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wiesenfa (Manuel Wiesenfarth)
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Mar 2 2020, 3:23 PM (46 w, 1 d)

Recent Activity

Dec 18 2020

wiesenfa created T28124: add line plot (like methods plot) across tasks to report.
Dec 18 2020, 6:28 PM · challengeR

Dec 17 2020

wiesenfa added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

platform is output with Sys.info(); linux and Mac systems are equal and windows may differ

Dec 17 2020, 5:55 PM · challengeR (v1.0)
wiesenfa added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

good idea!
otherwise you could use a platform dependent expect_equal but I think your idea is sufficient

Dec 17 2020, 5:53 PM · challengeR (v1.0)
wiesenfa added a comment to T28121: Remove parallel bootstrapping from quick-start scripts.

would mention it there at least though because bootstrapping may be time consuming

Dec 17 2020, 5:14 PM · challengeR (v1.0)
wiesenfa added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

don't think its necessary. there is anyway ordering applied to it in later stages.
otherwise ranking step (rank.aggregated.list()) could always do the ordering directly (then the test would check whether ordering is working). As mentioned before I avoided such change before the release because of (very unlikely) risk of breaking something in the first level hierarchy

Dec 17 2020, 5:13 PM · challengeR (v1.0)
wiesenfa added a comment to T28119: Unit tests are failing on Ubuntu due to mismatching messages.

I do see those as well on Mac

Dec 17 2020, 4:46 PM · challengeR (v1.0)
wiesenfa added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

R 4.0.2.
testthat previously 2.3.2, now 3.0.1.
the issue is however not connected to test_that I see that in the first 2 tests in aggregate-then-rank the ordering in the data set is not used but sorted

Dec 17 2020, 4:45 PM · challengeR (v1.0)

Dec 14 2020

wiesenfa added a comment to T28097: test errors in aggregateThenRank and rankThenAggregate.

seems to not fail on windows machines. but does on my Mac (and thus might also on linux). minor issue, defer to post 1.0.0

Dec 14 2020, 6:47 PM · challengeR (v1.0)
wiesenfa moved T28112: colors in box plots multitask not consistent from In Progress to Done on the challengeR (v1.0) board.
Dec 14 2020, 2:09 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER018edb100eae: T28112: respect algo colors in boxplots (authored by wiesenfa).
T28112: respect algo colors in boxplots
Dec 14 2020, 2:08 PM
wiesenfa moved T28112: colors in box plots multitask not consistent from Backlog to In Progress on the challengeR (v1.0) board.
Dec 14 2020, 2:07 PM · challengeR (v1.0)
wiesenfa created T28112: colors in box plots multitask not consistent.
Dec 14 2020, 1:33 PM · challengeR (v1.0)

Dec 10 2020

wiesenfa moved T27292: Fix toolkit authors from In Progress to Done on the challengeR (v1.0) board.
Dec 10 2020, 1:25 PM · challengeR (v1.0)
wiesenfa moved T27292: Fix toolkit authors from Backlog to In Progress on the challengeR (v1.0) board.
Dec 10 2020, 1:25 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER9217054b61ae: fix authors (authored by wiesenfa).
fix authors
Dec 10 2020, 1:25 PM
wiesenfa created T28097: test errors in aggregateThenRank and rankThenAggregate.
Dec 10 2020, 11:11 AM · challengeR (v1.0)
wiesenfa moved T28085: Report generation is broken from In Progress to Done on the challengeR (v1.0) board.
Dec 10 2020, 11:09 AM · challengeR (v1.0)
wiesenfa moved T28085: Report generation is broken from Backlog to In Progress on the challengeR (v1.0) board.
Dec 10 2020, 11:09 AM · challengeR (v1.0)
wiesenfa claimed T28085: Report generation is broken.
Dec 10 2020, 11:09 AM · challengeR (v1.0)
wiesenfa committed rCHALLENGER484d1c685a70: bug fixes (authored by wiesenfa).
bug fixes
Dec 10 2020, 11:08 AM
wiesenfa committed rCHALLENGER8fe6dd4d9574: ensure english warnings while testing (authored by wiesenfa).
ensure english warnings while testing
Dec 10 2020, 11:08 AM

Dec 7 2020

wiesenfa added a comment to T27925: Use cases of annotator option.

would defer to after release

Dec 7 2020, 3:58 PM · challengeR
wiesenfa added a comment to T27494: Check which files are still relevant.

please close if ok

Dec 7 2020, 3:58 PM · challengeR
wiesenfa committed rCHALLENGER77411271cd7a: fix podium (authored by wiesenfa).
fix podium
Dec 7 2020, 3:51 PM
wiesenfa committed rCHALLENGERd7c27e2a6dad: fix (authored by wiesenfa).
fix
Dec 7 2020, 3:51 PM
wiesenfa committed rCHALLENGER4a677bed212f: style (authored by wiesenfa).
style
Dec 7 2020, 3:51 PM
wiesenfa committed rCHALLENGER38ac623e8adc: add annotor (authored by wiesenfa).
add annotor
Dec 7 2020, 3:51 PM
wiesenfa added a comment to T27925: Use cases of annotator option.

added to documentation of as.challenge():
(arg annotator:) If multiple annotators annotated the test cases, a string specifying the name of the column that contains the annotator identifiers. Only applies to rang-then-aggregate. Use with caution: Currently not tested.

