Carbon Dioxide (CO₂) Fluxes from Terrestrial and Aquatic Environments in a High-Altitude Tropical Catchment

Authors: Chloe L. Schneider*, Maribel Herrera*, Megan L. Raisle*, Andrew R. Murray, Keridwen M. Whitmore, Andrea C. Encalada, Esteban Suárez, and Diego A. Riveros-Iregui

*These authors contributed equally to this work.

This repository serves to host data and analyses used in the research supporting the work in Carbon Dioxide (CO₂) Fluxes from Terrestrial and Aquatic Environments in a Tropical Alpine Catchment, submitted to Journal of Geophysical Research - Biogeosciences.

Purpose

To provide access to the data and make analyses reproducible for others. All figures presented in the paper were created using R statistical software. All scripts and data files for creating our figures are provided within this repository. If you have Rstudio installed on your computer, you should be able to 'fork' this repository and run it on your local computer to reproduce the anlayses in this paper without any alterations.

Instructions to run this code

This code was written and run with R version 3.6.2 and R Studio version 1.2.5001. You can fork or simply download this repository to your local computer and open the project file Schneider_et_al_2020.Rproj. We use the here package to ensure that the code will run on any computer without having to change any file paths.

Guide to Folders

Data

• File name: All_Stream_Data.csv

these data are used to create figures 2 & 4

Column Name	Description
DateTime	Date and Time of collection
Inj	denotes if data was collected during injection of CO2 gas
V1	raw partial pressure of CO2 at Station 1 (ppm)
V2	raw partial pressure of CO2 at Station 2 (ppm)
V3	raw partial pressure of CO2 at Station 3 (ppm)
V4	raw partial pressure of CO2 at Station 4 (ppm)
Turbidity_NTU	Turbidity (NTU)
Phycocyanin_ppb	Chlorophylla (ug.L)
CDOM_ppb	Colored Dissolved Organic Matter [parts per billion]
Flux_1	Carbon dioxide flux, unit no 1 (umole per m^2 per sec)
Temp_C_1	Temperature [Celsius] at station 1
Flux_2	Carbon dioxide flux, unit no 2 (umole per m^2 per sec)
Temp_C_2	Temperature [Celsius] at station 2
tempC_425	Temperature (C) at station:
tempC_430	Temperature (C) at station:
tempC_435	Temperature (C) at station:
tempC_436	Temperature (C) at station:
tempC_437	Temperature (C) at station:
tempC_442	Temperature (C) at station:
airTemp_c	Air Temperature (c)
EC1_uS	conductivity at station 1 (uS)
EC2_uS	conductivity at station 2 (uS)
DO1_mg.L	Dissolved Oxygen at station 1 (mg/l)
DO2_mg.L	Dissolved Oxygen at station 2 (mg/l)
DO4_mg.L	Dissolved Oxygen at station 4 (mg/l)
ppt24Tot	24-hour total precipitation [mm]
ppt48Tot	48-hour total precipitation [mm]
ppt72Tot	72-hour total precipitation [mm]
lvl_421_m	Corrected Water Level- Station 3 in meters
lvl_425_m	Corrected Water Level- Sensor 425 in meters
lvl_430_m	Corrected Water Level- Sensor 430 in meters
lvl_435_m	Corrected Water Level- Sensor 435 in meters
lvl_436_m	Corrected Water Level- Station 1 in meters
lvl_437_m	Corrected Water Level- Sensor 437 in meters
lvl_442_m	Corrected Water Level- Sensor 442 in meters
stn1_Q	Discharge at station 1 (m3s-1)
stn2_Q	Discharge at station 2 (m3s-1)
stn3_Q	Discharge at station 3 (m3s-1)
stn4_Q	Discharge at station 4 (m3s-1)
air_pressure_kPa	Air pressure (kPa)
tempC_421	Water Tempperature [C] at station 3
V1_adjusted	partial pressure of CO2 adjusted for temperature and pressure at Station 1 (ppm)
V3_adjusted	partial pressure of CO2 adjusted for temperature and pressure at Station 3 (ppm)
V4_adjusted	partial pressure of CO2 adjusted for temperature and pressure at Station 4 (ppm)
V2_adjusted	partial pressure of CO2 adjusted for temperature and pressure at Station 2 (ppm)
V1_CO2_mgC.L	mass equivalence of CO2 at Station 1 (mg/l)
V2_CO2_mgC.L	mass equivalence of CO2 at Station 2 (mg/l)
V3_CO2_mgC.L	mass equivalence of CO2 at Station 3 (mg/l)
V4_CO2_mgC.L	mass equivalence of CO2 at Station 4 (mg/l)
Flux_1_cleaned	Instantaneous flux [µmol m2s-1] between station 1 & 2

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sub folder: "Vaisala"

