Covid19Wastewater (version 1.0.1)

OffsetHeatmap: Outputs a heatmap of the offset for variant / time windows and population size / region

Description

Outputs a heatmap of the offset for variant / time windows and population size / region

Usage

OffsetHeatmap(
  method,
  timePeriods,
  waste_df,
  case_df,
  pop_df,
  covarstarts,
  covarends,
  covarnames,
  list,
  week,
  lod = FALSE,
  N1_column = N1,
  N2_column = N2,
  site_column = site,
  date_column = date,
  case_column = conf_case,
  pop_column = pop
)

Value

ggplot plot object

Arguments

method

Which analysis definds the offset (r squared, pearson, r squared offset, pearson offset, kendall offset, spearman offset)

timePeriods

Size of time windows in months (if 0 uses variants)

waste_df

DF of waste data must include: date, N1, N2

case_df

DF of case data must include: date, conf_case

pop_df

dataframe where region and population info is stored

covarstarts

start of each split period

covarends

end of each split period

covarnames

name of each split group

list

y axis bins (population size or regions)

week

if true applies 7-day smoothing to case data

lod

if true removes all values below LOD (default false)

N1_column

name of N1 column

N2_column

name of N2 column

site_column

name of site column

date_column

name of date column

case_column

name of case column

pop_column

name of pop column

Examples

data(WasteWater_data, package = "Covid19Wastewater")
data("Case_data", package = "Covid19Wastewater")
data(Pop_data, package = "Covid19Wastewater")
covarstarts <- c(as.Date("2020-08-17"),
                 as.Date("2021-03-29"))
covarends <- c(as.Date("2021-01-18"),
               as.Date("2021-05-24"))
covarnames <- c("Robin1",
                "Alpha.V1")
OffsetHeatmap("kendall_offset", 0, WasteWater_data, Case_data, Pop_data,
               covarstarts, covarends, covarnames, "pop", TRUE, TRUE)