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Aug 31 2020

wiesenfa added a comment to T27475: Legend of blob plot has missing legend title and algorithms.

@eisenman please close when finished

Aug 31 2020, 3:48 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER43b6f47337a1: missings warning message respects single tasks (authored by wiesenfa).
missings warning message respects single tasks
Aug 31 2020, 3:45 PM
wiesenfa moved T27657: When missing algorithm performances are added as NAs, task is also NA from Backlog to In Progress on the challengeR (v1.0) board.
Aug 31 2020, 3:37 PM · challengeR (v1.0)
wiesenfa claimed T27657: When missing algorithm performances are added as NAs, task is also NA.
Aug 31 2020, 3:37 PM · challengeR (v1.0)
wiesenfa moved T27253: Notify user when multi-task data set is interpreted as single-task data set from Backlog to In Progress on the challengeR (v1.0) board.
Aug 31 2020, 3:37 PM · challengeR (v1.0)
wiesenfa added a comment to T27253: Notify user when multi-task data set is interpreted as single-task data set.

if at least one quarter of cases have a duplicate, the error message is extended by "Or are you considering a multi-task challenge and forgot to specify argument 'by'? "
Otherwise the error message is now further improved, e.g. if it is a single task, the error message doesn't mention "in task dummyTask any more".
Example error message:

Aug 31 2020, 3:36 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER80d24ef83d16: informative message in case of duplicates (authored by wiesenfa).
informative message in case of duplicates
Aug 31 2020, 3:32 PM
wiesenfa claimed T27449: Consistent handling of plots created for multi-task data sets.
Aug 31 2020, 2:51 PM · challengeR (v1.0)
wiesenfa claimed T27338: Report contains misleading information on missing values.
Aug 31 2020, 2:51 PM · challengeR (v1.0)
wiesenfa claimed T27452: Provide plot function for dendrogram.
Aug 31 2020, 2:50 PM · challengeR (v1.0)
wiesenfa claimed T27411: Improve labels in cluster dendrogram.
Aug 31 2020, 2:50 PM · challengeR (v1.0)
wiesenfa claimed T27337: Report contains wrong ranking method when rank-then-aggregate is used.
Aug 31 2020, 2:50 PM · challengeR (v1.0)
wiesenfa added a comment to T27447: significanceMap function raises warning about deprecated function call.

@eisenman I don't get this warning. Could you give more details/ an example? or is this already solved/not relevant anymore?

Aug 31 2020, 2:48 PM · challengeR (v1.0)
wiesenfa lowered the priority of T27450: Consistent use of attribute indicating whether small metric values lead to a better rank from Normal to Low.
Aug 31 2020, 2:45 PM · challengeR (v1.0)
wiesenfa added a comment to T27450: Consistent use of attribute indicating whether small metric values lead to a better rank.

yes this has historical reasons (largeBetter had been "inverseOrder" in the beginning which was horrible;-))
smallBetter would have the advantage that the user interface would not change, modifying as.challenge with largeBetter would mean that existing scripts lead to wrong results which is problematic.
could someone of you please take care of this one?

Aug 31 2020, 2:43 PM · challengeR (v1.0)
wiesenfa lowered the priority of T27327: warning in docx report from Normal to Low.
Aug 31 2020, 2:39 PM · challengeR (v1.0)
wiesenfa added a comment to T27288: separate readme.md and readme.Rmd.

see comment in T27241

Aug 31 2020, 2:37 PM · challengeR (v1.0)
wiesenfa added a comment to T27288: separate readme.md and readme.Rmd.
Aug 31 2020, 2:32 PM · challengeR (v1.0)
wiesenfa added a comment to T27241: Readme improvements.

@aguilera
regarding issue 1: Rmd should be changed if we want to keep that the current package version at the beginning is automatically inserted. otherwise we could only work with the md file and drop the Rmd file. the readme.md file has to stay in the root directory such that GitHub finds it. If .Rmd file is also in root the easiest thing is to compile it such that it will be in the same directory. I don't remember, why do we need to change this?

