Page MenuHomePhabricator
Feed Advanced Search

Sep 30 2020

eisenman committed rCHALLENGERe70a83c00a2c: Rename directory (authored by eisenman).
Rename directory
Sep 30 2020, 1:56 PM
eisenman claimed T27686: tutorial can be added as vignette to embed it in the package .
Sep 30 2020, 1:36 PM · challengeR (v1.0)
eisenman merged task T27288: separate readme.md and readme.Rmd into T27241: Readme improvements.
Sep 30 2020, 1:23 PM · challengeR (v1.0)
eisenman merged T27288: separate readme.md and readme.Rmd into T27241: Readme improvements.
Sep 30 2020, 1:23 PM · challengeR (v1.0)
eisenman moved T27282: Implement tests for ranking method "test-then-rank" based on Wilcoxon signed rank test from In Progress to Done on the challengeR (v1.0) board.
Sep 30 2020, 1:21 PM · challengeR (v1.0)
eisenman added a comment to T27456: Extraction of task subset from (bootstrap) ranking does not raise an error for invalid task name.

The idea is to raise an error if the user tries to extract a task that is not contained in the set of tasks.

Sep 30 2020, 1:19 PM · challengeR (v1.0)
eisenman committed rCHALLENGERa9f26cb623be: Merge branch 'feature/T27282-AddTestsForTestThenRank' into develop (authored by eisenman).
Merge branch 'feature/T27282-AddTestsForTestThenRank' into develop
Sep 30 2020, 12:57 PM
eisenman committed rCHALLENGER4ba8b0ba84a7: Adapt column heading (authored by eisenman).
Adapt column heading
Sep 30 2020, 12:55 PM
eisenman committed rCHALLENGERb22ed4b2ebc8: Clean up (authored by eisenman).
Clean up
Sep 30 2020, 12:55 PM
eisenman added a comment to T27282: Implement tests for ranking method "test-then-rank" based on Wilcoxon signed rank test.

The function testThenRank has an argument FUN that is set to "significance" internally. The value that is actually passed is not used.
@wiesenfa Should "significance" be the default value in the signature already or should the argument be removed?

Sep 30 2020, 12:51 PM · challengeR (v1.0)
eisenman triaged T27802: Revise signature of function testThenRank as High priority.
Sep 30 2020, 12:50 PM · challengeR (v1.0)

Sep 29 2020

eisenman committed rCHALLENGER0d18d9a64990: Test that test-then-rank raises warning for one algorithm (authored by eisenman).
Test that test-then-rank raises warning for one algorithm
Sep 29 2020, 5:37 PM
eisenman committed rCHALLENGER16fec9a23aa9: Test that NAs are replaced by numeric value in multi-task data set (authored by eisenman).
Test that NAs are replaced by numeric value in multi-task data set
Sep 29 2020, 3:57 PM
eisenman committed rCHALLENGER186cda66338e: Test that test-then-rank raises error when no NA treatment specified but NAs… (authored by eisenman).
Test that test-then-rank raises error when no NA treatment specified but NAs…
Sep 29 2020, 3:57 PM
eisenman committed rCHALLENGERdf8b11ee1286: Test that test-then-rank works for multi-task data set with no missing data (authored by eisenman).
Test that test-then-rank works for multi-task data set with no missing data
Sep 29 2020, 3:57 PM
eisenman committed rCHALLENGERa0fadafa4197: Test options for handling of NAs (authored by eisenman).
Test options for handling of NAs
Sep 29 2020, 3:38 PM
eisenman committed rCHALLENGERf948633a42b8: Test that test-then-rank raises error for invalid ties method even when no ties… (authored by eisenman).
Test that test-then-rank raises error for invalid ties method even when no ties…
Sep 29 2020, 3:17 PM
eisenman committed rCHALLENGERe281136cf0a9: Test that test-then-rank works for ties method 'max' (authored by eisenman).
Test that test-then-rank works for ties method 'max'
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGER4d962dc2db24: Test that test-then-rank raises error for invalid ties method (authored by eisenman).
Test that test-then-rank raises error for invalid ties method
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGERb680f023acdc: Test that test-then-rank raises warning for one case (authored by eisenman).
Test that test-then-rank raises warning for one case
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGERa9b5e6e1c840: Test that test-then-rank works with two algorithms (authored by eisenman).
Test that test-then-rank works with two algorithms
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGERc1e510e404ba: Clean up (authored by eisenman).
Clean up
Sep 29 2020, 3:12 PM
eisenman committed rCHALLENGER3ac8798d0c48: Fix typos (authored by eisenman).
Fix typos
Sep 29 2020, 3:12 PM
eisenman added a comment to T27282: Implement tests for ranking method "test-then-rank" based on Wilcoxon signed rank test.