Dec 7 2020, 3:18 PM · challengeR
wiesenfa moved T27925: Use cases of annotator option from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 3:16 PM · challengeR
wiesenfa committed rCHALLENGER17905fc80c85: add man for annotator (authored by wiesenfa).
add man for annotator
Dec 7 2020, 3:16 PM
wiesenfa added a comment to T27971: Provide code for podium plot in vignette "Visualizations".

added

podium(ranking)

to vignette.
podium() does have a different syntax for layouting (it is not ggplot2 but base graphics) but vignette does not describe layouting for ggplot2 plots either

Dec 7 2020, 2:20 PM · challengeR (v1.0)
wiesenfa moved T27971: Provide code for podium plot in vignette "Visualizations" from Backlog to Done on the challengeR (v1.0) board.
Dec 7 2020, 2:18 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER6267c97aeb1b: T27971 podium in visualizations vignette (authored by wiesenfa).
T27971 podium in visualizations vignette
Dec 7 2020, 2:13 PM
wiesenfa committed rCHALLENGERf899ce83619a: add euclidean consensus man (authored by wiesenfa).
add euclidean consensus man
Dec 7 2020, 2:13 PM
wiesenfa committed rCHALLENGER269f169422a0: update man (authored by wiesenfa).
update man
Dec 7 2020, 2:13 PM
wiesenfa committed rCHALLENGERccd930a457fd: add details for euclidean consensus (authored by wiesenfa).
add details for euclidean consensus
Dec 7 2020, 2:13 PM
wiesenfa placed T27998: Interpretation of consensus ranking values needs further explanation up for grabs.
Dec 7 2020, 2:03 PM · challengeR (v1.0)
wiesenfa moved T27998: Interpretation of consensus ranking values needs further explanation from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 2:03 PM · challengeR (v1.0)
wiesenfa added a comment to T27998: Interpretation of consensus ranking values needs further explanation.

report() does not know what type of consensus ranking method had been used.
I added sentence
"Consensus ranking according to mean ranks across tasks if method="euclidean" where in case of ties (equal ranks for multiple algorithms) the average rank is used, i.e. ties.method="average"."
to help for consensus() and would suggest to also add this to the vignette/readme, but not to report. Could someone of you please take care of this?

Dec 7 2020, 2:03 PM · challengeR (v1.0)
wiesenfa added a comment to T27775: only export functions to be used by user.

@eisenman do you want to do this with roxygen?

Dec 7 2020, 1:10 PM · challengeR
wiesenfa assigned T27494: Check which files are still relevant to eisenman.
Dec 7 2020, 1:09 PM · challengeR
wiesenfa assigned T28016: embed web app in package to eisenman.
Dec 7 2020, 1:09 PM · challengeR (v1.0)
wiesenfa claimed T27998: Interpretation of consensus ranking values needs further explanation.
Dec 7 2020, 1:08 PM · challengeR (v1.0)
wiesenfa moved T28016: embed web app in package from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 1:08 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER2ade85d374f7: fix tests (authored by wiesenfa).
fix tests
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGER3578ab9be39c: allow consensus named numeric vector or ordered character vector (authored by wiesenfa).
allow consensus named numeric vector or ordered character vector
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGER6fc162a3bcde: remove compare.rank (authored by wiesenfa).
remove compare.rank
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGER019ec7bb9392: remove winner.ranked (authored by wiesenfa).
remove winner.ranked
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGERb925ab764dba: fix (authored by wiesenfa).
fix
Dec 7 2020, 1:07 PM
wiesenfa committed rCHALLENGERdeb1db150dac: T27943 allow ordering numeric (authored by wiesenfa).
T27943 allow ordering numeric
Dec 7 2020, 1:07 PM
wiesenfa moved T27943: Plot function stability() raises error when used with default values from In Progress to Done on the challengeR (v1.0) board.
Dec 7 2020, 1:07 PM · challengeR (v1.0)
wiesenfa added a comment to T27494: Check which files are still relevant.

kept select.if(), winner(), extract.workfolow and compareRanks()
and removed everything not supported anymore.
as.warehouse (benchmarkUtils) is not exported, recommend to leave because this may come handy for specific situations

