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wiesenfa (Manuel Wiesenfarth)
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Mar 2 2020, 3:23 PM (34 w, 1 d)

Recent Activity

Thu, Oct 15

wiesenfa added a comment to T27794: Stacked frequency plots should switch to single page layout.

stabilityByAlgorithmStacked is now replaced by stabilityByAlgorithm(....., stacked=TRUE)

Thu, Oct 15, 2:43 PM · challengeR (v1.0)
wiesenfa moved T27794: Stacked frequency plots should switch to single page layout from In Progress to Done on the challengeR (v1.0) board.
Thu, Oct 15, 2:40 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER2fd21713233a: Merge branch 'develop' of https://phabricator.mitk.org/source/challenger into… (authored by wiesenfa).
Merge branch 'develop' of https://phabricator.mitk.org/source/challenger into…
Thu, Oct 15, 2:40 PM
wiesenfa committed rCHALLENGER6a7e604bf5f8: Merge branch 'feature/T27794-stackedFrequencies' into develop (authored by wiesenfa).
Merge branch 'feature/T27794-stackedFrequencies' into develop
Thu, Oct 15, 2:40 PM
wiesenfa committed rCHALLENGER75ee76a039c2: use print.ggList (authored by wiesenfa).
use print.ggList
Thu, Oct 15, 2:40 PM
wiesenfa committed rCHALLENGERd6b7074d84e7: replace stabilityByAlgorithmStacked by stabilityByAlgorithm(...,stacked=T) (authored by wiesenfa).
replace stabilityByAlgorithmStacked by stabilityByAlgorithm(...,stacked=T)
Thu, Oct 15, 2:40 PM
wiesenfa moved T27794: Stacked frequency plots should switch to single page layout from Backlog to In Progress on the challengeR (v1.0) board.
Thu, Oct 15, 11:27 AM · challengeR (v1.0)
wiesenfa claimed T27794: Stacked frequency plots should switch to single page layout.
Thu, Oct 15, 11:27 AM · challengeR (v1.0)

Mon, Oct 12

wiesenfa added a comment to T27708: ggplot2 dendrogram .

disadvantage would be dependency on another package facilitating ggplot2 dendrograms

Mon, Oct 12, 2:30 PM · challengeR (v1.0)
wiesenfa added a comment to T27708: ggplot2 dendrogram .

current implementation is fine. However, we said it would be nice if all plots (if directly called by users and not within the report) would have the same syntax and could be layouted with ggplot2 syntax. current implementation is using basic R graphics.

Mon, Oct 12, 2:30 PM · challengeR (v1.0)
wiesenfa added a comment to T27326: autolayout networks in multi task report ugly.

turned off in v1.0, everything else postponed

Mon, Oct 12, 2:27 PM · challengeR

Thu, Oct 8

wiesenfa moved T27802: Revise signature of function testThenRank from In Progress to Done on the challengeR (v1.0) board.
Thu, Oct 8, 1:20 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER96a5812ece30: fix respect alpha (authored by wiesenfa).
fix respect alpha
Thu, Oct 8, 1:20 PM
wiesenfa added a comment to T27802: Revise signature of function testThenRank.

This was a tricky bug, thanks!
alpha is now respected, argument FUN is removed. significance ranking is considered an aggregation step, so testThenRank() is nothing else than aggregateThenRank(FUN="significance").
Note that testThenRank will pass all arguments to decision.challenge(), i.e. it will respect arguments:

