dylanhmorris/sars-cov-2-temp-humidity-1.0.zip
dylanhmorris-sars-cov-2-temp-humidity-d80dd01
.gitignore
758 Bytes
LICENSE.txt
1.9 kB
Makefile
26.1 kB
README.md
9.2 kB
dat
bibliography.bib
37.8 kB
cleaned
dmem-evaporation-data.csv
33.7 kB
literature-data.csv
38.7 kB
plastic-data.csv
1.3 MB
sars-mers-data.csv
283.9 kB
figure-prisma.pdf
22.3 kB
raw
dmem-evap-endpoints.csv
354 Bytes
dmem-evaporation-data.csv
8.3 kB
literature-data.csv
313.1 kB
th-data.csv
7.4 MB
schematic-icons
effloresced-droplet.png
197.6 kB
evaporating-droplet.png
366.5 kB
large-droplet.png
319.0 kB
small-droplet.png
254.7 kB
ms
bibliography.bib
37.8 kB
figures
figure-compare-activation-energies.pdf
40.8 kB
figure-concentration-factor-mech.pdf
52.8 kB
figure-concentration-factor-model.pdf
53.1 kB
figure-evaporation.pdf
600.1 kB
figure-extrapolation.pdf
389.2 kB
figure-halflives-compare.pdf
295.1 kB
figure-halflives-schematic.pdf
774.5 kB
figure-mechanistic-evaporation-evap-phase-fit.pdf
639.7 kB
figure-mechanistic-evaporation-modeled-evap-phase-fit.pdf
642.4 kB
figure-mechanistic-evaporation-modeled-qe-fit.pdf
1.7 MB
figure-mechanistic-evaporation-qe-fit.pdf
1.7 MB
figure-mechanistic-two-regime-meas-conc-evap-phase-fit.pdf
640.9 kB
figure-mechanistic-two-regime-meas-conc-qe-fit.pdf
1.7 MB
figure-mechanistic-two-regime-mod-conc-evap-phase-fit.pdf
640.0 kB
figure-mechanistic-two-regime-mod-conc-qe-fit.pdf
1.7 MB
figure-parameters.pdf
41.1 kB
figure-plastic-evap-phase-fit.pdf
823.2 kB
figure-plastic-qe-fit.pdf
1.7 MB
figure-predict-literature.pdf
523.7 kB
figure-prisma.pdf
22.3 kB
figure-sars-mers-regression.pdf
559.5 kB
posterior-checks
figure-evap-phase-mechanistic-evaporation-modeled-posterior-check.pdf
141.2 kB
figure-evap-phase-mechanistic-evaporation-posterior-check.pdf
141.4 kB
figure-evap-phase-mechanistic-two-regime-meas-conc-posterior-check.pdf
142.0 kB
figure-evap-phase-mechanistic-two-regime-mod-conc-posterior-check.pdf
141.4 kB
figure-evap-phase-plastic-posterior-check.pdf
140.2 kB
figure-evap-phase-sars-mers-posterior-check.pdf
34.2 kB
figure-literature-posterior-check.pdf
987.3 kB
figure-mechanistic-evaporation-modeled-posterior-check.pdf
253.8 kB
figure-mechanistic-evaporation-posterior-check.pdf
250.6 kB
figure-mechanistic-two-regime-meas-conc-posterior-check.pdf
246.8 kB
figure-mechanistic-two-regime-mod-conc-posterior-check.pdf
252.7 kB
figure-plastic-posterior-check.pdf
249.3 kB
figure-sars-mers-posterior-check.pdf
85.2 kB
prior-checks
figure-evap-phase-mechanistic-evaporation-modeled-prior-check.pdf
135.4 kB
figure-evap-phase-mechanistic-evaporation-prior-check.pdf
135.6 kB
figure-evap-phase-mechanistic-two-regime-meas-conc-prior-check.pdf
135.6 kB
figure-evap-phase-mechanistic-two-regime-mod-conc-prior-check.pdf
135.3 kB
figure-evap-phase-plastic-prior-check.pdf
124.0 kB
figure-evap-phase-sars-mers-prior-check.pdf
34.2 kB
figure-inferred-plastic-titers-prior-check.pdf
366.3 kB
figure-inferred-sars-mers-titers-prior-check.pdf
50.6 kB
figure-literature-prior-check.pdf
337.1 kB
figure-mechanistic-evaporation-modeled-prior-check.pdf
138.8 kB
figure-mechanistic-evaporation-prior-check.pdf
138.0 kB
figure-mechanistic-two-regime-meas-conc-prior-check.pdf