Dec 7 2020, 1:07 PM · challengeR
wiesenfa moved T27494: Check which files are still relevant from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 12:56 PM · challengeR
wiesenfa moved T27943: Plot function stability() raises error when used with default values from Backlog to In Progress on the challengeR (v1.0) board.
Dec 7 2020, 11:21 AM · challengeR (v1.0)
wiesenfa added a comment to T27494: Check which files are still relevant.

removed second()

Dec 7 2020, 11:19 AM · challengeR

Dec 4 2020

wiesenfa committed rCHALLENGER6144decf510d: delete funciton second() (unmaintained) (authored by wiesenfa).
delete funciton second() (unmaintained)
Dec 4 2020, 8:49 PM
wiesenfa placed T27971: Provide code for podium plot in vignette "Visualizations" up for grabs.
Dec 4 2020, 8:46 PM · challengeR (v1.0)
wiesenfa added a comment to T27971: Provide code for podium plot in vignette "Visualizations".

What is the problem?
in the extend of the vignette it would be simply

Dec 4 2020, 8:46 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER2e04538d9e1d: podium default topright legend (authored by wiesenfa).
podium default topright legend
Dec 4 2020, 8:44 PM
wiesenfa moved T27915: Podium plot shrinks for long algorithm names from In Progress to Done on the challengeR (v1.0) board.
Dec 4 2020, 8:40 PM · challengeR (v1.0)
wiesenfa added a comment to T27915: Podium plot shrinks for long algorithm names.

legend now always at bottom and dynamically adjusts to number of algorithms and algorithm name length.
Took me almost the day...

Dec 4 2020, 8:40 PM · challengeR (v1.0)
wiesenfa moved T27748: Decide on limit for algorithms in plot legends from In Progress to Done on the challengeR (v1.0) board.
Dec 4 2020, 8:39 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER26eb63cdef48: report podium plot dynamic legend bottom (authored by wiesenfa).
report podium plot dynamic legend bottom
Dec 4 2020, 8:38 PM
wiesenfa committed rCHALLENGER019b63757493: bottom legend in line plot if n.algorithms>20 (authored by wiesenfa).
bottom legend in line plot if n.algorithms>20
Dec 4 2020, 8:38 PM
wiesenfa committed rCHALLENGERdad94cd28be0: bottom legend in stacked frequency if n.tasks>20 (authored by wiesenfa).
bottom legend in stacked frequency if n.tasks>20
Dec 4 2020, 8:38 PM
wiesenfa added a comment to T27748: Decide on limit for algorithms in plot legends.

max number of tasks / algorithms now 20 in stacked frequency and line plots, respectively for legend appear on right, otherwise put on bottom of plot. could also be put to lower number

Dec 4 2020, 12:00 PM · challengeR (v1.0)
wiesenfa added a comment to T27748: Decide on limit for algorithms in plot legends.

only podium plots and line plots actually require algorithms in legend, otherwise algorithm is identifiable from x-axis or facet label. Now, these redundant legends are removed.
besides that stacked frequency plots have colored tasks and respective legend

Dec 4 2020, 11:52 AM · challengeR (v1.0)
wiesenfa committed rCHALLENGER126a4af6fa0c: remove legend if algorithm identifiable in x-axis (authored by wiesenfa).
remove legend if algorithm identifiable in x-axis
Dec 4 2020, 11:41 AM
wiesenfa committed rCHALLENGER4b396c8ddc14: introduce n.tasks in Rmd (authored by wiesenfa).
introduce n.tasks in Rmd
Dec 4 2020, 11:41 AM
wiesenfa committed rCHALLENGER527c8578ee15: introduce n.tasks and n.algorithms in Rmd files (authored by wiesenfa).
introduce n.tasks and n.algorithms in Rmd files
Dec 4 2020, 11:41 AM
wiesenfa committed rCHALLENGERced7c6c06339: improve reporting of used aggregation method (authored by wiesenfa).
improve reporting of used aggregation method
Dec 4 2020, 11:41 AM
wiesenfa committed rCHALLENGER11b645ebaac1: hide output of task names in report 4.2.1 (authored by wiesenfa).
hide output of task names in report 4.2.1
Dec 4 2020, 11:41 AM
wiesenfa moved T27915: Podium plot shrinks for long algorithm names from Backlog to In Progress on the challengeR (v1.0) board.
Dec 4 2020, 9:55 AM · challengeR (v1.0)
wiesenfa moved T27748: Decide on limit for algorithms in plot legends from Backlog to In Progress on the challengeR (v1.0) board.
Dec 4 2020, 9:55 AM · challengeR (v1.0)
wiesenfa moved T27707: na.treat obligatory for report from In Progress to Done on the challengeR (v1.0) board.
Dec 4 2020, 9:36 AM · challengeR (v1.0)
wiesenfa moved T27707: na.treat obligatory for report from Backlog to In Progress on the challengeR (v1.0) board.
Dec 4 2020, 9:36 AM · challengeR (v1.0)
wiesenfa committed rCHALLENGER6ee0e3a4dbd1: messages if na.treat not specified and NA present (authored by wiesenfa).
messages if na.treat not specified and NA present
Dec 4 2020, 9:35 AM