The function testThenRank has an argument FUN that is set to "significance" internally. The value that is actually passed is not used.
@wiesenfa Should "significance" be the default value in the signature already or should the argument be removed?

Sep 29 2020, 1:00 PM · challengeR (v1.0)

Sep 28 2020

eisenman updated the task description for T27794: Stacked frequency plots should switch to single page layout.
Sep 28 2020, 6:27 PM · challengeR (v1.0)
eisenman created T27794: Stacked frequency plots should switch to single page layout.
Sep 28 2020, 4:44 PM · challengeR (v1.0)
eisenman triaged T27793: Plot titles are missing in some line plots as High priority.
Sep 28 2020, 4:32 PM · challengeR (v1.0)
eisenman claimed T27282: Implement tests for ranking method "test-then-rank" based on Wilcoxon signed rank test.
Sep 28 2020, 3:48 PM · challengeR (v1.0)
eisenman moved T27770: Inconsistency in report description from In Progress to Done on the challengeR (v1.0) board.

We talked about this in the meeting this morning. It makes sense to proceed stepwise: First, having consistent descriptions and Lena's feedback (T27677) integrated for release v1.0. We should not reuse text from the paper until it is accepted. Once it is accepted, we can still decide on the revision of the report text (T27420).

Sep 28 2020, 12:45 PM · challengeR (v1.0)
eisenman committed rCHALLENGERe65b282c6076: Merge branch 'feature/T27770-FixInconsistentDescription' into develop (authored by eisenman).
Merge branch 'feature/T27770-FixInconsistentDescription' into develop
Sep 28 2020, 10:54 AM
eisenman committed rCHALLENGERd2a4438a74d1: Fix inconsistent description (authored by eisenman).
Fix inconsistent description
Sep 28 2020, 10:52 AM
eisenman claimed T27770: Inconsistency in report description.
Sep 28 2020, 10:36 AM · challengeR (v1.0)

Sep 25 2020

eisenman moved T27761: [shiny] Prevent generation of report if field "name" is empty from Done to Backlog on the webChallengeR board.

Whitespaces should be trimmed here as well, e.g. if a space character is entered and report generated, this error also occurs.

Sep 25 2020, 2:43 PM · webChallengeR
eisenman triaged T27788: [shiny] Several blocks for configuration of data structure appear when switching from options "head" and "all" as High priority.
Sep 25 2020, 11:39 AM · webChallengeR
eisenman created T27786: [shiny] Navigation from page "Uncertainty analysis" to "Generate report" without option selected.
Sep 25 2020, 11:20 AM · webChallengeR
eisenman added a comment to T27757: [shiny] Contradicting instruction on page "Uncertainty analysis".

Same for "Introduce the number of samples and click >>".

Sep 25 2020, 10:55 AM · webChallengeR
eisenman triaged T27783: [shiny] Typo in waiting pop-up as Low priority.
Sep 25 2020, 10:14 AM · webChallengeR
eisenman created T27782: [shiny] Success notification may be hidden.
Sep 25 2020, 10:10 AM · webChallengeR
eisenman moved T27757: [shiny] Contradicting instruction on page "Uncertainty analysis" from Done to Backlog on the webChallengeR board.

In my opinion, this sentence can be removed in general. At this stage the user should already know how to navigate. It does not add any valuable information.

Sep 25 2020, 10:04 AM · webChallengeR
eisenman created T27780: [shiny] Links should open in new tabs.
Sep 25 2020, 10:00 AM · webChallengeR
eisenman created T27779: [shiny] Clarifications on page "Configure ranking".
Sep 25 2020, 9:54 AM · webChallengeR
eisenman edited projects for T27326: autolayout networks in multi task report ugly, added: challengeR; removed challengeR (v1.0).

