OffsetHeatmap: Outputs a heatmap of the offset for variant / time windows...
In Covid19Wastewater: Prepare, Analyze, and Visualize Covid-19 Wastewater Data

View source: R/library--analysis_tools--time_offset--Offset_Analysis_Plot.R

OffsetHeatmap

R Documentation

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
)

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

Value

ggplot plot object

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)

Covid19Wastewater documentation built on Aug. 25, 2023, 1:07 a.m.