inst/check-appended-file.R

In carlbfrederick/ohiCovidMetrics: Used to calculate sub-state metrics relating to the COVID-19 pandemic

#check-appended-file.R
#
#Check Appended Files For Errors created by columns added
#

#Setup ----
library(tidyverse)
library(ohiCovidMetrics)
library(tinytest)

load(Sys.getenv("LOADAPPENDEDFILE"))

out <- out %>%
  group_by(Data_Period) %>%
  mutate(
    nocase = max(as.Date(Date)) - as.Date(Date) == 14,
    noessence = max(as.Date(Date)) - as.Date(Date) == 0 & RowType == "Daily",
  ) %>%
  ungroup(.)

non_cty <- c("Wisconsin", "Fox Valley Area", "North Central", "Northeast",
             "Northwest", "South Central", "Southeast", "Western")

##. . COLUMNS ADDED OR MODIFIED BY append_metric_files()----
macheck <- out %>%
  group_by(Region) %>%
  mutate(
    burn_obs = row_number(Date),
    ma_present = if_else(RowType == "Daily" & burn_obs > 6, TRUE, FALSE)
  )

###Hosp_DailyCOVID_PX_moving_avg
expect_true(inherits(macheck$Hosp_DailyCOVID_PX_moving_avg, 'numeric'),
            info = "Hosp_DailyCOVID_PX_moving_avg column is 'numeric' class")
expect_equal(sum(is.na(macheck$Hosp_DailyCOVID_PX_moving_avg[macheck$ma_present & macheck$Region %in% non_cty & !macheck$noessence])), 0,
             info = "Hosp_DailyCOVID_PX_moving_avg column has all expected nonmissing values")
expect_equal(sum(!is.na(macheck$Hosp_DailyCOVID_PX_moving_avg[!macheck$ma_present & !(out$Region %in% non_cty)])), 0,
             info = "Hosp_DailyCOVID_PX_moving_avg column is always NA/missing when expected")

###Hosp_DailyCOVID_ICU_moving_avg
expect_true(inherits(macheck$Hosp_DailyCOVID_ICU_moving_avg, 'numeric'),
            info = "Hosp_DailyCOVID_ICU_moving_avg column is 'numeric' class")
expect_equal(sum(is.na(macheck$Hosp_DailyCOVID_ICU_moving_avg[macheck$ma_present & out$Region %in% non_cty & !macheck$noessence])), 0,
             info = "Hosp_DailyCOVID_ICU_moving_avg column has all expected nonmissing values")
expect_equal(sum(!is.na(macheck$Hosp_DailyCOVID_ICU_moving_avg[!macheck$ma_present & !(out$Region %in% non_cty)])), 0,
             info = "Hosp_DailyCOVID_ICU_moving_avg column is always NA/missing when expected")

###Hosp_Beds_moving_avg
expect_true(inherits(macheck$Hosp_Beds_moving_avg, 'numeric'),
            info = "Hosp_Beds_moving_avg column is 'numeric' class")
expect_equal(sum(is.na(macheck$Hosp_Beds_moving_avg[macheck$ma_present & out$Region %in% non_cty & !macheck$noessence])), 0,
             info = "Hosp_Beds_moving_avg column has all expected nonmissing values")
expect_equal(sum(!is.na(macheck$Hosp_Beds_moving_avg[!macheck$ma_present & !(out$Region %in% non_cty)])), 0,
             info = "Hosp_Beds_moving_avg column is always NA/missing when expected")

###Hosp_ICU_moving_avg
expect_true(inherits(macheck$Hosp_ICU_moving_avg, 'numeric'),
            info = "Hosp_ICU_moving_avg column is 'numeric' class")
expect_equal(sum(is.na(macheck$Hosp_ICU_moving_avg[macheck$ma_present & out$Region %in% non_cty & !macheck$noessence])), 0,
             info = "Hosp_ICU_moving_avg column has all expected nonmissing values")
expect_equal(sum(!is.na(macheck$Hosp_ICU_moving_avg[!macheck$ma_present & !(out$Region %in% non_cty)])), 0,
             info = "Hosp_ICU_moving_avg column is always NA/missing when expected")

###Hosp_Vent_moving_avg
expect_true(inherits(macheck$Hosp_Vent_moving_avg, 'numeric'),
            info = "Hosp_Vent_moving_avg column is 'numeric' class")
expect_equal(sum(is.na(macheck$Hosp_Vent_moving_avg[macheck$ma_present & out$Region %in% non_cty & !macheck$noessence])), 0,
             info = "Hosp_Vent_moving_avg column has all expected nonmissing values")
expect_equal(sum(!is.na(macheck$Hosp_Vent_moving_avg[!macheck$ma_present & !(out$Region %in% non_cty)])), 0,
             info = "Hosp_Vent_moving_avg column is always NA/missing when expected")