I agree!

Sep 25 2020, 8:33 AM · challengeR

Sep 24 2020

eisenman moved T27774: wrong text in report on algorithm subsets from In Progress to Done on the challengeR (v1.0) board.

It's important to mention that the subset of algorithms should be drawn from the final ranking to avoid wrong results. So if bootstrapping should be performed, create the subset from the bootstrapped ranking, not from the initial ranking that is passed to perform bootstrapping.

Sep 24 2020, 5:15 PM · challengeR (v1.0)
eisenman committed rCHALLENGER595046260c52: Merge branch 'feature/T27774-FixReportingOfAlgorithmSubset' into develop (authored by eisenman).
Merge branch 'feature/T27774-FixReportingOfAlgorithmSubset' into develop
Sep 24 2020, 5:09 PM
eisenman committed rCHALLENGER6fbbc9bb3920: Test that full data set is preserved (authored by eisenman).
Test that full data set is preserved
Sep 24 2020, 5:08 PM
eisenman committed rCHALLENGERb55aaaf309cf: Fix reporting of algorithm subset (authored by eisenman).
Fix reporting of algorithm subset
Sep 24 2020, 5:08 PM
eisenman triaged T27777: Failing unit tests for challenge as High priority.
Sep 24 2020, 3:39 PM · challengeR (v1.0)
eisenman triaged T27776: Failing unit tests for subset of tasks as High priority.
Sep 24 2020, 3:38 PM · challengeR (v1.0)
eisenman added a comment to T27774: wrong text in report on algorithm subsets.

Ok, weird. For me it says: "The top 5 out of 5 algorithms are considered."

your result is strange given the fact that not the correct things are actually counted

Sep 24 2020, 1:16 PM · challengeR (v1.0)
eisenman claimed T27774: wrong text in report on algorithm subsets.
  1. I think it will be confusing if it writes "top 5 of 5 algorithms", I would put an if
  2. which changes? as.challenge does not have a full data attribute. The changes in subset have been done by you, see my comments in T27685.
Sep 24 2020, 12:53 PM · challengeR (v1.0)
eisenman added a comment to T27774: wrong text in report on algorithm subsets.

Ok, weird. For me it says: "The top 5 out of 5 algorithms are considered."

Sep 24 2020, 12:32 PM · challengeR (v1.0)
eisenman moved T27773: package dependencies from In Progress to Done on the challengeR (v1.0) board.
Sep 24 2020, 12:23 PM · challengeR (v1.0)
eisenman committed rCHALLENGER64f2452c0f45: Merge branch 'feature/T27773-FixPackageDependencies' into develop (authored by eisenman).
Merge branch 'feature/T27773-FixPackageDependencies' into develop
Sep 24 2020, 12:23 PM
eisenman committed rCHALLENGERce606a59b22c: Move ggplot2 and purrr to Depends (authored by eisenman).
Move ggplot2 and purrr to Depends
Sep 24 2020, 12:20 PM
eisenman claimed T27773: package dependencies.
Sep 24 2020, 12:12 PM · challengeR (v1.0)
eisenman added a comment to T27774: wrong text in report on algorithm subsets.

currently It says "The top 0 out of 0 algorithms are considered." in my latest example

Sep 24 2020, 12:07 PM · challengeR (v1.0)
eisenman added a comment to T27774: wrong text in report on algorithm subsets.
  1. This is on purpose as I wanted to avoid further nested ifs, but can be discussed.
  2. This was the only variable where I found all algorithm factors. How can they be accessed now? fulldata is not working anymore after you latest changes.
Sep 24 2020, 11:40 AM · challengeR (v1.0)
eisenman added a comment to T27773: package dependencies.

Are you using the latest develop branch? There everything works for me.

Sep 24 2020, 11:34 AM · challengeR (v1.0)

Sep 23 2020

eisenman moved T27769: Top x performing algorithms are not mentioned in the reports anymore from In Progress to Done on the challengeR (v1.0) board.

