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Missing limit argument in dag_paths() #65

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henningte opened this issue Apr 6, 2022 · 2 comments
Closed

Missing limit argument in dag_paths() #65

henningte opened this issue Apr 6, 2022 · 2 comments

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@henningte
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dag_paths() internally uses dagitty::paths() to identify open paths. dagitty::paths() has an argument limit which specifies how many of all existing distinct paths are considered. By default, limit = 100, meaning that only the first 100 paths are considered.

Could the limit argument be added also to dag_paths()? I think this should be quite straightforward to implement:

library(magrittr)
library(ggdag)
#> 
#> Attaching package: 'ggdag'
#> The following object is masked from 'package:stats':
#> 
#>     filter

# updated version of dag_paths
dag_paths <- function (.dag, from = NULL, to = NULL, adjust_for = NULL, limit = 100, directed = FALSE, 
          paths_only = FALSE, ...) 
{
  .tdy_dag <- ggdag:::if_not_tidy_daggity(.dag, ...)
  if (is.null(from)) 
    from <- dagitty::exposures(.tdy_dag$dag)
  if (is.null(to)) 
    to <- dagitty::outcomes(.tdy_dag$dag)
  if (is.null(from) || is.null(to)) 
    stop("`exposure` and `outcome` must be set!")
  pathways <- dagitty::paths(.tdy_dag$dag, from, to, Z = adjust_for, limit = limit,
                             directed = directed) %>% dplyr::as_tibble() %>% dplyr::filter(open) %>% 
    dplyr::pull(paths)
  vars <- c(from = from, to = to)
  .tdy_dag$data <- pathways %>% purrr::map_df(function(.x) {
    path_df <- .x %>% ggdag:::dag2() %>% dagitty::edges() %>% dplyr::select(.from = v, 
                                                                    .to = w) %>% dplyr::mutate(.from = as.character(.from), 
                                                                                               .to = as.character(.to), path = "open path") %>% 
      dplyr::left_join(.tdy_dag$data, ., by = c(name = ".from", 
                                                to = ".to"))
    any_x_unopend <- any(path_df$name == vars[[1]] & is.na(path_df$path))
    if (any_x_unopend) {
      x_has_no_children <- any(path_df$name == vars[[1]] & 
                                 is.na(path_df$to))
      if (x_has_no_children) {
        path_df[path_df$name == vars[[1]], "path"] <- "open path"
      }
      else {
        path_df <- path_df %>% filter(name == vars[[1]]) %>% 
          dplyr::slice(1) %>% dplyr::mutate(path = "open path") %>% 
          dplyr::bind_rows(path_df, .)
      }
    }
    y_has_no_children <- any(path_df$name == vars[[2]] & 
                               is.na(path_df$to))
    if (y_has_no_children) {
      path_df[path_df$name == vars[[2]], "path"] <- "open path"
    }
    else {
      path_df <- path_df %>% filter(name == vars[[2]]) %>% 
        dplyr::slice(1) %>% dplyr::mutate(path = "open path") %>% 
        dplyr::bind_rows(path_df, .)
    }
    path_df
  }, .id = "set")
  if (paths_only) 
    .tdy_dag$data <- filter(.tdy_dag$data, path == "open path")
  .tdy_dag
}

# example
x_td <- 
  ggdag::dag("x1 -> x2
           x1 -> x3
           x2 -> x3
           x2 -> x4
           x3 -> x4
           x3 -> x5
           x4 -> x5
           x4 -> x6
           x4 -> x7
           x5 -> x7
           x5 -> x8
           x6 -> x8
           x1 -> x6
           x4 -> x9
           x2 -> x9
           x5 -> x9
           x9 -> x10
           x9 -> x3
           x10 -> x6
           x3 -> x10
           x5 -> x11") %>%
  ggdag::tidy_dagitty(seed = 345)
  
# more than 100 paths with dagitty::paths when limit is set appropriately 
x_td_paths1 <- dagitty::paths(x_td$dag, limit = 200, from = "x5", to = "x8")
length(x_td_paths1$paths)
#> [1] 115

# no option available in ggdag
x_td_paths2 <- 
  ggdag::dag_paths(x_td, from = "x5", to = "x8")

# updated version
x_td_paths3 <- 
  dag_paths(x_td, from = "x5", to = "x8", limit = 200)

identical(x_td_paths2$data$path, x_td_paths3$data$path)
#> [1] FALSE

Created on 2022-04-06 by the reprex package (v2.0.1)

Session info 
sessioninfo::session_info()
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In addition, I think there's a typo in the documentation for dag_paths(): The first line starts with:

node_paths finds the ...

But should probably be

dag_paths finds the ...
@malcolmbarrett
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Yes, I agree. Happy to accept a PR for this and and ggdag_paths() if you want to expedite the process

@henningte henningte mentioned this issue Apr 7, 2022
Merged
@henningte
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@malcolmbarrett Thanks for your quick reply. I actually plan to use this feature in the near future!

I have made a pull request. If there are any issues, please let me know.

malcolmbarrett added a commit that referenced this issue Apr 14, 2022
@malcolmbarrett
Merge pull request #66 from henningte/main
fd8d668 
Missing `limit` argument in `dag_paths()` (#65)
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@malcolmbarrett @henningte