Aug 31 2020, 2:22 PM · challengeR (v1.0)
wiesenfa added a comment to T27474: Legend of line plot has missing legend title and algorithm.

@eisenman can larger number of algorithms be checked? what's your opinion? please close otherwise.

Aug 31 2020, 2:05 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER1b5c2b17a680: adapt figure heights to avoid crop (authored by wiesenfa).
adapt figure heights to avoid crop
Aug 31 2020, 1:58 PM
wiesenfa added a comment to T27475: Legend of blob plot has missing legend title and algorithms.

solved (at least for 19 tasks) in merge for T27474

Aug 31 2020, 1:56 PM · challengeR (v1.0)
wiesenfa added a comment to T27420: report text.

items 3 and 4 solved (see separate tasks).
solved at least for 19 algorithms.

Aug 31 2020, 1:55 PM · challengeR (v1.0)
wiesenfa moved T27474: Legend of line plot has missing legend title and algorithm from Backlog to In Progress on the challengeR (v1.0) board.
Aug 31 2020, 1:53 PM · challengeR (v1.0)
wiesenfa moved T27475: Legend of blob plot has missing legend title and algorithms from Backlog to In Progress on the challengeR (v1.0) board.
Aug 31 2020, 1:53 PM · challengeR (v1.0)
wiesenfa added a comment to T27474: Legend of line plot has missing legend title and algorithm.

solved at least for 19 algorithms (MSD data).

Aug 31 2020, 1:52 PM · challengeR (v1.0)
wiesenfa added a comment to T27449: Consistent handling of plots created for multi-task data sets.

maybe introduce some utility function that takes care of it

Aug 31 2020, 10:02 AM · challengeR (v1.0)
wiesenfa lowered the priority of T27286: interactive plots from Normal to Wishlist.
Aug 31 2020, 9:54 AM · challengeR

Aug 27 2020

wiesenfa updated subscribers of T27686: tutorial can be added as vignette to embed it in the package .
Aug 27 2020, 10:54 AM · challengeR (v1.0)
wiesenfa created T27686: tutorial can be added as vignette to embed it in the package .
Aug 27 2020, 10:53 AM · challengeR (v1.0)
wiesenfa created T27685: changes in subset().
Aug 27 2020, 10:44 AM · challengeR (v1.0)

Aug 7 2020

wiesenfa reassigned T27252: Multiple cases per algorithm are not detected when missing data was added before from wiesenfa to eisenman.
Aug 7 2020, 2:49 PM · challengeR (v1.0)
wiesenfa added a comment to T27252: Multiple cases per algorithm are not detected when missing data was added before.

should work now, tests successful.
However warning is

Performance of not all algorithms is observed for all cases in task 'dummyTask'

despite being single task challenge. see also separate task #T27657

Aug 7 2020, 2:47 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER4a2a4d181421: always check both for missings and duplicates (authored by wiesenfa).
always check both for missings and duplicates
Aug 7 2020, 2:41 PM
wiesenfa created T27658: LaTeX Warning: There were undefined references.
Aug 7 2020, 2:31 PM · challengeR (v1.0)
wiesenfa moved T27252: Multiple cases per algorithm are not detected when missing data was added before from Backlog to In Progress on the challengeR (v1.0) board.
Aug 7 2020, 2:10 PM · challengeR (v1.0)
wiesenfa created T27657: When missing algorithm performances are added as NAs, task is also NA.
Aug 7 2020, 2:10 PM · challengeR (v1.0)
wiesenfa moved T27453: Create complete network plot in its function from Backlog to In Progress on the challengeR (v1.0) board.
Aug 7 2020, 1:05 PM · challengeR (v1.0)
wiesenfa moved T27494: Check which files are still relevant from Backlog to In Progress on the challengeR (v1.0) board.
Aug 7 2020, 1:03 PM · challengeR
wiesenfa moved T27407: Warnings are shown in multi-task challenge report for violin plot from Backlog to Done on the challengeR (v1.0) board.
Aug 7 2020, 12:59 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER48b7e35505c6: handle warnings in violin (authored by wiesenfa).
handle warnings in violin
Aug 7 2020, 12:57 PM
wiesenfa added a comment to T27494: Check which files are still relevant.
  • compareRanks() allows to compare 2 ranking lists and compute Kendall's tau, would leave it in package
  • benchmarkUtils allows to link with benchmark package (CRAN archived) which has some more features, but is not maintained anymore. might be dropped
Aug 7 2020, 12:36 PM · challengeR
wiesenfa committed rCHALLENGER4520859fe0f3: ensure that challenge object is data.frame (authored by wiesenfa).
ensure that challenge object is data.frame
Aug 7 2020, 12:10 PM
wiesenfa moved T27656: make sure data set is data.frame from In Progress to Done on the challengeR (v1.0) board.
Aug 7 2020, 12:00 PM · challengeR (v1.0)
wiesenfa moved T27656: make sure data set is data.frame from Backlog to In Progress on the challengeR (v1.0) board.
Aug 7 2020, 12:00 PM · challengeR (v1.0)
wiesenfa created T27656: make sure data set is data.frame.
Aug 7 2020, 11:48 AM · challengeR (v1.0)

