collateral

November 1, 2018
By

(This article was first published on James Goldie (rstats posts), and kindly contributed to R-bloggers)

Toward the end of my PhD analysis, I’ve started leaning on purrr more and more to get analysis done on small multiples quickly and safely. Where before I might have used nested loops and potentially missed a lot of problems, I now split data frames out, build statistical models, extract model parameters and print plots all in one workflow.

This has incredible benefits for workflow: instead of having to track group identifiers across each output you produce, data and outputs and are linked to group identifiers by row, and you can do further tidying to summarise these complex outputs. You essentially have a summary of your analysis right there in the data frame.

In particular, purrr::safely() and purrr::quietly() wrap a number of R’s output and error handling systems, allowing you to push through errors as you iterate and capture them along with warnings, messages and other output. Instead of getting zero output until every group is behaving, you can get to the end of your analysis and then review to see what didn’t work out.

These two functions already lend themselves well to mapping, but since they return nested lists with each component of the output, it’s not always easy to tell until you burrow in to the returned column which groups returned output, which stopped with errors and which flagged other warnings or messages.

In response, I built the collateral package. Collateral provides two new map variants:

  • map_safely() wraps safely() and,
  • map_quietly() wraps quietly().

As well as automatically wrapping these functions (so you can use them exactly as you would the vanilla map()), these functions style the resulting list (or list-column) using pillar—the same system that provides enhanced tibble output. You can scan down the column and see which mapped elements returned a result, which stopped with errors, and which returned warnings, messages or other output. If you’d like to inspect these kinds of output in more detail (for example, retrieve an error or read returned warnings), you can do so just as you would a manually mapped-and-wrapped function call, using components like $result, $error or $warning.

Here’s a quick example, using a safe version of log (as in the safely() documentation):

library(tidyverse)
library(collateral)

test =
  # tidy up and trim down for the example
  mtcars %>%
  rownames_to_column(var = "car") %>%
  as_data_frame() %>%
  select(car, cyl, disp, wt) %>%
  # spike some rows in cyl == 4 to make them fail
  mutate(wt = dplyr::case_when(
    wt < 2 ~ -wt,
    TRUE ~ wt)) %>%
  # nest and do some operations quietly()
  nest(-cyl) %>%
  mutate(qlog = map_quietly(data, ~ log(.$wt)))

test
#> # A tibble: 3 x 4
#>     cyl data              qlog
#>                
#> 1     6   R O _ _
#> 2     4  R O _ W
#> 3     8  R O _ _

The captured side effects appear in the tibble columns: (R)results, (O)utput, (M)essages and (W)arnings. If you’re using map_safely() instead, you’ll see (R)esults and (E)rrors. if we investigate row 2 further, we can see the problem:

test$qlog[[2]]$warnings
# [1] "NaNs produced"
test$qlog[[2]]$result
#  [1] 0.8415672 1.1600209 1.1474025 0.7884574       NaN       NaN 0.9021918       NaN 0.7608058
# [10]       NaN 1.0224509

Even better: because collateral plugs into pillar, which powers enhanced tibble output, you get color in the terminal!

A stickylabeller plot, including multiple faceting variables and automatic numbering

(Next on the to-do list: getting this going with knitted output!)

You can find and install collateral on GitHub. If you have ideas or bugs, please get in touch or
file an issue!

To leave a comment for the author, please follow the link and comment on their blog: James Goldie (rstats posts).

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.

Search R-bloggers


Sponsors

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)