This repository contains code associated with the manuscript Venolia et al. (in press). Any questions about this code or data should be directed towards Celeste Venolia ([email protected]) and Austin Humphries ([email protected]).
Code files key:
KelpDEB_Run.R: The runfile for the Kelp DEB model which contains most of the plot codes.
KelpDEB_model.R: The Kelp DEB model turned into a function using the R package deSolve.
SolveR_R.R: The Newton-Raphson solver for the net specific growth rate (r) in the Kelp DEB model.
Photosynthesis_Calibration.R: Function code used to calibrate the photosynthesis parameters for the Kelp DEB model.
N_uptake_Calibration.R: Function code used to calibrate the N parameters for the Kelp DEB model.
SensitivityAnalyses_FME.R: Function code and run code for sensitivity analysis of the Kelp DEB parameters using the R package FME.
Field data key:
Dredge_Y1_hobo.csv: Temperature data for Dredge (Pt Judith Pond S) in 2017-2018
Dredge_Y2_HoboTempLight.csv: Temperature data for Dredge (Pt Judith Pond S) in 2018-2019
RomePoint_Y1_hobotemp.csv: Temperature data for Rome Pt (Narragansett Bay S) in 2017-2018
RomePt_Y2_HoboTempLight.csv: Temperature data for Rome Pt (Narragansett Bay S) in 2018-2019
Sled_Y1_TempLogger2.csv: Temperature data for Sled (Pt Judith Pond N) in 2017-2018
Sled_Y2_HoboLightTemp.csv: Temperature data for Sled (Pt Judith Pond N) in 2018-2019
WaterSampleAnalysis2Y1.csv: Nitrate and nitrite concentration from all sites in 2017-2018
WaterSamplesY2.csv: Nitrate and nitrite concentration from all sites in 2018-2019
Wickford_Y1_hobo.csv: Temperature data for Wickford (Narragansett Bay N) in 2017-2018
Wickford_Y2_HoboLightTemp.csv: Temperature data for Wickford (Narragansett Bay N) in 2018-2019
Year1kelpdata.csv: Kelp blade length growth from all sites in 2017-2018
Year2kelpdata.csv: Kelp blade length growth from all sites in 2018-2019
Literature data key: for references see Venolia et al. (in press)
BrentonPoint_Segarra2002CarbonData.csv: Dissolved inorganic carbon concentration used for Narragansett Bay sites (Segarra, 2002)
EspinozaChapman1983_Nuptake_9C_StMargaretsBay.csv: Nitrate uptake data for kelp from St Margarets Bay with an experimental temperature of 9 degrees C from Espinoza and Chapman (1983)
EspinozaChapman1983_Nuptake_18C_StMargaretsBay.csv: Nitrate uptake data for kelp from St Margarets Bay with an experimental temperature of 18 degrees C from Espinoza and Chapman (1983)
Johansson2002.csv: Oxygen production rate for kelp from Johansson and Snoeijs (2002)
Ninigret_EPA_DIC.csv: Dissolved inorganic carbon concentration used for Pt Judith sites (J. Grear, unpublished data)
NOAASurfaceIrradiance.csv: radiative forcing from the North American Regional Reanalysis (Mesinger et al., 2006) used to estimate photosynthetically active radiation