138.6 kB
figure-mechanistic-two-regime-mod-conc-prior-check.pdf
138.5 kB
figure-plastic-prior-check.pdf
72.2 kB
figure-sars-mers-prior-check.pdf
19.9 kB
macros
macros-energy-comparison.sty
312 Bytes
macros-infer-hyperparams.sty
106 Bytes
macros-literature-hyperparams.sty
202 Bytes
macros-meas-parameters.sty
144 Bytes
macros-mod-parameters.sty
141 Bytes
macros-plastic-halflives.sty
2.2 kB
macros-plastic-hyperparams.sty
1.3 kB
macros-sars-mers-halflives.sty
369 Bytes
tables
table-absolute-predictions.csv
4.6 kB
table-literature-halflives.tex
6.3 kB
table-meas-parameters.tex
912 Bytes
table-mod-parameters.tex
918 Bytes
table-plastic-halflives.tex
1.1 kB
table-relative-predictions.csv
5.8 kB
table-sars-mers-halflives.tex
847 Bytes
out
chain_diagnostics.csv
2.4 kB
figures
figure-compare-activation-energies.pdf
40.8 kB
figure-concentration-factor-mech.pdf
52.8 kB
figure-concentration-factor-model.pdf
53.1 kB
figure-evaporation.pdf
600.1 kB
figure-extrapolation.pdf
389.2 kB
figure-halflives-compare.pdf
295.1 kB
figure-halflives-schematic.pdf
774.5 kB
figure-mechanistic-evaporation-evap-phase-fit.pdf
639.7 kB
figure-mechanistic-evaporation-modeled-evap-phase-fit.pdf
642.4 kB
figure-mechanistic-evaporation-modeled-qe-fit.pdf
1.7 MB
figure-mechanistic-evaporation-qe-fit.pdf
1.7 MB
figure-mechanistic-two-regime-meas-conc-evap-phase-fit.pdf
640.9 kB
figure-mechanistic-two-regime-meas-conc-qe-fit.pdf
1.7 MB
figure-mechanistic-two-regime-mod-conc-evap-phase-fit.pdf
640.0 kB
figure-mechanistic-two-regime-mod-conc-qe-fit.pdf
1.7 MB
figure-parameters.pdf
41.1 kB
figure-plastic-evap-phase-fit.pdf
823.2 kB
figure-plastic-qe-fit.pdf
1.7 MB
figure-predict-literature.pdf
523.7 kB
figure-prisma.pdf
22.3 kB
figure-sars-mers-regression.pdf
559.5 kB
posterior-checks
figure-evap-phase-mechanistic-evaporation-modeled-posterior-check.pdf
141.2 kB
figure-evap-phase-mechanistic-evaporation-posterior-check.pdf
141.4 kB
figure-evap-phase-mechanistic-two-regime-meas-conc-posterior-check.pdf
142.0 kB
figure-evap-phase-mechanistic-two-regime-mod-conc-posterior-check.pdf
141.4 kB
figure-evap-phase-plastic-posterior-check.pdf
140.2 kB
figure-evap-phase-sars-mers-posterior-check.pdf
34.2 kB
figure-literature-posterior-check.pdf
987.3 kB
figure-mechanistic-evaporation-modeled-posterior-check.pdf
253.8 kB
figure-mechanistic-evaporation-posterior-check.pdf
250.6 kB
figure-mechanistic-two-regime-meas-conc-posterior-check.pdf
246.8 kB
figure-mechanistic-two-regime-mod-conc-posterior-check.pdf
252.7 kB
figure-plastic-posterior-check.pdf
249.3 kB
figure-sars-mers-posterior-check.pdf
85.2 kB
prior-checks
figure-evap-phase-mechanistic-evaporation-modeled-prior-check.pdf
135.4 kB
figure-evap-phase-mechanistic-evaporation-prior-check.pdf
135.6 kB
figure-evap-phase-mechanistic-two-regime-meas-conc-prior-check.pdf
135.6 kB
figure-evap-phase-mechanistic-two-regime-mod-conc-prior-check.pdf
135.3 kB
figure-evap-phase-plastic-prior-check.pdf
124.0 kB
figure-evap-phase-sars-mers-prior-check.pdf
34.2 kB
figure-inferred-plastic-titers-prior-check.pdf
366.3 kB
figure-inferred-sars-mers-titers-prior-check.pdf
50.6 kB
figure-literature-prior-check.pdf
337.1 kB
