Interactive Shiny application for exploration and QA/QC of eddy covariance data.
Streamlines post-processing of eddy covariance datasets (e.g., after EddyPro) to detect and remove outliers, enforce physical ranges, and generate reproducible R code for AmeriFlux submissions.
Fluxtools is an independent project and is not affiliated with or endorsed by the AmeriFlux Network. “AmeriFlux” is a registered trademark of Lawrence Berkeley National Laboratory and is used here for identification purposes only.
If you use fluxtools in your workflow, please cite:
Key, K. (2025). fluxtools (version 0.5.0) [Computer software]. Zenodo.
https://doi.org/10.5281/zenodo.15597159
- Key Features
- Installation
- Quickstart
- Data Requirements
- How It Works
- Download & Reset
- Vignette & Docs
- Citation
- License
#key-features
-
Interactive scatter
Choose TIMESTAMP_START (time) or any numeric variable for X; choose any numeric variable for Y. Drag a box or lasso to flag points -
Multi-year support
Upload up to ~1GB CSV (all years by default, or select one/more years) -
±σ outlier highlighting
Slider marks points beyond n standard deviations from a linear fit; click Select ±σ outliers to add them -
Accumulate & undo
Add selections to an accumulated list and remove them later if needed Use Apply removals to commit NA changes, and Reload original data to revert -
Physical Range Module (PRM)
Clamp variables to physically reasonable ranges (AmeriFlux Technical Note, Table A1) Out-of-range → NA. QC columns are ignored by PRM by default Undo PRM reverts only PRM-applied changes -
Reproducible outputs
Export a cleaned CSV (removed values set to NA) and an R script with the exact transformations If PRM was applied, a summary table, audit CSV, and a manual replay script are included -
Dark/Light mode
Toggle theme on the fly
#installation
# From CRAN
install.packages("fluxtools")
# Newest version from GitHub
library(devtools)
devtools::install_github("kesondrakey/fluxtools")#quickstart
library(fluxtools)
# Launch the QA/QC Shiny app
run_fluxtools()#data-requirements
- Input: AmeriFlux BASE (or Fluxnet) CSV
- Must include TIMESTAMP_START (e.g., YYYYMMDDHHMM for 30-min or hourly data)
- Missing values like -9999 are treated as NA
#how-it-works Timestamp Parsing & Time Zones #timestamp-parsing--time-zones
- TIMESTAMP_START is parsed automatically
- Viewer can display times with a fixed UTC±offset (no DST)
- Selections, code, and exports are keyed to the original timestamp string. Underlying values and exported timestamps are preserved
Interactive QC & Selection #interactive-qc--selection
- Box or lasso to select points
- Click Flag Data to add selected points to the accumulated removal set
- Click Unflag Data or Clear Selection to remove from the current set
- Click Apply removals to set Y-values to NA_real_ (not reversible except through Reload original data)
Outlier Detection #outlier-detection
- Fit a simple linear model between X and Y, compute residuals, and highlight points exceeding ±σ (user-controlled)
- Select all ±σ outliers to add them to your accumulated code; clear ±σ outliers if needed
Time Slider (Inside / Outside) #time-slider-inside--outside
- Adjustable time window on TIMESTAMP_START
- Flag inside: add only points within the chosen time range
- Flag outside: add all points except those within the chosen range
- The slider snaps to your data cadence (30 min / 60 min) and supports multi-year files
Manual Range Filters #manual-range-filters
- Define custom min/max for any variable
- Flag values outside range to add out-of-bounds points to the accumulated set
- Complements PRM by allowing site- or project-specific thresholds
Physical Range Module (PRM) #physical-range-module-prm'
- Available in the app or through fluxtools directly in R
- Applies canonical physical bounds to variables (e.g., SWC, P, TA, CO2) using name-family matching (e.g., ^SWC($|_).)
- Example: the "SWC" family refers to all variables starting with SWC (e.g., SWC_1_1_1, SWC_2_1_3)
- Out-of-range values are set to NA and summarized with counts and percentages replaced
- Apply to all variables or limit to selected families
- Undo PRM reverts only the last PRM operation.
Example:
# View PRM rule table
get_prm_rules()
# Apply to all present families
res <- apply_prm(df)
res$data # clamped data
res$summary # per-column stats (min, max, n_replaced, pct_replaced)
# Apply to selected families
res2 <- apply_prm(df, include = c("SWC", "P"))PRM ranges (and name) were sourced from Ameriflux
Code Generation & Copy-All #code-generation--copy-all
- The app continuously builds tidy dplyr code that sets selected Y-values to NA via case_when()
- Switch between Current and Accumulated snippets; click Copy code to paste into your own scripts and version control
-
Export cleaned data: downloads a ZIP containing
-
raw_df.csv (original upload, unchanged)
-
fluxtools_processed_df_.csv (cleaned, NA applied)
-
fluxtools_removal_script.R (replays removals)
-
If PRM was applied:
-
prm_summary.csv (bounds + replacements)
-
prm_removed_values.csv (audit of values removed)
-
manual_prm_removed.R (cell-level replay)
-
Reload original data: restores the initial CSV to start over
browseVignettes("fluxtools")
# or
vignette("introduction", package = "fluxtools")If you use fluxtools in publications, please cite:
Key, K. (2025). fluxtools (version 0.4.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.15597159
This package is free software, released under the GNU General Public License v3 (GPL-3). See the LICENSE file for details.
Fluxtools is an independent project and is not affiliated with or endorsed by the AmeriFlux Network. “AmeriFlux” is a registered trademark of Lawrence Berkeley National Laboratory and is used here for identification purposes only.