Thu, Oct 8, 1:15 PM · challengeR (v1.0)
wiesenfa moved T27494: Check which files are still relevant from In Progress to Backlog on the challengeR (v1.0) board.
Thu, Oct 8, 12:36 PM · challengeR (v1.0)
wiesenfa moved T27802: Revise signature of function testThenRank from Backlog to In Progress on the challengeR (v1.0) board.
Thu, Oct 8, 12:34 PM · challengeR (v1.0)
wiesenfa moved T27456: Extraction of task subset from (bootstrap) ranking does not raise an error for invalid task name from In Progress to Done on the challengeR (v1.0) board.
Thu, Oct 8, 12:33 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER7b50eff1c116: subset error messages (authored by wiesenfa).
subset error messages
Thu, Oct 8, 12:32 PM
wiesenfa committed rCHALLENGER356105ac93b4: fix test for invalid task name (authored by wiesenfa).
fix test for invalid task name
Thu, Oct 8, 12:32 PM
wiesenfa committed rCHALLENGER4d4c7820d18f: adapt test for invalid task names (authored by wiesenfa).
adapt test for invalid task names
Thu, Oct 8, 12:32 PM
wiesenfa committed rCHALLENGER85d2f7a263b1: error messages invalid task names (authored by wiesenfa).
error messages invalid task names
Thu, Oct 8, 12:32 PM
wiesenfa moved T27456: Extraction of task subset from (bootstrap) ranking does not raise an error for invalid task name from Backlog to In Progress on the challengeR (v1.0) board.
Thu, Oct 8, 12:16 PM · challengeR (v1.0)
wiesenfa moved T27793: Plot titles are missing in some line plots from In Progress to Done on the challengeR (v1.0) board.
Thu, Oct 8, 11:55 AM · challengeR (v1.0)
wiesenfa committed rCHALLENGER7ae1fb0d69e3: task title in line plot (authored by wiesenfa).
task title in line plot
Thu, Oct 8, 11:55 AM
wiesenfa moved T27793: Plot titles are missing in some line plots from Backlog to In Progress on the challengeR (v1.0) board.
Thu, Oct 8, 11:30 AM · challengeR (v1.0)
wiesenfa moved T27778: turn off networks from In Progress to Done on the challengeR (v1.0) board.
Thu, Oct 8, 11:29 AM · challengeR (v1.0)
wiesenfa committed rCHALLENGERce25f3551296: outcomment networks (authored by wiesenfa).
outcomment networks
Thu, Oct 8, 11:29 AM
wiesenfa moved T27778: turn off networks from Backlog to In Progress on the challengeR (v1.0) board.
Thu, Oct 8, 11:25 AM · challengeR (v1.0)
wiesenfa moved T27804: Message text from violin plot is cut off in the PDF report from In Progress to Done on the challengeR (v1.0) board.
Thu, Oct 8, 10:58 AM · challengeR (v1.0)
wiesenfa committed rCHALLENGER885d495f0efe: violin text improve (authored by wiesenfa).
violin text improve
Thu, Oct 8, 10:57 AM
wiesenfa moved T27804: Message text from violin plot is cut off in the PDF report from Backlog to In Progress on the challengeR (v1.0) board.
Thu, Oct 8, 7:47 AM · challengeR (v1.0)

Mon, Oct 5

wiesenfa claimed T27778: turn off networks.
Mon, Oct 5, 10:16 AM · challengeR (v1.0)

Fri, Oct 2

wiesenfa closed T27811: turn off networks in report as Invalid.

redundant

Fri, Oct 2, 9:45 PM · challengeR (v1.0)
wiesenfa created T27811: turn off networks in report.
Fri, Oct 2, 1:05 PM · challengeR (v1.0)
wiesenfa moved T27286: interactive plots from v1.0 to Backlog on the challengeR board.
Fri, Oct 2, 12:58 PM · challengeR
wiesenfa claimed T27456: Extraction of task subset from (bootstrap) ranking does not raise an error for invalid task name.
Fri, Oct 2, 12:57 PM · challengeR (v1.0)
wiesenfa claimed T27793: Plot titles are missing in some line plots.
Fri, Oct 2, 11:19 AM · challengeR (v1.0)
wiesenfa claimed T27802: Revise signature of function testThenRank.
Fri, Oct 2, 11:18 AM · challengeR (v1.0)
wiesenfa claimed T27804: Message text from violin plot is cut off in the PDF report.
Fri, Oct 2, 11:18 AM · challengeR (v1.0)

Thu, Oct 1

wiesenfa added a comment to T27794: Stacked frequency plots should switch to single page layout.

stacked frequency plots are quite neglected. They are not mentioned in the paper. Are they interesting or should they be removed entirely?

Thu, Oct 1, 12:05 PM · challengeR (v1.0)
wiesenfa added a comment to T27494: Check which files are still relevant.

what about
keep S3, compareRanks and extract.workflow
but do not export (i.e. remove from namespace) compareRanks and extract.workflow. they can then only be accessed e.g. by challengeR:::compareRanks(). These might be of practical use.
?

Thu, Oct 1, 12:03 PM · challengeR (v1.0)

Sep 25 2020

wiesenfa moved T27447: significanceMap function raises warning about deprecated function call from In Progress to Done on the challengeR (v1.0) board.
Sep 25 2020, 12:08 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER2691d1ba70a6: fix grid in significancePlot (authored by wiesenfa).
fix grid in significancePlot
Sep 25 2020, 12:06 PM
wiesenfa committed rCHALLENGER0ab46fb7c444: Merge branch 'develop' of https://phabricator.mitk.org/source/challenger into… (authored by wiesenfa).
Merge branch 'develop' of https://phabricator.mitk.org/source/challenger into…
Sep 25 2020, 12:06 PM
wiesenfa moved T27447: significanceMap function raises warning about deprecated function call from Backlog to In Progress on the challengeR (v1.0) board.
Sep 25 2020, 10:17 AM · challengeR (v1.0)
wiesenfa claimed T27447: significanceMap function raises warning about deprecated function call.
Sep 25 2020, 9:47 AM · challengeR (v1.0)
wiesenfa created T27778: turn off networks.
Sep 25 2020, 9:45 AM · challengeR (v1.0)

Sep 24 2020

wiesenfa added a comment to T27326: autolayout networks in multi task report ugly.

