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Lo Iacono, Giovanni Dr (School of Vet Med.)'s avatar
- /PAPER_Conditional_probability_quantile_original_MEDMI_4_variables_quarter.Rout
- /PAPER_Conditional_probability_quantile_original_MEDMI_quarters.R
- /PAPER_Conditional_probability_quantile_original_MEDMI_quarters.Rout
- /PAPER_Conditional_probability_quantile_original_one_variable_quantile.R
- /PAPER_Conditional_probability_quantile_original_two_variables_MEDMI_high_resolution.R
- /PAPER_Conditional_probability_quantile_original_two_variables_MEDMI_high_resolution.Rout
- /PAPER_Conditional_probability_quantile_original_two_variables_MEDMI_lab.R
- /PAPER_Conditional_probability_quantile_original_two_variables_MEDMI.R
- /PAPER_Conditional_probability_quantile_original_two_variables_MEDMI.Rout
- /PAPER_Efficient_Simulated_Campylobacter_environment_analysis_subset_3_variables_for_reconstruction.R
- /PAPER_Efficient_Simulated_Campylobacter_environment_analysis_subset_3_variables_for_reconstruction.Rout
- /PAPER_Pathogen_Linkage_fixed_time_lag.R
- /PAPER_Pathogen_Linkage_fixed_time_lag.Rout
- /Paper_plot_Simulated_Reconstruct_3_var.R
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_daylength.R
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_daylength.Rout
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_except_daylength.R
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_except_daylength.Rout
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_except_humidity.R
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_except_humidity.Rout
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_except_temperature.R
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_except_temperature.Rout
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_humidity.R
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_humidity.Rout
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_temperature.R
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_constant_temperature.Rout
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_PHE_centre.R
- /Paper_Reconstruct_Campylobacter_environment_light_hum_max_for_rec_PHE_centre.Rout
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_fixed_lag_original_MEDMI_max_hum_light.R
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_fixed_lag_original_MEDMI_max_rain_light.R
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_fixed_lag_original_MEDMI_max_rain_light.Rout
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_fixed_lag_original_MEDMI_min_hum_light.R
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_fixed_lag_original_MEDMI.Rout
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_fixed_lag_original_MEDMI2.R
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_fixed_lag_original_MEDMI2.Rout
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_light_hum_max_for_rec_multiple_delays_half_year.R
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_light_hum_max_for_rec_multiple_delays_half_year.Rout
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_light_hum_max_for_rec_multiple_delays.R
- /PAPER_Reconstruct_Simulated_Campylobacter_environment_light_hum_max_for_rec_multiple_delays.Rout
- /Paper_Taylor_Campylobacter_environment_hum_max_for_rec_delay_original.R
- /Paper_time_lag_3_var_Simulated.R
- /Paper_time_lag_3_var_Simulated.Rout
- /Paper_time_lag.R
- /Taylor_Simulated_Campylobacter_environment_light_hum_max_for_rec_delay_original_modified.R
- /Taylor_Simulated_Campylobacter_environment_light_hum_max_for_rec_delay_original_modified.Rout
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History

Paper_data_extraction_from_MEDMI.R: The code extracts the environmental variable provided by the MetOffice

Paper_Campylobacter_correction.R: The code correct the Campylobacter data, to remove the incubation period and reporting delay. Incubation period based on log-normal, which is better. This is not the best way to remove reporting delay as it depends on time, season etc. Contacted Nouflay but no reply. So I cannot be bother to do this. Use simple Sartwell instead.

PAPER_campy_correction_plot: The code associates the value of the environmental variables to the Campylobacter cases at the location (diagnostic postcode) and date of occurrence with a chosen time-lag

PAPER_Conditional_Probability.R: To find the conditional probability

PAPER_Reconstruction_from_Conditional_probability_light_hum_max (and all other variables): To reconstruct the time-series

PAPER_Plots_Campylobacter_Conditional_probability_quantile.r. PAPER_Reconstruction_from_Conditional_probability_light_hum_max_quantile.r paper_plot_Simulated_Reconstruct_3_var_quantile.R The sameas above with quantiles