###Testing_Perc_Pos_moving_avg
expect_true(inherits(macheck$Testing_Perc_Pos_moving_avg, 'numeric'),
            info = "Testing_Perc_Pos_moving_avg column is 'numeric' class")
expect_equal(sum(is.na(macheck$Testing_Perc_Pos_moving_avg[macheck$ma_present & !macheck$noessence])), 0,
             info = "Testing_Perc_Pos_moving_avg column has all expected nonmissing values")
expect_equal(sum(!is.na(macheck$Testing_Perc_Pos_moving_avg[!macheck$ma_present])), 0,
             info = "Testing_Perc_Pos_moving_avg column is always NA/missing when expected")
expect_true(all(dplyr::between(macheck$Testing_Perc_Pos_moving_avg[macheck$ma_present & !macheck$noessence], left = 0.0, right = 100.0)),
            info = "Testing_Perc_Pos_moving_avg columns values are all between 0 and 100 inclusive.")
expect_true(any(macheck$Testing_Perc_Pos_moving_avg[macheck$ma_present] > 1.0),
            info = "Testing_Perc_Pos_moving_avg columns values are scaled between 0 and 100 (not 0 and 1).")

###Testing_Tot_Enc_moving_avg
expect_true(inherits(macheck$Testing_Tot_Enc_moving_avg, 'numeric'),
            info = "Testing_Tot_Enc_moving_avg column is 'numeric' class")
expect_equal(sum(is.na(macheck$Testing_Tot_Enc_moving_avg[macheck$ma_present & !macheck$noessence])), 0,
             info = "Testing_Tot_Enc_moving_avg column has all expected nonmissing values")
expect_equal(sum(!is.na(macheck$Testing_Tot_Enc_moving_avg[!macheck$ma_present])), 0,
             info = "Testing_Tot_Enc_moving_avg column is always NA/missing when expected")

###CLI_Count_moving_avg
expect_true(inherits(macheck$CLI_Count_moving_avg, 'numeric'),
            info = "CLI_Count_moving_avg column is 'numeric' class")
expect_equal(sum(is.na(macheck$CLI_Count_moving_avg[macheck$ma_present & !macheck$noessence])), 0,
             info = "CLI_Count_moving_avg column has all expected nonmissing values")
expect_equal(sum(!is.na(macheck$CLI_Count_moving_avg[!macheck$ma_present])), 0,
             info = "CLI_Count_moving_avg column is always NA/missing when expected")

###Conf_Case_Count_moving_avg
expect_true(inherits(macheck$Conf_Case_Count_moving_avg, 'numeric'),
            info = "Conf_Case_Count_moving_avg column is 'numeric' class")
expect_equal(sum(is.na(macheck$Conf_Case_Count_moving_avg[macheck$ma_present & !macheck$nocase & macheck$burn_obs > 7])), 0,
             info = "Conf_Case_Count_moving_avg column has all expected nonmissing values")
expect_equal(sum(!is.na(macheck$Conf_Case_Count_moving_avg[!macheck$ma_present])), 0,
             info = "Conf_Case_Count_moving_avg column is always NA/missing when expected")

###ILI_Moving_Avg
ili_ma <- out %>%
  group_by(Region) %>%
  mutate(
    burn_obs = row_number(Date),
    ma_present = if_else(RowType == "Daily" & burn_obs > 2 & Date != max(Date), TRUE, FALSE)
  )

expect_true(inherits(ili_ma$ILI_Moving_Avg, 'numeric'),
            info = "ILI_Moving_Avg column is 'numeric' class")
expect_equal(sum(is.na(ili_ma$ILI_Moving_Avg[ili_ma$ma_present])), 0,
             info = "ILI_Moving_Avg column has no NA/missings for Daily rows that are not first 2 dates of period per geo-unit")
expect_equal(sum(!is.na(ili_ma$ILI_Moving_Avg[!ili_ma$ma_present])), 0,
             info = "ILI_Moving_Avg column has ONLY NA/missings for Summary rows and first 2 dates of period per geo-unit")
expect_true(all(dplyr::between(ili_ma$ILI_Moving_Avg[ili_ma$ma_present], left = 0.0, right = 100.0)),
            info = "ILI_Moving_Avg columns values are all between 0 and 100 inclusive.")
expect_true(any(ili_ma$ILI_Moving_Avg[ili_ma$ma_present] > 1.0),
            info = "ILI_Moving_Avg columns values are scaled between 0 and 100 (not 0 and 1).")

###ILI_Status
expect_true(inherits(ili_ma$ILI_Status, 'character'),
            info = "ILI_Status column is 'character' class")
expect_equal(sum(is.na(ili_ma$ILI_Status[ili_ma$ma_present & ili_ma$Region != "Florence" & !ili_ma$noessence])), 0,
             info = "ILI_Status column has no NA/missings for Daily rows outside of Florence County and first 2 dates of period per geo-unit")
expect_equal(sum(!is.na(ili_ma$ILI_Status[ili_ma$RowType == "Summary" | ili_ma$Region == "Florence" | ili_ma$burn_obs <= 2])), 0,
             info = "ILI_Status column has ONLY NA/missings for Summary rows and Florence County and first 2 dates of period per geo-unit")
expect_true(all(unique(ili_ma$ILI_Status[ili_ma$ma_present & ili_ma$Region != "Florence" & !ili_ma$noessence]) %in%
                  c("Elevated", "Low", "Moderate")),
            info = "ILI_Status column has only correct unique values")