectively
- The discharge must be in m3/s
The import options allows the user to define:
Name: will be used for export file names and plot displaysTime step: time step of the imported time seriesSkip row: number of rows to skip at the beginning of the fileSheet: sheet number if Excel fileDecimal mark: decimal mark of the discharge valuesDelimiter: delimiter of the columnsHeader: presence of header or not (if no header, column names will be defaulted todateanddischarge)Compute and use daily mean: only for hourly time step. If checked, compute and use daily mean from (infra) hourly dataDate format: format of the date (e.g.%Y-%m-%d %H:%M:%Sfor a date-time format)
After defining the import options, the user can click on Load dataset
to import his data. The application will:
- Look for missing date entries (adapted to the time step of the time series) and fill the blanks if necessary
- Interpolate missing discharge values if the user want to
- Apply a daily or hourly mean depending on the user preference and the initial time step
- Display the hydrograph on the import page
It is also possible to use a “test dataset” as demonstrated below.
It is possible to interpolate missing values when importing discharge data:
Max interpolation gap size: define the maximum gap (in days) which will be interpolated with a spline functionKeep NA values: define the behaviour when there are still missing values after the interpolation (even if no interpolation). If checked, the whole time series with missing values will be loaded. If unchecked, only the longest part of the time series without missing values will be loaded
The recession curves analysis tab allows to select recession curves and apply recession model. The recession selection is done with a slider and four buttons:
Select a time interval: define the time interval of the plotZoom: zoom on the plot according to the dimensions of the mouse brushReset: reset the default (full) time intervalAdd: add the selected recession curve (dimensions of the mouse brush) to the KarstID workspace. A recap of the information is displayed in the table belowDelete: delete the selected recession curve in the table from the KarstID workspace
It is possible to save the time series of the selected recession curves
with the Download selected recession button and save the recap table
with the Download table button. It is possible to save and import the
entire KarstID workspace with the Save KarstID recession workspace and
Upload KarstID recession workspace, respectively.
Once the recession curves are saved, they all appear in the table below and can be selected. When selected, the recession model interface is displayed on the right. The workflow is:
- Remove potential perturbations on the recession with the
Remove spikes in the recession curvecheckbox - Click on the plot or enter a number in the
Breakpoint valuenumeric input to define the inflexion point of the Mangin model (Mangin, 1975) - Calculate and retain indicators of functioning with the
Save indicatorsbutton. The indicators appear in the recap table. It is possible to cancel the results withClear selection
The simple correlational and spectral analyses tab allows to visualize the results of these signal analyses proposed by Mangin (1984). The results are calculated automatically once a dataset is imported. It is possible to change the cutting point (in days) with the slider input below the graphs.
The analysis of classified discharges tab allows to visualize the results of the classic approach and the Mangin (1971) approach. The results are calculated automatically once a dataset is imported.
The classification tab can be appreciated in four parts:
- The top left text (i) reminds the values of the indicators, (ii) gives the distance to other classes, and (iii) displays a description of the hydrological functioning of the system according to its class
- The top right flowchart indicates how the system is classified according to the values of the indicators of functioning
- The bottom right table contains the classes and indicators values of 78 karst systems located worldwide. By default, they are ordered by distance to the investigated system
- The bottom left plot shows the investigated system (highlighted in red) alongside the 78 other karst systems. It is possible to select a system in the table to highlight it in yellow on the plot The axis correspond to the three indicators of functioning used for the classification
This work is licensed under a Creative Commons Attribution 4.0 International License
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