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tinatownestinatownes
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updates to DUA, Quidel
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‎scripts/quidelMissingness.R

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library(epidatr)
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library(dplyr)
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signals <- c(
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#"covid_ag_raw_pct_positive", #"county", "state"
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#"covid_ag_raw_pct_positive_age_0_4", #"county", "state"
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#"covid_ag_smoothed_pct_positive", #"county", "state"
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#"covid_ag_smoothed_pct_positive_age_0_4", #"county", "state"
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#"covid_ag_smoothed_pct_positive_age_18_49" #"county", "state"
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#"covid_ag_smoothed_pct_positive_age_65plus" #"county", "state"
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"covid_ag_raw_pct_positive", #"hrr", "msa", "hhs", "nation"
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"covid_ag_smoothed_pct_positive" #"hrr", "msa", "hhs", "nation"
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#"raw_pct_negative", #FLU
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#"raw_tests_per_device", #FLU
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#"smoothed_pct_negative", #FLU
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#"smoothed_tests_per_device" #FLU
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)
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names(signals) <- signals
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lapply(signals, function(signal) {
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source <- "quidel"
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signal <- signals
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geo_type <- "msa" #"county", "state", "hrr", "msa", "hhs", "nation"
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time_type <- "day"
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print(signal)
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print(geo_type)
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epidata <- pub_covidcast(
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source,
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signal,
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geo_type = geo_type,
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geo_values = "*",
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time_type = time_type,
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time_values = c(
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"2021-03-01",
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"2021-03-02",
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"2021-03-03",
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"2021-03-04",
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"2021-03-05",
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"2021-03-06",
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"2021-03-07",
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"2021-03-08",
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"2021-03-09",
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"2021-03-10",
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"2021-03-11",
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"2021-03-12",
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"2021-03-13",
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"2021-03-14",
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"2021-03-15",
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"2021-03-16",
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"2021-03-17",
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"2021-03-18",
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"2021-03-19",
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"2021-03-20",
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"2021-03-21",
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"2021-03-22",
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"2021-03-23",
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"2021-03-24",
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"2021-03-25",
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"2021-03-26",
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"2021-03-27",
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"2021-03-28",
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"2021-03-29",
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"2021-03-30"
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)
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)
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# Number of locations reported for each reference date
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count_geos_by_date <- count(epidata, time_value)
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# print(count_geos_by_date)
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print(max(count_geos_by_date$n) / 3143 * 100)
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print(mean(count_geos_by_date$n) / 3143 * 100)
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return(max(count_geos_by_date$n) / 3143 * 100)
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})
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####################################### geo_type = "county"
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "county"
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# [1] 76.32835
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# [1] 72.70973
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "county"
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# [1] 76.32835
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# [1] 72.70973
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "county"
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# [1] 76.32835
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# [1] 72.70973
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "county"
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# [1] 76.32835
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# [1] 72.70973
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "county"
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# [1] 76.32835
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# [1] 72.70973
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# $covid_ag_raw_pct_positive
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# [1] 76.32835
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#
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# $covid_ag_raw_pct_positive_age_0_4
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# [1] 76.32835
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#
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# $covid_ag_smoothed_pct_positive
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# [1] 76.32835
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#
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# $covid_ag_smoothed_pct_positive_age_0_4
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# [1] 76.32835
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#
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# $covid_ag_smoothed_pct_positive_age_18_49
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# [1] 76.32835
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####################################### geo_type = "state"
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "state"
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# [1] 6.04518
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# [1] 5.738679
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "state"
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# [1] 6.04518
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# [1] 5.738679
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "state"
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# [1] 6.04518
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# [1] 5.738679
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "state"
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# [1] 6.04518
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# [1] 5.738679
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# covid_ag_raw_pct_positive
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# "covid_ag_raw_pct_positive"
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# covid_ag_raw_pct_positive_age_0_4
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# "covid_ag_raw_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive
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# "covid_ag_smoothed_pct_positive"
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# covid_ag_smoothed_pct_positive_age_0_4
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# "covid_ag_smoothed_pct_positive_age_0_4"
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# covid_ag_smoothed_pct_positive_age_18_49
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# "covid_ag_smoothed_pct_positive_age_18_49"
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# [1] "state"
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# [1] 6.04518
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# [1] 5.738679
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# $covid_ag_raw_pct_positive
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# [1] 6.04518
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#
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# $covid_ag_raw_pct_positive_age_0_4
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# [1] 6.04518
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#
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# $covid_ag_smoothed_pct_positive
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# [1] 6.04518
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#
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# $covid_ag_smoothed_pct_positive_age_0_4
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# [1] 6.04518
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#
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# $covid_ag_smoothed_pct_positive_age_18_49
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# [1] 6.04518
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####################################### geo_type = "state"
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