figure-mechanistic-evaporation-modeled-prior-check.pdf
138.8 kB
figure-mechanistic-evaporation-prior-check.pdf
138.0 kB
figure-mechanistic-two-regime-meas-conc-prior-check.pdf
138.6 kB
figure-mechanistic-two-regime-mod-conc-prior-check.pdf
138.5 kB
figure-plastic-prior-check.pdf
72.2 kB
figure-sars-mers-prior-check.pdf
19.9 kB
tables
table-absolute-predictions.csv
4.6 kB
table-literature-halflives.tex
6.3 kB
table-meas-parameters.tex
912 Bytes
table-mod-parameters.tex
918 Bytes
table-plastic-halflives.tex
1.1 kB
table-relative-predictions.csv
5.8 kB
table-sars-mers-halflives.tex
847 Bytes
src
chain_diagnostics.R
2.9 kB
cleaning
clean-dmem-evap-data.R
2.1 kB
clean-excel-metadata.R
9.2 kB
clean-literature-data.R
4.3 kB
clean-plastic-data.R
3.8 kB
figures
figure-compare-activation-energies.R
5.0 kB
figure-concentration-factor.R
5.5 kB
figure-evaporation.R
4.1 kB
figure-extrapolation.R
28.1 kB
figure-halflives-compare.R
7.4 kB
figure-halflives-schematic.R
24.0 kB
figure-inference-predictive-check.R
6.0 kB
figure-literature-predictive-check.R
5.0 kB
figure-parameters.R
4.5 kB
figure-predict-literature.R
12.6 kB
figure-prediction-error.R
9.4 kB
figure-predictive-check.R
7.5 kB
figure-regression.R
11.2 kB
figure-sars-mers-regression.R
6.3 kB
fitting
fit_literature_model.R
3.7 kB
fit_plastic_evap_model.R
6.1 kB
fit_plastic_model.R
4.3 kB
install_needed_packages.R
1.4 kB
parameters
infer_hyperparams.R
478 Bytes
literature_hyperparams.R
502 Bytes
make-parameter-macros.R
1.4 kB
plastic_hyperparams.R
1.5 kB
stan
evaporation_rate
evaporation_rate_data.stan
849 Bytes
evaporation_rate_functions.stan
298 Bytes
evaporation_rate_model.stan
580 Bytes
evaporation_rate_parameters.stan
127 Bytes
evaporation_rate_transformed_data.stan
69 Bytes
evaporation_rate_transformed_parameters.stan
92 Bytes
evaporation_rate.stan
474 Bytes
functions
poisson_single_hit.stan
612 Bytes
general
flags.stan
36 Bytes
temp_humidity_data.stan
97 Bytes
well_data.stan
488 Bytes
well_observation_process.stan
248 Bytes
halflife
calculate_halflife_transformed_parameters.stan
47 Bytes
calculate_halflife_transient_transformed_parameters.stan
208 Bytes
halflife_data.stan
62 Bytes
halflife_parameters.stan
43 Bytes
halflife_priors.stan
87 Bytes
halflife_transformed_parameters.stan
36 Bytes
halflife_transient_data.stan
200 Bytes
halflife_transient_parameters.stan
59 Bytes
halflife_transient_priors.stan
130 Bytes
halflife_transient_transformed_parameters.stan
94 Bytes
halflives_explicit_evaporation.stan
2.0 kB
halflives_fraction_viable.stan
2.5 kB
halflives_no_evaporation.stan
1.3 kB
halflives_true_replicate.stan
1.2 kB
infer_titers.stan
780 Bytes
mass
mass_data.stan
122 Bytes
mass_parameters.stan
45 Bytes
mass_priors.stan
163 Bytes
mass_transformed_parameters.stan
306 Bytes
mechanistic
calculate_mechanistic_transformed_parameters.stan
2.8 kB
calculate_mechanistic_transient_transformed_parameters.stan
270 Bytes
concentration_observation_process.stan
441 Bytes
mechanistic_data.stan
511 Bytes
mechanistic_flags.stan
218 Bytes
mechanistic_functions.stan
4.4 kB
mechanistic_parameters.stan
310 Bytes
mechanistic_priors.stan
821 Bytes
mechanistic_transformed_parameters.stan
297 Bytes