Aug 6 2020

wiesenfa added a comment to T27453: Create complete network plot in its function.

can be closed?

Aug 6 2020, 12:29 PM · challengeR (v1.0)
wiesenfa added a comment to T27453: Create complete network plot in its function.

the complication arises to handle the automatic sizing of the plot, which is why in the first chunk it reads out the width without plotting and in the second chunk the figure width is adapted

Aug 6 2020, 12:28 PM · challengeR (v1.0)
wiesenfa added a comment to T27453: Create complete network plot in its function.

the function is network() and is already in the report

Aug 6 2020, 10:09 AM · challengeR (v1.0)

May 14 2020

wiesenfa added a comment to T27396: Represent single-task challenge as multi-task challenge with one task.

Something important I think is also, that all plot functions work outside of the report as intended (it is desirable that users can also create their own reports). This includes choosing the correct function and giving an error if a function does not work with single tasks, e.g.

May 14 2020, 2:25 PM · challengeR (v1.0)
wiesenfa added a comment to T27396: Represent single-task challenge as multi-task challenge with one task.

Thanks.
In a single task situation, in practice a task will not have a name, so there should be no title and there should not be the need to set a task name I think....
I'll have a look at it, but please give me some time

May 14 2020, 2:20 PM · challengeR (v1.0)
wiesenfa added a comment to T27396: Represent single-task challenge as multi-task challenge with one task.

I think this should be well thought through before putting into action

May 14 2020, 11:42 AM · challengeR (v1.0)
wiesenfa created T27420: report text.
May 14 2020, 10:58 AM · challengeR (v1.0)
wiesenfa added a comment to T27407: Warnings are shown in multi-task challenge report for violin plot.

it's not because of missing test cases. It is because in certain situation no Kendall can be computed. Don't use treat.na for this.

May 14 2020, 10:53 AM · challengeR (v1.0)

May 11 2020

wiesenfa added a comment to T27338: Report contains misleading information on missing values.

I agree, it would be nice if the actual number of NAs would be reported (together with the na.treat method) and not the number after na.treat which is then obviously 0.

May 11 2020, 2:05 PM · challengeR (v1.0)
wiesenfa added a comment to T27326: autolayout networks in multi task report ugly.

layouting (circle sizes, distances, font sizes, size of plot) needs to be automatically optimized which I failed so far

May 11 2020, 2:04 PM · challengeR
wiesenfa added a comment to T27385: Variables holding the aggregated value are named differently for single- and multi-task challenges.

Did you take care that FUN="mean" and FUN=mean is handled differently (in the former case it is a name, in the latter case it is a function)?

