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Transpose coords #54

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xrobin opened this issue May 19, 2019 · 8 comments
Closed

Transpose coords #54

xrobin opened this issue May 19, 2019 · 8 comments

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@xrobin
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@xrobin xrobin commented May 19, 2019

Coords returns a matrix with thresholds in columns, and the measurement in rows.

This has always been a bit weird but is becoming problematic with pipelines where a data.frame in transposed form would be better suited.

Expected behavior

> library(dplyr)
> roc(aSAH, outcome, wfns) %>% coords()
Setting levels: control = Good, case = Poor
Setting direction: controls < cases
                threshold specificity sensitivity
      -Inf   0.0000000   1.0000000
       1.5   0.5138889   0.9512195
       2.5   0.7916667   0.6585366
       3.5   0.8333333   0.6341463
       4.5   0.9444444   0.4390244
       Inf   1.0000000   0.0000000
xrobin added a commit that referenced this issue May 19, 2019
xrobin added a commit that referenced this issue May 19, 2019
xrobin added a commit that referenced this issue May 19, 2019
@xrobin
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@xrobin xrobin commented May 21, 2019

See wiki page Updating coords for an assessment of potential impact on dependent packages.

xrobin added a commit that referenced this issue May 23, 2019
@xrobin
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@xrobin xrobin commented May 23, 2019

  • TODO: add an FAQ entry documenting this change, the warning, and how to silence it.

xrobin added a commit that referenced this issue May 23, 2019
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xrobin added a commit that referenced this issue May 31, 2019
@xrobin
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@xrobin xrobin commented Jun 1, 2019

Email sent to 49 maintainers of reverse dependencies.

Delivery failures for EFS (Ursula Neumann, mailbox quota exceeded), blkbox (Boris Guennewig, 550 Address rejected), and sambia (Norbert Krautenbacher, 550 Recipient address rejected).

@xrobin
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@xrobin xrobin commented Jun 10, 2019

4 emails and 2 PR sent to authors of packages found using coords:

lwaldron added a commit to waldronlab/doppelgangR that referenced this issue Jun 10, 2019
Use tidy version of coords (xrobin/pROC#54)
DavisVaughan added a commit to tidymodels/yardstick that referenced this issue Jul 30, 2019
Use tidy version of coords (xrobin/pROC#54)
@xrobin
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@xrobin xrobin commented Dec 4, 2019

Email sent now to 57 reverse depends/imports (5 delivery failures) and 21 reverse suggests (1 delivery failure).

Reminder diff sent to Colin Tredoux (r4lineups) and bug report for biomod2 (bug #6650), which are the last 2 packages detected as impacted that haven't been fixed yet.

xrobin added a commit that referenced this issue Dec 8, 2019
Needed to drop row names which are not allowed to be duplicated. Update doc with latest changes.
xrobin added a commit that referenced this issue Dec 8, 2019
Needed to drop row names which are not allowed to be duplicated. Update doc with latest changes. Turn off dropping dimensions by default.
@xrobin
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@xrobin xrobin commented Dec 8, 2019

The coords function now uses a data.frame internally too. Following Tibble's Overview, I dropped row names which are sometimes duplicated, and turned off dropping dimensions by default. This required some adaptation of the tests and examples.

@xrobin
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@xrobin xrobin commented Jan 4, 2020

The use of a data.frame internally came with a significant performance hit (apparently related to row indexing/updating operations, which are used a lot here). CI operations became unacceptably slow. Reverted to use matrix internally and added an as.matrix option, used in CI. Still defaults to returning a data.frame, but conversion happens in the end.

xrobin added a commit that referenced this issue Jan 4, 2020
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@xrobin xrobin commented Jan 12, 2020

pROC 1.16.0 is on CRAN with transpose = FALSE by default.

Closing, future changes to remove the warning (probably in ~ 1 year) and potentially drop transpose = TRUE altogether will go to new issues.

@xrobin xrobin closed this Jan 12, 2020
xrobin added a commit that referenced this issue Dec 27, 2020
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