mechanistic_transient_transformed_parameters.stan
57 Bytes
mechanistic_explicit_evaporation.stan
2.5 kB
predictive_checks
titer_inference_predictive_checks.stan
178 Bytes
titer_predictive_checks_basic.stan
477 Bytes
titer_predictive_checks_declarations.stan
76 Bytes
titer_predictive_checks_drying.stan
772 Bytes
titer_predictive_checks_evap_equation.stan
1.1 kB
pseudoreplicates
pseudoreplicates_data.stan
139 Bytes
pseudoreplicates_parameters.stan
125 Bytes
pseudoreplicates_priors.stan
223 Bytes
titer_inference
titer_inference_data.stan
58 Bytes
titer_inference_parameters.stan
32 Bytes
titer_inference_priors.stan
97 Bytes
titer_prediction
predict_titers_basic.stan
451 Bytes
predict_titers_drying_time.stan
741 Bytes
predict_titers_mechanistic_evap.stan
1.2 kB
predict_titers_true_replicate.stan
409 Bytes
titer_prediction_transformed_parameters.stan
74 Bytes
true_replicates
true_replicates_data.stan
154 Bytes
true_replicates_parameters.stan
53 Bytes
true_replicates_priors.stan
132 Bytes
tables
macros-energy-comparison.R
2.8 kB
table-halflives.R
7.0 kB
table-literature-halflives.R
4.1 kB
table-parameters.R
4.8 kB
table-predicted-actual.R
4.2 kB
virusenv
.Rbuildignore
28 Bytes
.gitignore
650 Bytes
DESCRIPTION
1.0 kB
NAMESPACE
1.5 kB
R
droplet_kinetics.R
19.6 kB
inactivation_kinetics.R
14.2 kB
math.R
2.5 kB
metaanalysis.R
270 Bytes
physical_constants.R
1.5 kB
plotting_style.R
11.5 kB
utilities.R
1.5 kB
man
A_phi.Rd
448 Bytes
R.Rd
291 Bytes
add_titer_metadata.Rd
608 Bytes
buck_eqn.Rd
388 Bytes
cohen_RH_of_molality.Rd
509 Bytes
cohen_molality_of_RH.Rd
531 Bytes
decay_rate_pred.Rd
708 Bytes
decay_ratio_pred.Rd
625 Bytes
density_pure_water.Rd
482 Bytes
fraction_change_to_log_concentration_factor.Rd
712 Bytes
get_params.Rd
896 Bytes
half_life_hum.Rd
1.3 kB
half_life_pred.Rd
731 Bytes
hl_ratio_pred.Rd
610 Bytes
log_arrenhius_A.Rd
698 Bytes
log_arrhenius_rate.Rd
646 Bytes
log_eq_molality_pitzer.Rd
1.4 kB
log_pred_molality_pitzer.Rd
775 Bytes
mass_change_to_log_concentration_factor.Rd
749 Bytes
mass_frac.Rd
588 Bytes
mass_frac_to_molality.Rd
535 Bytes
mass_frac_to_molar_frac.Rd
666 Bytes
mechanistic_decay_rate.Rd
1.7 kB
molality.Rd
687 Bytes
molality_to_mass_frac.Rd
532 Bytes
pitzer_phi.Rd
688 Bytes
pitzer_phi_nacl.Rd
586 Bytes
predict_log_concentration_factor.Rd
1.1 kB
predict_titers_explicit_evaporation.Rd
1.2 kB
predict_titers_exponential_decay.Rd
639 Bytes
predict_titers_implicit_evaporation.Rd
996 Bytes
read_data_for_plotting.Rd
427 Bytes
save_plot.Rd
429 Bytes
scale_color_temperature.Rd
756 Bytes
scale_color_virus.Rd
360 Bytes
scale_fill_temperature.Rd
749 Bytes
scale_fill_virus.Rd
353 Bytes
scale_shape_virus.Rd
360 Bytes
scale_size_virus.Rd
770 Bytes
scale_x_log10_mathformat.Rd
417 Bytes
scale_y_log10_mathformat.Rd
466 Bytes
solute_to_solvent_mole_ratio.Rd
1.0 kB
solve_quartic.Rd
428 Bytes
solve_tang_quartic.Rd
554 Bytes
strain_order.Rd
323 Bytes
tang_aw.Rd
463 Bytes
tang_mass_frac.Rd
494 Bytes
theme_default_legend.Rd
293 Bytes
theme_project.Rd
449 Bytes
to_AH.Rd
397 Bytes
to_Celsius.Rd
327 Bytes
to_Kelvin.Rd
323 Bytes
to_decay_rate.Rd
707 Bytes
to_fractional_life.Rd
624 Bytes
to_half_life.Rd
479 Bytes
virus_order.Rd
318 Bytes