README

Tyler Hampton 2020-02-14

Intro

This R Markdown README file accompanies Hampton et al. (2020): Experimental shifts of hydrologic residence time in a sandy urban stream sediment-water interface alter nitrate removal and nitrous oxide fluxes

Corresponding Author Information: Tyler B. Hampton Email: tyler.hampton@uwaterloo.ca; ORCID: https://orcid.org/0000-0003-1087-2059

This document details the scripts and data accompanying this Rproject

Scripts

r list.files(pattern=".R")

## [1] "README.Rmd"                          
## [2] "SawmillBrook_dataanalysis_20200214.R"
## [3] "SawmillBrook_paperfigures_20200214.R"
## [4] "SawmillBrook_Rproj.Rproj"

“SawmillBrook_dataanalysis_20200214.R” This is the primary script accompanying this publication. Running it in its entirety will process all the raw data, create figures in the figures folder and write all datasets to the outdata folder.

“SawmillBrook_dataanalysis_20200214.R” This script is called by dataanalysis and processes the input data for a given subset of parameters.

Input Files

r list.files(path="input")

## [1] "otherstudiesDENrates.csv"  "otherstudiesDENrates.xlsx"
## [3] "SawB_rawdata.csv"          "SawB_timedata.csv"        
## [5] "SMBcaption.png"

“SMBcaption.png”
A PNG file that serves as a caption for all plots

“otherstudiesDENrates.csv” This data accompanies Figure 9. The columns are:

• study: A shortened name of the study. See the manuscript for paper citations

• Denrate: Areal denitrification rates from the study, all units are (\mu)mol m^-2 hr^-1

“otherstudiesDENrates.xlsx” This xlsx file contains the same data in the csv sorted by study, including calculations to convert study units to the units used in the csv file

“SawB_timedata.csv” This csv contains the fluid residence times (in hours) measured at each sediment depth (0,5,10,15,20 cm) for each experiment. The columns are:

• Exp: a text string with the experiment flux rate appended with the ring, so 3 m/d US is for the short residence time experiment in ring US

• Depth [cm]: the sediment depth in centimeters

• time [hr]: the fluid residence time in hours

“SawB_rawdata.csv” This csv file contains all the chemical concentrations used in this study. Though the data are from different sources or instruments, see methods section of paper, they are all sorted by individual sample. The columns are:

• Flux.Ring: a text string with the experiment flux rate appended with the ring, so 3 m/d US is for the short residence time experiment in ring US. Same as “Exp” column for “SawB_timedata.csv”

• Depth.cm.: the sediment depth in centimeters

• Time.hours.: the fluid residence time in hours

• XsampleN2: measured ¹⁵N atom percent (15/(15+14)) in N₂ gas from solution

• XsampleN2O: measured ¹⁵N atom percent (15/(15+14)) in N₂O gas from solution

• XsampleNO3: measured ¹⁵N atom percent (15/(15+14)) in NO₃ in solution

• d15N2: measured del ¹⁵N enrichment in N₂ gas from solution

• N2.uM: concentration of N₂ gas in porewater, in (\mu)mol N L^-1. See methods for calculation in Hampton MS Thesis: https://d.lib.msu.edu/etd/16393

• N2O.uM: concentration of N₂O gas in porewater, in (\mu)mol N L^-1. See methods for calculation in Hampton MS Thesis

• N2x15N2: concentration of N₂ gas in porewater multiplied by XsampleN2, in (\mu)mol N L^-1

• N2Ox15N2O: concentration of N₂O gas in porewater multiplied by XsampleN2O, in (\mu)mol N L^-1

• NO3.uM: concentration of NO₃ in solution in (\mu)mol N L^-1

• NO3x15NO3: concentration of NO\~3 in porewater multiplied by XsampleNO3, in (\mu)mol N L^-1

• O2.uM: concentration of dissolved O₂ in porewater, in in (\mu)mol O2 L^-1

• C.uM: concentration of dissolved organic carbon (DOC) in porewater, in in (\mu)mol C L^-1

Output Files

r list.files(path="outdata")

## [1] "publish_means2.csv"    "publish_Ratesk.csv"    "publish_RatesU.csv"   
## [4] "SawB_means.csv"        "SawB_N2Oexport.csv"    "SawB_uptakewhole.csv" 
## [7] "SawB_uptakewholeK.csv" "TableSM1.csv"          "TableSM2.csv"

“TableSM1.csv” This csv file contains the data from Supplementary Materials Table 1, showing sediment percent sand and organic carbon with depth for the two rings.

“TableSM2.csv” This csv file contains reaction rates as k and U from the experiments, rounded with error estimates in parentheses next to each measurement.

“SawB_means.csv” This csv file contains mean concentrations and standard deviation for each chemical, per experiment and depth. Columns are the same as for “SawB_rawdata.csv” except for column “type”.

• type: one of “M” or “sd” for mean or standard deviation.

“publish_means2.csv” This csv is the same as “SawB_means.csv” but means are rounded and grouped with standard deviation in parentheses

“SawB_uptakewhole.csv” This csv file contains reaction rates (U) summarized in TableSM2, tall format Columns:

• chem: one of the chemical columns from “SawB_rawdata.csv”, specifying the reaction rates for that species.

• plot: the reaction rate, in (\mu)mol m^-2 hr^-1

• err: the reaction rate standard error, in (\mu)mol m^-2 hr^-1

“SawB_uptakewholeK.csv” This csv file contains reaction rates (k) summarized in TableSM2, tall format

“SawB_N2Oexport.csv” This csv contains the output data summarized for N₂O in TableSM2 Columns:

• N2O.umold: the concentration of N₂O multiplied by the flux rate, units are (\mu)mol d^-1

• N2O.umold.stdev: the standard deviation of N₂O concentrations, multiplied by the flux rate, units are (\mu)mol d^-1

• print: the rounded values shown in TableSM2, derived from the prior two columns

“publish_RatesU.csv” This csv file contains rounded reaction rates with error (U) summarized in TableSM2, wide format

“publish_Ratesk.csv” This csv file contains rounded reaction rates with error (k) summarized in TableSM2, wide format