Basic idea for a linelist class

linelist_class.R

  

library(outbreaks)
library(tidyverse)

make_linelist <- function(x, date, interval = 1L, date_start = NULL, date_stop = NULL) {

  ## TODO: add tests on inputs
  
  x <- tibble::as_tibble(x)
  out <- dplyr::select(x, date, everything())
  dates <- pull(out, date)

  if (is.null(date_start)) {
    date_start <- min(dates, na.rm = TRUE)
  }

  if (is.null(date_stop)) {
    date_stop <- max(dates, na.rm = TRUE)
  }
  
  x_info <- list(
    date = names(out)[1],
    interval = interval,
    date_start = date_start,
    date_stop = date_stop
  )

  ## append class and add attributes
  class(out) <- c("linelist", class(x))
  attr(out, "linelist_info") <- x_info
  
  out  
}


x <- make_linelist(ebola_sim_clean$linelist, "date_of_onset")
x


## some operations are okay preserving attributes
x %>%
  select(1:10) %>%
  attr("linelist_info")

x %>%
  select(1:10) %>%
  group_by(gender) %>%
  attr("linelist_info")

x %>%
  select(1:10) %>%
  filter(date_of_onset < as.Date("2015-01-01")) %>%
  attr("linelist_info")

## some are not
x %>%
  select(1:10) %>%
  group_by(gender) %>%
  filter(date_of_onset < as.Date("2015-01-01")) %>%
  attr("linelist_info")

Yes it makes total sense, and I think it is a nice way to do things. We may need to add:

interval_function <- function(dat_var, interval, date_start, date_stop) {
 ...
}

+1 to naming the output of that function date_group inside incidence::incidence, probably clearer like this.