inst/doc/my-vignette.R

In dlmwwbe: Dynamic Linear Model for Wastewater-Based Epidemiology

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  comment = "#>",
  fig.width = 7.2,
  fig.height = 4.8,
  fig.align = "center"
)

## ----setup--------------------------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
library(dlmwwbe)
data(wastewater)
data(wastewaterhealthworker)

## -----------------------------------------------------------------------------
data_TC <- wastewater[wastewater$Code == "TC",]
data_TC$SampleDate <- as.Date(data_TC$SampleDate)
fit <- dllm(
  equal.state.var=FALSE,
  equal.obs.var=FALSE,
  log10=TRUE,
  data = data_TC,
  date = "SampleDate",
  obs_cols = c("ORFlab", "Nlab"),
  S = c('kvariate')
)

summary(fit)
plot(fit, type='smoother', conf.int = TRUE)

## -----------------------------------------------------------------------------
data_TC <- wastewaterhealthworker[wastewaterhealthworker$Code == "TC",]
data_TC$SampleDate <- as.Date(data_TC$SampleDate)
fit <- pdlm(
  data=data_TC,
  formula=HealthWorkerCaseCount ~ WW.tuesday + WW.thursday,
  lags=0,
  log10=TRUE,
  date = NULL,
  equal.state.var = TRUE,
  equal.obs.var = FALSE,
  auto_init = TRUE,
  control = list(maxit = 100))
summary(fit)
plot(fit, conf.int=TRUE)


## -----------------------------------------------------------------------------
data_TC <- wastewaterhealthworker[wastewaterhealthworker$Code == "TC",]
data_TC$SampleDate <- as.Date(data_TC$SampleDate)
fit <- pdlm(
  data=data_TC,
  formula=HealthWorkerCaseCount ~ WW.tuesday + WW.thursday,
  lags=2,
  log10=TRUE,
  date = NULL,
  equal.state.var = FALSE,
  equal.obs.var = TRUE,
  auto_init = TRUE,
  control = list(maxit = 100))
summary(fit)
plot(fit, conf.int=TRUE)