This issue is fixed in T27677.

Sep 23 2020, 11:24 PM · challengeR (v1.0)
eisenman moved T27677: Update text in reports (feedback from Lena) from In Progress to Done on the challengeR (v1.0) board.
Sep 23 2020, 11:24 PM · challengeR (v1.0)
eisenman added a comment to T27677: Update text in reports (feedback from Lena).

In section 3.2.1 "Visualizing bootstrap results", two visualization methods are mentioned, but only one is contained in the report: "To investigate which tasks separate algorithms well (i.e., lead to a stable ranking), two visualization methods
are recommended."

Do we add a second plot or adapt the text?

Sep 23 2020, 11:24 PM · challengeR (v1.0)
eisenman created T27770: Inconsistency in report description.
Sep 23 2020, 11:22 PM · challengeR (v1.0)
eisenman committed rCHALLENGER53cad48c02bb: Merge branch 'feature/T27677-RestructureReports' into develop (authored by eisenman).
Merge branch 'feature/T27677-RestructureReports' into develop
Sep 23 2020, 11:20 PM
eisenman committed rCHALLENGER3487afdc60ae: Rephrase some explanations (authored by eisenman).
Rephrase some explanations
Sep 23 2020, 11:17 PM
eisenman committed rCHALLENGERce659d3df8a2: Mention top x performing algorithms in the single-task reports (authored by eisenman).
Mention top x performing algorithms in the single-task reports
Sep 23 2020, 11:17 PM
eisenman claimed T27769: Top x performing algorithms are not mentioned in the reports anymore.
Sep 23 2020, 6:58 PM · challengeR (v1.0)
eisenman triaged T27769: Top x performing algorithms are not mentioned in the reports anymore as High priority.
Sep 23 2020, 6:39 PM · challengeR (v1.0)
eisenman committed rCHALLENGER4edfe8f3555b: Complete overview of plots (authored by eisenman).
Complete overview of plots
Sep 23 2020, 5:18 PM
eisenman created T27766: [shiny] Update workflow figure.
Sep 23 2020, 12:16 PM · webChallengeR
eisenman triaged T27765: [shiny] Make sure that column specified for metric values has numeric values as High priority.
Sep 23 2020, 12:12 PM · webChallengeR
eisenman triaged T27764: [shiny] Detect early when insufficient number of columns are loaded as High priority.
Sep 23 2020, 12:11 PM · webChallengeR
eisenman triaged T27761: [shiny] Prevent generation of report if field "name" is empty as High priority.
Sep 23 2020, 11:40 AM · webChallengeR
eisenman created T27758: [shiny] Remove "next" button from page "Generate report".
Sep 23 2020, 11:17 AM · webChallengeR
eisenman created T27757: [shiny] Contradicting instruction on page "Uncertainty analysis".
Sep 23 2020, 11:14 AM · webChallengeR

Sep 21 2020

eisenman committed rCHALLENGERe3ef40f37895: Adapt sections (authored by eisenman).
Adapt sections
Sep 21 2020, 11:48 PM
eisenman committed rCHALLENGER8ba1c489befb: Cite paper (authored by eisenman).
Cite paper
Sep 21 2020, 11:48 PM
eisenman committed rCHALLENGER71695c6b7ffa: Use challenge name in description (authored by eisenman).
Use challenge name in description
Sep 21 2020, 11:48 PM
eisenman added a comment to T27677: Update text in reports (feedback from Lena).

In section 3.2.1 "Visualizing bootstrap results", two visualization methods are mentioned, but only one is contained in the report: "To investigate which tasks separate algorithms well (i.e., lead to a stable ranking), two visualization methods
are recommended."

Sep 21 2020, 7:01 PM · challengeR (v1.0)
eisenman claimed T27677: Update text in reports (feedback from Lena).
Sep 21 2020, 6:58 PM · challengeR (v1.0)
eisenman added a comment to T27748: Decide on limit for algorithms in plot legends.

The plots can already be limited to the top x performing algorithms. This can be reused in that case. Then the question is how many legend items are we going to "guarantee" appearing nicely?

