Data and code from: Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints
Data files
Feb 04, 2020 version files 1.33 MB
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dataset_for_marine_TPC_MCMCglmms.csv
116.86 KB
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dataset_for_TPC_MCMCglmms.csv
40.36 KB
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dataset_of_B0_B_pk_and_cell_volume.csv
25.20 KB
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final_calibrated_tree.phy
27.97 KB
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growth_rate_dataset.csv
927.05 KB
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Lagrangian_trajectory_simulation.py
6.08 KB
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ReadMe.txt
1.86 KB
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run_B_0_or_B_pk_against_cell_volume_MCMCglmms.R
9.73 KB
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run_marine_TPC_MCMCglmms.R
146.51 KB
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run_TPC_MCMCglmms.R
7.16 KB
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TPC_fitting.py
19.69 KB
Abstract
Usage notes
CONTENTS OF THIS DATASET
Data files:
1) growth_rate_dataset.csv
Phytoplankton growth rate vs temperature measurements, extracted
from the literature.
2) final_calibrated_tree.phy
The relative time-calibrated phylogeny reconstructed for this
study.
3) dataset_for_TPC_MCMCglmms.csv
Reliable TPC parameter estimates (along with measures of
uncertainty), latitude/longitude values, and habitat (marine or
freshwater) for all phytoplankton strains of this study.
4) dataset_for_marine_TPC_MCMCglmms.csv
As above, but only for marine strains. Besides lat/lon values,
this dataset also includes temperature data (from Lagrangian
simulations and from the NOAA OISST dataset) for each isolation
location.
5) dataset_of_B_0_B_pk_and_cell_volume.csv
B_0 and B_pk estimates for all phytoplankton along with cell
volume measurements in units of cubic meters.
Source code:
1) TPC_fitting.py
Python 2 script for fitting the 4-parameter variant of the
Sharpe-Schoolfield model to the data in growth_rate_dataset.csv.
2) Lagrangian_trajectory_simulation.py
Python 2 script for simulating backwards-in-time Lagrangian
trajectories of drifting particles (marine phytoplankton) from a
list of latide/longitude locations.
3) run_TPC_MCMCglmms.R
R script for fitting regression models to the entire TPC dataset
with all TPC parameters forming a combined response.
4) run_marine_TPC_MCMCglmms.R
R script for fitting regression models to the TPC dataset of
marine phytoplankton only.
5) run_B_0_or_B_pk_against_cell_volume_MCMCglmms.R
R script for estimating the influence of cell volume on B_0 or
B_pk values.