TJ Mahr tjmahr Madison, WI tjmahr.com Language and data scientist

issue openedstan-dev/bayesplot

rank-based alternative to traceplot

As described by Dan here https://statmodeling.stat.columbia.edu/2019/03/19/maybe-its-time-to-let-the-old-ways-die-or-we-broke-r-hat-so-now-we-have-to-fix-it/

If we take the input into mcmc_trace(), we know the chain id and values of the iterations. Then we can compute ranks with dplyr::row_number() and facet by by chain id.

Sanity check: Plot should be perfectly uniform when mode has just one chain.

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issue closedtjmahr/textgrid

accented characters throw an error with textgrid::TextGrid()

If in my Praat .TextGrid file I have accented characters, as is the case often in Spanish, for example with "está", the textgrid::TextGrid() function throws this error message:

Error in mapply(FUN = f, ..., SIMPLIFY = FALSE) : 
  zero-length inputs cannot be mixed with those of non-zero length
In addition: There were 50 or more warnings (use warnings() to see the first 50)

If I remove the accented characters, say "esta", no error.

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ekbrown

issue closedtjmahr/textgrid

unit test for point text

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tjmahr

issue closedtjmahr/textgrid

unit test for interval text

see praat's own unit testing https://github.com/jjatria/praat/blob/master/dwtest/test_TextGrid_extensions.praat

https://github.com/jjatria/praat/blob/master/test/fon/TextGrid.praat

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tjmahr

issue closedtjmahr/textgrid

write_textgrid

Should be able to reproduce a convert from a textgrid file to an R object back to textgrid file.

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issue commenttjmahr/textgrid

Unable to open textgrid files

I've been using textgRid by @patrickreidy for my textgrid needs. this package (mine) was a fork of that one (pat's). https://github.com/patrickreidy/textgRid It's on CRAN and has the same API, so I recommend it. (I should probably take this package offline...)

ANYWAY, both of our packages have this problem. My fix has been to temporarily fix the file before reading it in.



u <- "~/../Downloads/LM_BTT_37_Mother.TextGrid"

temp_fix_textgrid <- function(x) {
  temp <- tempfile(fileext = ".TextGrid")
  
  lines <- readr::read_lines(x)
  lines <- stringr::str_replace_all(lines, "\t{4}", "\t\t\t")
  lines <- stringr::str_replace_all(lines, "\t", "    ")
  readr::write_lines(lines, temp)
  temp
}

textgRid::TextGrid(u)
#> Error in mapply(FUN = f, ..., SIMPLIFY = FALSE): zero-length inputs cannot be mixed with those of non-zero length
textgRid::TextGrid(temp_fix_textgrid(u))
#> An object of class "TextGrid"
#> [[1]]
#> An object of class "IntervalTier"
#> Slot "startTimes":
#> [1] 0.000 0.013 0.122 0.383 0.552 0.722 0.752 0.882
#> 
#> Slot "endTimes":
#> [1] 0.013 0.122 0.383 0.552 0.722 0.752 0.882 0.889
#> 
#> Slot "labels":
#> [1] "sp"    "sp"    "s"     "¹ʌ"  "d"     "â\201°Ã¦" "n"     "sp"   
#> 
#> Slot "name":
#> [1] "default - phone"
#> 
#> Slot "number":
#> [1] 1
#> 
#> 
#> [[2]]
#> An object of class "IntervalTier"
#> Slot "startTimes":
#> [1] 0.000 0.013 0.122 0.882
#> 
#> Slot "endTimes":
#> [1] 0.013 0.122 0.882 0.889
#> 
#> Slot "labels":
#> [1] "sp"     "sp"     "SÃ…DAN" "sp"    
#> 
#> Slot "name":
#> [1] "default - word"
#> 
#> Slot "number":
#> [1] 2
#> 
#> 
#> Slot "startTime":
#> [1] 0
#> 
#> Slot "endTime":
#> [1] 0.889

<sup>Created on 2019-03-14 by the reprex package (v0.2.1)</sup>

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issue commentropensci/drake

use_drake()

What do you think about using usethis to implement this? They provide a use_template() function that apply the usual usethis steps and checks. That way we can satisfy both the checks (for the project root and for preventing overwriting) for free.

To avoid dependency, we can suggest the package and do a require() in the function.

The only change to your proposal would be that usethis wants the templates to live inst/templates.

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issue commentropensci/drake

Deprecate drake_cache_log_file()

preprocess-config.R refers to the function and the default filename. We can remove its mention from the documentation but should make sure that the behavior described here is accurate.