I propose to turn off networks and exclude them from the report for now.
if this is solved, we can reintroduce them.
they are not essential I think. what do you think?

Sep 24 2020, 5:24 PM · challengeR
wiesenfa placed T27326: autolayout networks in multi task report ugly up for grabs.
Sep 24 2020, 4:26 PM · challengeR
wiesenfa moved T27777: Failing unit tests for challenge from Backlog to Done on the challengeR (v1.0) board.
Sep 24 2020, 4:24 PM · challengeR (v1.0)
wiesenfa claimed T27777: Failing unit tests for challenge.
Sep 24 2020, 4:24 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER083f7c671f05: fix test for as.challenge (authored by wiesenfa).
fix test for as.challenge
Sep 24 2020, 4:24 PM
wiesenfa moved T27776: Failing unit tests for subset of tasks from Backlog to Done on the challengeR (v1.0) board.
Sep 24 2020, 4:18 PM · challengeR (v1.0)
wiesenfa claimed T27776: Failing unit tests for subset of tasks.
Sep 24 2020, 4:18 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER08deba103b9e: fix subset (authored by wiesenfa).
fix subset
Sep 24 2020, 4:17 PM
wiesenfa moved T27708: ggplot2 dendrogram from In Progress to Backlog on the challengeR (v1.0) board.
Sep 24 2020, 3:28 PM · challengeR (v1.0)
wiesenfa added a comment to T27708: ggplot2 dendrogram .

this will require a further package, put on hold for the moment

Sep 24 2020, 3:28 PM · challengeR (v1.0)
wiesenfa moved T27685: changes in subset() from In Progress to Done on the challengeR (v1.0) board.
Sep 24 2020, 3:23 PM · challengeR (v1.0)
wiesenfa added a comment to T27685: changes in subset().

taskSubset is deprecated
there is now
subset(x, top, tasks)

  • if top is specified subset to top algorithms (only applicable to single task challenges)
  • if tasks is specified subset of tasks (only applicable to multi task challenges)
Sep 24 2020, 3:22 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGERaf8f561d7b94: fix subset(), remove taskSubset() (authored by wiesenfa).
fix subset(), remove taskSubset()
Sep 24 2020, 3:20 PM
wiesenfa updated subscribers of T27775: only export functions to be used by user.
Sep 24 2020, 3:17 PM · challengeR (v1.0)
wiesenfa triaged T27775: only export functions to be used by user as Low priority.
Sep 24 2020, 3:17 PM · challengeR (v1.0)
wiesenfa claimed T27326: autolayout networks in multi task report ugly.
Sep 24 2020, 2:43 PM · challengeR
wiesenfa moved T27708: ggplot2 dendrogram from Backlog to In Progress on the challengeR (v1.0) board.
Sep 24 2020, 2:42 PM · challengeR (v1.0)
wiesenfa added a comment to T27748: Decide on limit for algorithms in plot legends.

20 might be a sensible number

Sep 24 2020, 2:42 PM · challengeR (v1.0)
wiesenfa moved T27714: Report contains weird R output from In Progress to Done on the challengeR (v1.0) board.
Sep 24 2020, 2:40 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGERd34e4efe8ea5: fix output classes (authored by wiesenfa).
fix output classes
Sep 24 2020, 2:40 PM
wiesenfa placed T27288: separate readme.md and readme.Rmd up for grabs.
Sep 24 2020, 2:27 PM · challengeR (v1.0)
wiesenfa claimed T27708: ggplot2 dendrogram .
Sep 24 2020, 2:26 PM · challengeR (v1.0)
wiesenfa moved T27714: Report contains weird R output from Backlog to In Progress on the challengeR (v1.0) board.
Sep 24 2020, 2:26 PM · challengeR (v1.0)
wiesenfa claimed T27714: Report contains weird R output.
Sep 24 2020, 2:26 PM · challengeR (v1.0)
wiesenfa added a comment to T27770: Inconsistency in report description.

the sentence can be dropped. But wasn't it planned to revise the text in line with the paper in total?

