Data, scripts and simulations for ProxyOH-[OH] analysis using ATom data and F0AM and AM3 simulations

This dataset provides the simulations and analysis code used in Baublitz et al., An observation-based, reduced-form model for oxidation in the remote marine troposphere, Proceedings of the National Academy of Sciences, 120.

Code, package versions

The code is generally written in Python and saved to a Jupyter Notebook (.ipynb) format, except for the component developing the Bayesian regressions, which is written in R. For improved accessibility, the code has also been printed to PDF format so that it may be readable without requiring access to Jupyter. The code used to create the main text figures is specified in the file names. When the primary focus of a script is to create supplemental figures, the figure names have also been specified in the script file name. The code for creating other supplemental figures is also available in the script corresponding to the section where that figure is referenced. 

The following packages and package versions were used to develop this analysis:

Python (v3.10.0)

anaconda 4.13.0

collections (native to anaconda installation)

datetime

os 

random

jupyter 1.0.0, jupyter-core 4.9.1

matplotlib (visualization) 3.5.1

notebook 6.4.6

numpy 1.21.4

pandas 1.3.4

scipy 1.7.3

seaborn (figure formatting) 0.11.2

The full environment is specified in the YAML file "atom_env.yml." Anaconda users (not tested, potentially restricted to Windows) may load this environment with this file and the following command:

$ conda env create -f atom_env.yml

R  (v4.1.2, includes package parallel)

tidyverse 1.3.1

rjags 4-12

runjags 2.2.0-3

lattice 0.20-45

lme4 1.1-31

loo 2.4.1

ggpubr 0.4.0

matrixStats 0.61.0

Zipped directory contents

The full set of global, hourly AM3 model simulations developed for this project are included in this repository (AM3_hourly_simulations_global_ATom1-4.zip) for reference and potential future application, though they are not used in the code. They are described here (vs listed) and span the dates for each campaign leg and are broken into four variable categories, concentrations and met fields ('stp_conc_v2'), individual reaction rates ('ind_rate'), integrated reaction rates ('all_rate') and deposition velocities or photolysis rates ('dep_jval'). Some of these files include all days in the range, while others include only the days that the campaign took measurements.

In addition, a subset of the AM3 simulations that specifically include variables used in the manuscript analysis that have been sampled along the ATom flight is included, along with the 10 s ATom merge  data (AM3_model_simulations_sampled.zip). This is the file that should be downloaded for reproducing the manuscript in the analysis.