• File: "synoptics2.csv"

these data are used to create figure 8

Column Name	Description
Distance	distance from the outlet of the wetland (meters)
Syn1_071819	Carbon dioxide partial pressure (ppm) collected on 2019-07-18
Syn2_072519	Carbon dioxide partial pressure (ppm) collected on 2019-07-25
Syn3_072919	Carbon dioxide partial pressure (ppm) collected on 2019-07-29
Syn4_073119	Carbon dioxide partial pressure (ppm) collected on 2019-07-31
Syn5_080619	Carbon dioxide partial pressure (ppm) collected on 2019-08-06
Syn6_081219	Carbon dioxide partial pressure (ppm) collected on 2019-08-12

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sub folder: "EosFD"

• File: "All_Synoptic_Flux_Data.csv"

*these data are used to create figure *

Column Name	Description
Eos#	EosFd unit no.
Date	date of collection
Flux	Carbon dioxide flux (umole per m^2 per sec)
Distance From 35	distance from the outlet of the wetland (meters)
Syn7-18	synoptic site number, collection date July 18th
Syn7-25	synoptic site number, collection date July 25th
Syn7-31	synoptic site number, collection date July 31th
Syn8-6	synoptic site number, collection date August 6th
Syn8-12	synoptic site number, collection date August 12th

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• Files:
  "eos2_07182019.csv" CO₂ evasion data from soil collected on 2019-07-18 using EosFD no 2
  "eos2_07222019.csv" CO₂ evasion data from soil collected on 2019-07-22 using EosFD no 2
  "eos2_07292019.csv" CO₂ evasion data from soil collected on 2019-07-29 using EosFD no 2
  "eos2_07312019.csv" CO₂ evasion data from soil collected on 2019-07-31 using EosFD no 2
  "eos2_08012019.csv" CO₂ evasion data from soil collected on 2019-08-12 using EosFD no 2
  "eos1_08132019.1.csv" CO₂ evasion data from soil collected on 2019-08-13 using EosFD no 1
  "eos2_08142019.csv" CO₂ evasion data from soil collected on 2019-08-14 using EosFD no 2
  these data are used to create figures 3 & 5

  Column Name	Description
  Month	Month of collection
  Day	Day of collection
  Year	Year of collection
  Time	Time of collection
  Flux	Carbon dioxide flux (umole per m^2 per sec)
  Temperature (C)	soil temerature (celcius)
  CO2 Soil (ppm)	Partial pressure of carbon dioxide in soil / water (ppm)
  CO2 Soil STD (ppm)	standard deviation of carbon dioxide in soil / water (ppm)
  CO2 ATM (ppm)	Atmospheric CO2
  CO2 ATM STD (ppm)	Standard deviation of atmospheric CO2
  Mode	Mode flag for eosFD

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• File: "eos1_FIX_07312019.csv

these data are used to create figures 3 & 5

Column Name	Description
DateTime	Date and time of collection
Flux_1	Carbon dioxide flux (umole per m^2 per sec)
CO2_Soil_1	Partial pressure of carbon dioxide in soil / water (ppm)
CO2_Soil_STD_1	standard deviation of carbon dioxide in soil / water (ppm)
CO2_ATM_1	Atmospheric CO2
CO2_ATM_STD_1	Standard deviation of atmospheric CO2
Mode_1	Mode flag for eosFD

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sub folder: "picarro"

• File:

"col1statistics.csv"
"col2statistics.csv"
"col3statistics.csv"
"col4statistics.csv"
"col5statistics.csv"
"col6statistics.csv"
"col7statistics.csv"
"col8statistics.csv"

these data were used to create figure 7

Column Name	Description
Sample	collar number/name
day	day of collection
CorrectedAverage	average value for the collar with the linearity correction
StdDev_iCO2	standard deviation of all the values that went into making the average
CV	coefficient of variation
RelativeStdDev	relative standard deviation (%)

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• File: "synoptics.csv"

these data were used to create figure 6

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figures

File Name	Type	Description
figure_02.pdf	pdf	Figure 2
figure_03.pdf	pdf	Figure 3
figure_04.pdf	pdf	Figure 4
figure_05a.pdf	pdf	Figure 5 a
figure_05b.pdf	pdf	Figure 5 b
figure_06.pdf	pdf	Figure 6
figure_07.pdf	pdf	Figure 7
figure_08.pdf	pdf	Figure 8

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scripts

File Name	Type	Description
figure_02.R	R code	figure 3
figure_03.Rmd	R markdown	figure 3
figure_03.html	html	figure 3 image rendered in html
figure_04.R	R code	figure 04
figure_05.R	R code	figure 04
figure_06.R	R code	figure 07
figure_07.R	R code	figure 07
figure_08.R	R code	figure 08

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Points of contact

Direct questions about the paper to Dr. Diego Riveros-Iregui: [email protected]

Direct questions about the code to:

Andrew Murray: [email protected]

or

Kriddie Whitmore: [email protected]