May 11 2020, 2:02 PM · challengeR (v1.0)
wiesenfa added a comment to T27396: Represent single-task challenge as multi-task challenge with one task.

might indeed reduce complexity, however,

  • many functions need to be adapted requiring some care
  • behavior is sometimes by purpose different, e.g. there are plot titles with the task name in multi-task challenges while there is none in single task challenges
  • many visualizations apply only to multi-task challenges and trying to use them in single task challenges throws an error, this would be needed to be handled
  • also reports for multi task challenges contain more visualizations which would be uninformative for single task challenges (could however be handled by checking the number of tasks internally)
  • a workaround would be necessary adding a task column to single class challenges (with the same label in every row)
May 11 2020, 1:59 PM · challengeR (v1.0)

Apr 29 2020

wiesenfa moved T27252: Multiple cases per algorithm are not detected when missing data was added before from In Progress to Backlog on the challengeR (v1.0) board.
Apr 29 2020, 4:03 PM · challengeR (v1.0)
wiesenfa added a comment to T27252: Multiple cases per algorithm are not detected when missing data was added before.

ok

Apr 29 2020, 4:03 PM · challengeR (v1.0)

Apr 27 2020

wiesenfa created T27360: compatibility with R4.0.0.
Apr 27 2020, 5:27 PM · challengeR (v1.0)
wiesenfa placed T27287: is warning given if na.treat unspecified in rank-first and obligatory otherwise up for grabs.
Apr 27 2020, 4:25 PM · challengeR (v1.0)
wiesenfa added a comment to T27287: is warning given if na.treat unspecified in rank-first and obligatory otherwise.

@eisenman : could you please check whether there is something to be done?

Apr 27 2020, 4:24 PM · challengeR (v1.0)
wiesenfa added a comment to T27323: Found bug for report with rankThenAggregate.

can this be closed?

Apr 27 2020, 4:23 PM · challengeR (v1.0)
wiesenfa added a comment to T27252: Multiple cases per algorithm are not detected when missing data was added before.

@eisenman: did you take over solving this task? Or should I still do something here?

Apr 27 2020, 4:21 PM · challengeR (v1.0)

Apr 20 2020

wiesenfa added a comment to T27323: Found bug for report with rankThenAggregate.

This is strange. This should normally not happen only if there is a strange package interfering . It is helpful to run sessionInfo() or slightly more detailed devtools::session_info() after a bug happened and report that in the task

Apr 20 2020, 8:55 AM · challengeR (v1.0)

Apr 17 2020

wiesenfa created T27327: warning in docx report.
Apr 17 2020, 2:19 PM · challengeR (v1.0)
wiesenfa created T27326: autolayout networks in multi task report ugly.
Apr 17 2020, 2:14 PM · challengeR
wiesenfa created T27325: Plot titles in rankingHeatmap missing in multi task report.
Apr 17 2020, 2:12 PM · challengeR (v1.0)

Apr 3 2020

wiesenfa created T27294: add multiple figure output formats in report with option clean=TRUE.
Apr 3 2020, 5:06 PM · challengeR (v1.0)
wiesenfa created T27291: update license file.
Apr 3 2020, 4:11 PM · challengeR (v1.0)

Apr 2 2020

wiesenfa claimed T27253: Notify user when multi-task data set is interpreted as single-task data set.
Apr 2 2020, 11:32 AM · challengeR (v1.0)
wiesenfa created T27288: separate readme.md and readme.Rmd.
Apr 2 2020, 11:32 AM · challengeR (v1.0)
wiesenfa created T27287: is warning given if na.treat unspecified in rank-first and obligatory otherwise.
Apr 2 2020, 11:31 AM · challengeR (v1.0)
wiesenfa updated subscribers of T27286: interactive plots.
Apr 2 2020, 11:29 AM · challengeR
wiesenfa created T27286: interactive plots.
Apr 2 2020, 11:29 AM · challengeR

Mar 27 2020

wiesenfa added a comment to T27241: Readme improvements.

There should be a team section where all of you are acknowledged

Mar 27 2020, 10:48 AM · challengeR (v1.0)
wiesenfa added a comment to T27256: Changes during sanity check can constradict NA handling option.

in my opinion this is a desirable feature

Mar 27 2020, 10:43 AM · challengeR