AM3_model_simulations_sampled.zip

atom1_10s_ss_030122.csv

atom2_10s_ss_030122.csv

atom3_10s_ss_030122.csv

atom4_10s_ss_030122.csv

bayes_data.zip

bayes_atom_10s_model_122022.csv

bayes_ats_10s_remNOlsth2sigma_highlogNO_emulate_122022.csv

bayes_ats_10s_remNOlsth2sigma_highlogNO_emulate_allPOH_030723.csv

base/

.Rhistory

atom_jags_010723.R

atom_lmer_model_122122.R

atom_sens_030723.R

dat1_bins.csv

dat1_OH.csv

gelman_list_base.csv

levels.csv

log_pd.csv

model_b0.csv

model_b1.csv

p.fit.csv

p.mu.csv

p.sd.csv

r_prx_ytrue.pkl

rjmt_B0.csv

rjmt_B1.csv

rjmt_proxy.csv

rjmt_y_true.csv

CH4_CO_HCHO_MHP/

.Rhistory

atom_altCH4_CO_HCHO_MHP_031423.R

atom_jags_altCH4_CO_HCHO_MHP_031423.R

dat1_bins.csv

dat1_OH.csv

dat1_proxy_ch4_co_hcho_mhp.csv

levels.csv

log_pd.csv

p.fit.csv

p.mu.csv

p.sd.csv

r_prx_ytrue.pkl

rjmt_B0.csv

rjmt_B1.csv

rjmt_proxy_ch4_co_hcho_mhp.csv

rjmt_y_true.csv

CO_HCHO/

.Rhistory

atom_altCO_HCHO_031423.R

atom_jags_altCO_HCHO_031423.R

dat1_bins.csv

dat1_OH.csv

dat1_proxy_CO_HCHO.csv

levels.csv

r_prx_ytrue.pkl

rjmt_B0.csv

rjmt_B1.csv

rjmt_proxy_co_hcho.csv

rjmt_y_true.csv

CO_HCHO_MHP/

atom_altCO_HCHO_MHP_031423.R

atom_jags_altCO_HCHO_MHP_031423.R

dat1_bins.csv

dat1_OH.csv

dat1_proxy_CO_HCHO_MHP.csv

levels.csv

r_prx_ytrue.pkl

rjmt_B0.csv

rjmt_B1.csv

rjmt_proxy_CO_HCHO_MHP.csv

rjmt_y_true.csv

H2O2_O3_CH4_CO_HCHO_MHP/

.Rhistory

atom_altH2O2_O2_CH4_CO_HCHO_MHP_122122.R

atom_jags_altH2O2_O3_CH4_CO_HCHO_MHP_030723.R

dat1_bins.csv

dat1_OH.csv

dat1_proxy_h2o2_o3_ch4_co_hcho_mhp.csv

levels.csv

r_prx_ytrue.pkl

rjmt_B0.csv

rjmt_B1.csv

rjmt_proxy_h2o2_o3_ch4_co_hcho_mhp.csv

rjmt_y_true.csv

HCHO/

atom_altHCHO_031423.R

atom_jags_altHCHO_031423.R

dat1_bins.csv

dat1_OH.csv

dat1_proxy_HCHO.csv

levels.csv

r_prx_ytrue.pkl

rjmt_B0.csv

rjmt_B1.csv

rjmt_proxy_HCHO.csv

rjmt_y_true.csv

MHP/

atom_altMHP_122122.R

atom_jags_altMHP_122122.R

dat1_bins.csv

dat1_OH.csv

dat1_proxy_MHP.csv

levels.csv

r_prx_ytrue.pkl

rjmt_B0.csv

rjmt_B1.csv

rjmt_proxy_MHP.csv

rjmt_y_true.csv

F0AMv3.2.zip

mean_ratio_OH_loss_bins_oce.npy

mean_ratio_OH_prod_bins_oce.npy

mean_ratio_OH_prod_loss_bins_oce.npy

Data/

atom1/

atom1_output_alt.cs

atom1_output_CO.csv

atom1_output_H2O.csv

atom1_output_lat.csv

atom1_output_lon.csv

atom1_output_lossOH_ppt_lump15.csv

atom1_output_M.csv

atom1_output_NO.csv

atom1_output_OH.csv

atom1_output_prodOH_ppt_lump15.csv

atom1_output_startTime.csv

atom1_output_sza.csv

atom2/

atom2_output_alt.csv

atom2_output_CO.csv

atom2_output_H2O.csv

atom2_output_lat.csv

atom2_output_lon.csv

atom2_output_lossOH_ppt_lump15.csv

atom2_output_M.csv

atom2_output_NO.csv

atom2_output_OH.csv

atom2_output_prodOH_ppt_lump15.csv

atom2_output_startTime.csv

atom2_output_sza.csv

atom3/

atom3_output_alt.csv

atom3_output_CO.csv

atom3_output_H2O.csv

atom3_output_lat.csv

atom3_output_lon.csv

atom3_output_lossOH_ppt_lump15.csv

atom3_output_M.csv

atom3_output_NO.csv

atom3_output_OH.csv

atom3_output_prodOH_ppt_lump15.csv

atom3_output_startTime.csv

atom3_output_sza.csv

atom4/

atom4_output_alt.cs

atom4_output_CO.csv

atom4_output_H2O.csv

atom4_output_lat.cs

atom4_output_lon.cs

atom4_output_lossOH_ppt_lump15.csv

atom4_output_M.csv

atom4_output_NO.csv

atom4_output_OH.csv

atom4_output_prodOH_ppt_lump15.csv

atom4_output_startTime.csv

atom4_output_sza.csv

For any further questions on the model simulations or code included here, please contact the corresponding author (Colleen Baublitz, [e-mail]).