Assam NobBS Onset date calculation

NobBS-Experiments/Experiment1.R

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+library(jsonlite)
+library(magrittr)
+library(dplyr)
+library(fGarch)
+library(NobBS)
+
+# Get raw patient data
+raw_patient_df <- data.frame(fromJSON("https://api.covid19india.org/raw_data.json"))
+
+# Get names of all districts with patients
+district_wise_data <- fromJSON("https://api.covid19india.org/state_district_wise.json")
+districts_list = list()
+for(p in district_wise_data) { districts_list[names(p$districtData)] <- FALSE}
+districts_list[["Unknown"]] <- NULL
+districts_df = data.frame(names(districts_list))
+colnames(districts_df) <- c("district")
+
+# cleaning up patient data to remove tourist related data and retaining only the columns needed
+patient_clean_df = merge(x=districts_df, y=raw_patient_df, by.x='district', by.y='raw_data.detecteddistrict')
+patient_data <- patient_clean_df %>% select(district, raw_data.dateannounced, raw_data.gender)
+patient_data_reliable <- patient_data %>% filter(raw_data.dateannounced >= "01/03/2020")
+
+#### Calculation of onset date based on announcement date
+num_patients <- nrow(patient_data_reliable)
+# Using Skewed Gaussian with a mean of 14 days and standard deviation 1 to get the incubation time
+incubation_times <- floor(rsnorm(num_patients, mean=14, sd=1, xi=-10))
+# Using Uniform Random sample in the interval of [1-3] to get the testing time
+testing_time <- floor(runif(num_patients, min=1, max=4))
+delay <- incubation_times + testing_time
+onset_date <- as.Date(patient_data_reliable$raw_data.dateannounced, format ="%d/%m/%Y") - delay
+
+# Create dataframe for all districts
+report_date <- as.Date(patient_data_reliable$raw_data.dateannounced, format="%d/%m/%Y")
+district <- patient_data_reliable$district
+all_districts_data <- data.frame(district, onset_date, report_date)
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