Kerry Flux Data

Standardised flux data for the IE-Kil (Killorglin - Glencar) site in Co. Kerry, Ireland collected during the CarboEuropeIP (EU-FP6) (http://carboeurope.org/ceip/) project.

Existing standardised data for IE-Kil for the years 2002-2012 can be downloaded from the European Fluxes Database Cluster.

This repository details steps taken to standardise the remaining data (i.e. 2012-2016) to complete the archive in the European Fluxes Database.

Site details

IE-Kil (Killorglin)

• An Atlantic blanket bog
• Located near Glencar, Co. Kerry, in south-west Ireland
• Latitude: 51.9683611, Longitude: -9.9003056
• Area: ~450 ha
• Lies on sandstone bedrock
• Located in a valley at an elevation 145-170 m above sea level
• Composed of a large central pristine part (~220 ha), surrounded by disturbed peatland areas
• Instruments: Campbell Scientific dataloggers, ...
• Status: ...

Source: Sottocornola (2007)

Variables

The IE-Kil data already archived on the European Fluxes Database Cluster are Level 2 data, i.e. data provided by the PIs, half-hourly, not gap-filled or filtered but quality checked by the PIs. The variables are listed here. They are also listed in a TSV file in the data folder.

Variables for the raw data and flux data are also available in the data folder. These have been compiled from the data headers with additional descriptions from Jaimes (2014) and Cantero et al. (2019). A number of these variables cite Webb et al. (1980).

Variables used in the REddyProc R package are listed in another TSV file and are mapped to AmeriFlux variables.

Raw and flux data formats

The data (DAT) files come from Campbell Scientific dataloggers.

To view a DAT file's contents (first 10 lines), run the following:

sed -n '1,10p' 'filename.dat'

If the DAT file is binary, the output looks something like this:

"TOB3","1541","CR5000","1541","2.3","CPU:3D_LI_EB_DFnew.CR5","52197","2014-12-22 11:34:18"
"ts_data","100 MSEC","1024","57237140","26132","Sec100Usec","           0","   790944810"
"Ux","Uy","Uz","co2","h2o","Ts","press","diag_csat","diag_irga"
"m/s","m/s","m/s","mg/(m^3)","g/(m^3)","C","kPa","unitless","unitless"
"Smp","Smp","Smp","Smp","Smp","Smp","Smp","Smp","Smp"
"IEEE4B","IEEE4B","IEEE4B","IEEE4B","IEEE4B","IEEE4B","IEEE4B","IEEE4B","IEEE4B"
Pd�.�@������:D)�@ݿbA3M�B�$A
`B��󷾩��D)�T@ݟ�A4Z�B�$@�A��      G�?�x�D)��@�v�A6��B�$@���=%�T@.D)��@ݞ�A3�!B�$@�A�����?y�_D)�h@�oA4�B��A��?Ұ!?|��D)��@ޢ�A=7BB��A
�?�`B�p�D*�@�DA1�rB��@��@89Y�� �D*l@�*
                                      A3�B�@��?��ؾ�t�D)�F@���A�B�$@�;e?����|�   D)�(@��mA6��B�1R@��i@J����D)��@�]�A5��B�,k@�fg@���>�SD)�@޷�A2U�B�$@�@G
>��WD)�d@ކ@A4��B�$@�+@V�Ϳ2�!D)�@ޗA2�B�$@ӗ�@����XD)��@�|/A4��B�@|v�?�~���-D)�@ޖ<A3ipB�(�@�hs>D�>�XD)�@ނ�A5�B�:@�%�A��?\I�D)�t@�A3��B�$@��?��D)֎@�d�A3��B�$@�bN?*�=�ȵD)��@�tNA3F�B�$@��>��
                                                                                           C�D)��@߸9A5Y�B�$@���>�o���D)�@�.�A50]B�$@�K�?��>.�D)ܩ@ތVA4��B�$@p�>�?D�kD)��@�,�A5D�B�$@���>�1(>�E�D)�]@�$A3�B�$@����bN?�&�D)�@��

If the DAT file is a text file, the output looks something like this:

"TOA5","2806","CR1000","2806","CR1000.Std.06","CPU:3D_LI_TGA_VNOTDNEW.CR1","21445","ts_data"
"TIMESTAMP","RECORD","Ux","Uy","Uz","co2","h2o","n2o","Ts","press","diag_csat","t_hmp","e_hmp"
"TS","RN","m/s","m/s","m/s","mg/m^3","g/m^3","umol/mol","C","kPa","unitless","C","kPa"
"","","Smp","Smp","Smp","Smp","Smp","Smp","Smp","Smp","Smp","Smp","Smp"
"2014-12-22 11:47:39.3",761139393,1.69375,0.68975,0.8642501,760.738,8.81152,"NAN",12.08542,99.28229,0,11.51643,1.219314
"2014-12-22 11:47:39.4",761139394,1.551,0.1625,1.36275,760.2671,8.790375,"NAN",12.10226,99.24676,0,11.51643,1.220242
"2014-12-22 11:47:39.5",761139395,1.51725,-0.11075,1.74625,760.1978,8.794267,"NAN",12.16629,99.24676,0,11.80331,1.2455
"2014-12-22 11:47:39.6",761139396,1.95925,-0.34375,0.6390001,760.7865,8.813287,"NAN",12.07193,99.24676,0,11.61206,1.227055
"2014-12-22 11:47:39.7",761139397,1.3605,-0.455,1.206,760.8245,8.806199,"NAN",12.12418,99.25624,0,11.70769,1.235777
"2014-12-22 11:47:39.8",761139398,0.5765,-0.9160001,1.22775,760.9031,8.796409,"NAN",12.12582,99.22072,0,11.70769,1.236716

The first header row should tell us the format of the data, e.g. TOA5 or TOB3. Binary data are in the TOB3 (Table Oriented Binary 3) format, while the text-based data are in the TOA5 (Table Oriented ASCII 5) format. Binary data can be viewed and converted into TOA5 by installing the free PC400 software (Windows only; requires admin rights to install) from Campbell Scientific and using the Card Convert utility. More information can be found in this LI-COR EddyPro guide. TOA5 files can be processed just like any other CSV file.

Notebooks

Notebooks demonstrating the methods used can be found here.

Installation

Clone this Git repository:

git clone https://github.com/nmstreethran/kerry-flux-data.git
cd kerry-flux-data

Set-up a Conda virtual environment:

conda env create
conda activate kerry-flux
R -e "IRkernel::installspec()"

Note

On Windows, use R.exe instead of R.

Install R packages:

install.packages("REddyProc")

Further reading

References and links related to this topic can be found in this Zotero library: https://www.zotero.org/groups/4706660/climag/collections/2ITV79EF

Licence

Scripts are licenced under the Apache License, Version 2.0.