Sep 21 2020, 9:32 AM · challengeR (v1.0)

Sep 18 2020

eisenman committed rCHALLENGERcfb5ffa0fa05: Keep cases generic (authored by eisenman).
Keep cases generic
Sep 18 2020, 7:01 PM
eisenman moved T27677: Update text in reports (feedback from Lena) from Backlog to In Progress on the challengeR (v1.0) board.
Sep 18 2020, 6:55 PM · challengeR (v1.0)
eisenman moved T27474: Legend of line plot has missing legend title and algorithm from In Progress to Done on the challengeR (v1.0) board.

The 19 algorithms are shown correctly. The strategy for more algorithms is discussed in T27748.

Sep 18 2020, 6:52 PM · challengeR (v1.0)
eisenman created T27748: Decide on limit for algorithms in plot legends.
Sep 18 2020, 6:51 PM · challengeR (v1.0)
eisenman moved T27475: Legend of blob plot has missing legend title and algorithms from In Progress to Done on the challengeR (v1.0) board.

The 19 algorithms are shown correctly.

Sep 18 2020, 6:39 PM · challengeR (v1.0)
eisenman added a comment to T27294: add multiple figure output formats in report with option clean=TRUE.

It works with the vector. The generated jpeg and png files have a quite low resolution and are as such not really reusable (e.g. in a presentation slide). Can you increase the resolution?

Sep 18 2020, 5:42 PM · challengeR (v1.0)
eisenman moved T27658: LaTeX Warning: There were undefined references from In Progress to Done on the challengeR (v1.0) board.
Sep 18 2020, 5:14 PM · challengeR (v1.0)
eisenman committed rCHALLENGERbf889b00d8e6: Merge branch 'feature/T27658-FixUndefinedReference' into develop (authored by eisenman).
Merge branch 'feature/T27658-FixUndefinedReference' into develop
Sep 18 2020, 5:08 PM
eisenman committed rCHALLENGER91d75517df45: Add individual plot description without need of referencing (authored by eisenman).
Add individual plot description without need of referencing
Sep 18 2020, 5:06 PM
eisenman added a comment to T27658: LaTeX Warning: There were undefined references.

The warning is raised because the label is defined when bootstrapping is used but also referenced when bootstrapping is not used.

Sep 18 2020, 4:44 PM · challengeR (v1.0)
eisenman moved T27658: LaTeX Warning: There were undefined references from Backlog to In Progress on the challengeR (v1.0) board.
Sep 18 2020, 2:29 PM · challengeR (v1.0)

Sep 17 2020

eisenman added a comment to T27677: Update text in reports (feedback from Lena).

Almost all suggestions from Lena can be realized, apart from listing the metrics in the meta data which we don't know.

Sep 17 2020, 3:41 PM · challengeR (v1.0)
eisenman placed T27360: compatibility with R4.0.0 up for grabs.
Sep 17 2020, 2:55 PM · challengeR (v1.0)
eisenman moved T27740: Add missing imports from In Progress to Done on the challengeR (v1.0) board.
Sep 17 2020, 2:53 PM · challengeR (v1.0)
eisenman moved T27252: Multiple cases per algorithm are not detected when missing data was added before from In Progress to Done on the challengeR (v1.0) board.
Sep 17 2020, 2:52 PM · challengeR (v1.0)
eisenman committed rCHALLENGER6a9fa7994fc2: Merge branch 'feature/T27740-AddMissingImports' into develop (authored by eisenman).
Merge branch 'feature/T27740-AddMissingImports' into develop
Sep 17 2020, 2:51 PM
eisenman committed rCHALLENGER5070907484ec: Add missing imports (authored by eisenman).
Add missing imports
Sep 17 2020, 2:49 PM
eisenman moved T27740: Add missing imports from Backlog to In Progress on the challengeR (v1.0) board.
Sep 17 2020, 2:48 PM · challengeR (v1.0)
eisenman triaged T27740: Add missing imports as High priority.
Sep 17 2020, 2:48 PM · challengeR (v1.0)
eisenman added a comment to T27453: Create complete network plot in its function.

Is it not possible to create a plot first on a canvas that contains everything and as a second step add the scaled plot to the report?

Sep 17 2020, 1:45 PM · challengeR (v1.0)