#' @param cache_log_file Name of the cache log file to write.
#'   If `TRUE`, the default file name is used (`drake_cache.log`).
#'   If `NULL`, no file is written.
#'   If activated, this option uses
#'   [drake_cache_log_file()] to write a flat text file
#'   to represent the state of the cache
#'   (fingerprints of all the targets and imports).
#'   If you put the log file under version control, your commit history
#'   will give you an easy representation of how your results change
#'   over time as the rest of your project changes. Hopefully,
#'   this is a step in the right direction for data reproducibility.
#' ...
drake_config <- function(
# ...
wlandau

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PR opened ropensci/drake

WIP deprecating drake_cache_log()

Summary

Deprecating drake_cache_log()

Related GitHub issues and pull requests

  • Ref: #741

Checklist

  • [x] I have read drake's code of conduct, and I agree to follow its rules.
  • [ ] I have listed any substantial changes in the development news.
  • [ ] I have added testthat unit tests to tests/testthat to confirm that any new features or functionality work correctly.
  • [ ] I have tested this pull request locally with devtools::check()
  • [ ] This pull request is ready for review.
  • [ ] I think this pull request is ready to merge.
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Merge pull request #775 from tjmahr/master added a `progress` argument to filter the results of `progress()`

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Pull request review commentropensci/drake

added a `progress` argument to filter the results of `progress()`

 progress <- function(   if (!length(targets)) {     targets <- cache$list(namespace = "progress")   }-  progress <- vapply(+  progress_results <- vapply(     targets,     get_progress_single,     cache = cache,     FUN.VALUE = character(1)   )-  out <- weak_tibble(target = targets, progress = progress)+  out <- weak_tibble(target = targets, progress = progress_results)   rownames(out) <- NULL++  if (!is.null(progress)) {

done

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Pull request review commentropensci/drake

added a `progress` argument to filter the results of `progress()`

 test_with_dir("loadd() does not load imports", {     regexp = "No targets to load"   ) })++test_with_dir("can filter progress", {+  skip_on_cran() # CRAN gets whitelist tests only (check time limits).+  plan <- drake_plan(a = TRUE, b = TRUE, c = stop())++  expect_error(make(plan))++  expect_equal(nrow(progress()), 3)+  expect_equal(nrow(progress(progress = c("done", "failed"))), 3)

done

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PR opened ropensci/drake

added a `progress` argument to filter the results of `progress()`

Summary

I added a progress argument to filter the results of progress().

Related GitHub issues and pull requests

  • Ref: #743

Checklist

  • [x] I have read drake's code of conduct, and I agree to follow its rules.
  • [x] I have listed any substantial changes in the development news.
  • [ ] I have added testthat unit tests to tests/testthat to confirm that any new features or functionality work correctly.
  • [ ] I have tested this pull request locally with devtools::check()
  • [x] This pull request is ready for review.
  • [] I think this pull request is ready to merge.

An unrelated x86 test failed on my Windows machine.

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An R-focused pipeline toolkit for reproducibility and high-performance computing

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issue commentchirunconf/chirunconf19

Add option to `broom` tidiers to standardize parameters

If we are doing stuff on posterior samples, then tidybayes might be better. I think of that as the Bayesian broom. (Sorry Alex 😅.)

What would we need to standardize the coefficients? Is there some magic we can do with a variance-covariance matrix? Or do we have to dig inside the model's data/matrix, take the SD of the numeric variables and do Gelman's thing to the binary variables?

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issue openedchirunconf/chirunconf19

usethis issue clinic

I love the usethis package. It lets you set up common pieces of R projects using standardized templates. Want to add a unit test a package? usethis::use_test() will create a file in tests/testthat and open it in RStudio for you. usethis::use_logo() will take an image file, resize it and store it man/figures/logo.png, which is a good spot for a logo file in an R package.

I see two routes here.

1. We show the package some care and try to take out some issues with one of the package's contributer's onsite as a coach (Jim Hester)

2. usethis is geared towards package developers, so we think about what pieces of boilerplate we would want to automate as data analysts. For example, use_database(connection) would create the configuration files needed to manage a database connection, add them to .gitignore, etc.

The main limitations for this proposal I think are that

  • This would be developing and improving tools instead of making something new and cool.
  • We don't own the package so our suggestions for new features could be ruled out by RStudio people.

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issue commentchirunconf/chirunconf19

Going to/from mixed model formulas and Hasse diagrams

The Hasse diagram is inscrutable, but the decomposition rivers are nice. Can we leverage D3 and r2d3 at all?

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Update README.md
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Datasets from "Nonlinear Models for Repeated Measurements Data" (Davidian & Giltinan, 1995)

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