Dec 3 2020

wiesenfa claimed T27748: Decide on limit for algorithms in plot legends.
Dec 3 2020, 10:22 PM · challengeR (v1.0)
wiesenfa moved T27963: Task names printed as R output in Sec. 3.1 of multi-task report from In Progress to Done on the challengeR (v1.0) board.
Dec 3 2020, 10:21 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER1df7fcff2ba7: hide unnecessary text (authored by wiesenfa).
hide unnecessary text
Dec 3 2020, 10:21 PM
wiesenfa moved T27963: Task names printed as R output in Sec. 3.1 of multi-task report from Backlog to In Progress on the challengeR (v1.0) board.
Dec 3 2020, 10:14 PM · challengeR (v1.0)
wiesenfa moved T28033: +scale_* seems to not work in combination with ggList objects from In Progress to Done on the challengeR (v1.0) board.
Dec 3 2020, 10:11 PM · challengeR (v1.0)
wiesenfa added a comment to T28033: +scale_* seems to not work in combination with ggList objects.

works again for single task visualizations. in case multiple plots (a list of plots) is created %++% instead of + must be used for scale_*_() etc
mention in vignette

Dec 3 2020, 10:09 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER2c873612bef5: return gg object if single task (authored by wiesenfa).
return gg object if single task
Dec 3 2020, 10:06 PM
wiesenfa moved T28033: +scale_* seems to not work in combination with ggList objects from Backlog to In Progress on the challengeR (v1.0) board.
Dec 3 2020, 9:52 PM · challengeR (v1.0)
wiesenfa added a comment to T28016: embed web app in package.

ok. just an idea, thought this might help issues with the server because people can run stuff by themselves and still seize the user interface.
can be closed or considered later

Dec 3 2020, 8:48 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGEReaba380339a2: podium: allow linetype and symbol depend on algo (authored by wiesenfa).
podium: allow linetype and symbol depend on algo
Dec 3 2020, 3:38 PM
wiesenfa moved T28055: respect color scheme also for box plots from In Progress to Done on the challengeR (v1.0) board.
Dec 3 2020, 1:57 PM · challengeR (v1.0)
wiesenfa moved T28055: respect color scheme also for box plots from Backlog to In Progress on the challengeR (v1.0) board.
Dec 3 2020, 1:57 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER403c0cc189b4: return gg object for single tasks, respect color scheme (authored by wiesenfa).
return gg object for single tasks, respect color scheme
Dec 3 2020, 1:56 PM
wiesenfa created T28055: respect color scheme also for box plots.
Dec 3 2020, 12:03 PM · challengeR (v1.0)

Nov 27 2020

wiesenfa claimed T28033: +scale_* seems to not work in combination with ggList objects.
Nov 27 2020, 3:23 PM · challengeR (v1.0)
wiesenfa created T28033: +scale_* seems to not work in combination with ggList objects.
Nov 27 2020, 1:55 PM · challengeR (v1.0)

Nov 26 2020

wiesenfa created T28016: embed web app in package.
Nov 26 2020, 8:48 AM · challengeR (v1.0)

Nov 23 2020

wiesenfa claimed T27971: Provide code for podium plot in vignette "Visualizations".
Nov 23 2020, 12:08 PM · challengeR (v1.0)
wiesenfa claimed T27963: Task names printed as R output in Sec. 3.1 of multi-task report.
Nov 23 2020, 12:07 PM · challengeR (v1.0)

Nov 12 2020

wiesenfa claimed T27943: Plot function stability() raises error when used with default values.
Nov 12 2020, 1:20 PM · challengeR (v1.0)
wiesenfa added a comment to T27943: Plot function stability() raises error when used with default values.

It has to be
ordering= names(meanRanks)
i.e. a vector of algorithm names in the ranking order
see reportMultiple.Rmd: ordering_consensus=names(params$consensus)

Nov 12 2020, 1:20 PM · challengeR (v1.0)

Nov 9 2020

wiesenfa claimed T27925: Use cases of annotator option.
Nov 9 2020, 9:48 AM · challengeR
wiesenfa added a comment to T27925: Use cases of annotator option.

will check old documentation/nature communications example

Nov 9 2020, 9:48 AM · challengeR