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

authors in italics contributed equally to this work.

This repository serves to host data and analyses used in the research supporting the work in:

Schneider, Chloe L., et al. "Carbon dioxide (CO₂) fluxes from terrestrial and aquatic environments in a high‐altitude tropical catchment." Journal of Geophysical Research: Biogeosciences 125.8 (2020): e2020JG005844.

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 use this repository 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: diegori@email.unc.edu

Direct questions about the code to:

Andrew Murray: armurray@live.unc.edu

or

Kriddie Whitmore: kriddie@email.unc.edu