## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup, output=FALSE, message=FALSE, warning=FALSE------------------------
library(serosv)
library(dplyr)
library(magrittr)
library(ggplot2)

## -----------------------------------------------------------------------------
# Prepare data 
tb_nl <- tb_nl_1966_1973 %>% 
  mutate(
    survey_year = age + birthyr,
    survey_time = as.Date(paste0(survey_year, "-01-01"))
  ) %>% select(-birthyr) %>% 
  filter(survey_year > 1966) %>% 
  group_by(age, survey_year, survey_time) %>% 
  summarize(pos = sum(pos), tot = sum(tot), .groups = "drop")

head(tb_nl)

## -----------------------------------------------------------------------------
out_pava <- tb_nl %>% 
  age_time_model(
    time_col = "survey_time", 
    grouping_col = "survey_year",
    age_correct = F,
    monotonize_method = "pava"
  ) %>% 
  suppressWarnings()

out_scam <- tb_nl %>% 
  age_time_model(
    time_col = "survey_time", 
    grouping_col = "survey_year",
    age_correct = T,
    monotonize_method = "scam"
  ) %>% 
  suppressWarnings()

## -----------------------------------------------------------------------------
out_pava
out_scam

## ----warning=FALSE, message=FALSE---------------------------------------------
plot(out_pava, facet = TRUE, modtype = "non-monotonized") + ylim(c(0, 0.07))
plot(out_pava, facet = TRUE, modtype = "monotonized") + ylim(c(0, 0.07))

plot(out_pava, facet = FALSE, modtype = "monotonized") + ylim(c(0, 0.07))

## ----warning=FALSE, message=FALSE---------------------------------------------
plot(out_scam, facet = TRUE, modtype = "non-monotonized") + ylim(c(0, 0.07))
plot(out_scam, facet = TRUE, modtype = "monotonized") + ylim(c(0, 0.07))