Sep 24 2020, 2:23 PM · challengeR (v1.0)
wiesenfa moved T27685: changes in subset() from Backlog to In Progress on the challengeR (v1.0) board.
Sep 24 2020, 1:16 PM · challengeR (v1.0)
wiesenfa claimed T27685: changes in subset().
Sep 24 2020, 1:16 PM · challengeR (v1.0)
wiesenfa 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, 1:13 PM · challengeR (v1.0)
wiesenfa added a comment to T27774: wrong text in report on algorithm subsets.
  1. it won't be more that I needed for the missing data description I guess;-) I still think that this sentence should be avoided if no subset is in fact used
Sep 24 2020, 1:11 PM · challengeR (v1.0)
wiesenfa moved T27453: Create complete network plot in its function from In Progress to Done on the challengeR (v1.0) board.
Sep 24 2020, 1:09 PM · challengeR (v1.0)
wiesenfa added a comment to T27453: Create complete network plot in its function.

this is more or less what I tried, ugliness is T27326. I think a ggplot solution mentioned there would be better

Sep 24 2020, 1:08 PM · challengeR (v1.0)
wiesenfa moved T27452: Provide plot function for dendrogram from In Progress to Done on the challengeR (v1.0) board.
Sep 24 2020, 1:07 PM · challengeR (v1.0)
wiesenfa moved T27337: Report contains wrong ranking method when rank-then-aggregate is used from In Progress to Done on the challengeR (v1.0) board.
Sep 24 2020, 1:06 PM · challengeR (v1.0)
wiesenfa moved T27294: add multiple figure output formats in report with option clean=TRUE from In Progress to Done on the challengeR (v1.0) board.
Sep 24 2020, 1:05 PM · challengeR (v1.0)
wiesenfa added a comment to T27294: add multiple figure output formats in report with option clean=TRUE.

report gains new argument "dpi" to change resolution

Sep 24 2020, 1:05 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER88b673042288: set dpi default to 150 (authored by wiesenfa).
set dpi default to 150
Sep 24 2020, 1:05 PM
wiesenfa committed rCHALLENGER88e1de7d8cc3: set dpi default to 300 (authored by wiesenfa).
set dpi default to 300
Sep 24 2020, 1:05 PM
wiesenfa committed rCHALLENGERb2891c3b4f02: Merge branch 'develop' of https://phabricator.mitk.org/source/challenger into… (authored by wiesenfa).
Merge branch 'develop' of https://phabricator.mitk.org/source/challenger into…
Sep 24 2020, 1:00 PM
wiesenfa committed rCHALLENGERc66c18f1fbcd: allow setting dpi (authored by wiesenfa).
allow setting dpi
Sep 24 2020, 1:00 PM
wiesenfa added a comment to T27774: wrong text in report on algorithm subsets.
set.seed(4)
strip=runif(n,.9,1)
c_ideal=cbind(task="c_ideal",
              rbind(
                      data.frame(alg_name="A1",value=runif(n,.9,1),case=1:n),
                      data.frame(alg_name="A2",value=runif(n,.8,.89),case=1:n),
                      data.frame(alg_name="A3",value=runif(n,.7,.79),case=1:n),
                      data.frame(alg_name="A4",value=runif(n,.6,.69),case=1:n),
                      data.frame(alg_name="A5",value=runif(n,.5,.59),case=1:n)
              ))
challenge=as.challenge(c_ideal, 
                       algorithm="alg_name", case="case", value="value",
                       smallBetter = T)
ranking=challenge%>%aggregateThenRank(FUN = "mean", # aggregation function, 
                                      na.treat="na.rm", # either "na.rm" to remove missing data, 
                                      ties.method = "min" # a character string specifying 
)
Sep 24 2020, 12:18 PM · challengeR (v1.0)
wiesenfa moved T27338: Report contains misleading information on missing values from In Progress to Done on the challengeR (v1.0) board.
Sep 24 2020, 12:07 PM · challengeR (v1.0)
wiesenfa committed rCHALLENGER0e1a1e5dae75: description of missings in reports+as.challenge (authored by wiesenfa).
description of missings in reports+as.challenge
Sep 24 2020, 12:06 PM
wiesenfa 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, 11:46 AM · challengeR (v1.0)
wiesenfa added a comment to 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, 11:45 AM · challengeR (v1.0)
wiesenfa added a comment to T27773: package dependencies.

yes I think so. maybe you have purrr (or dplyr) and ggplot loaded in the workspace.
packages in depends are loaded at startup (and we need these package to be available by the user). imports does not load the packages, functions of challengeR can however call them.
it is true that packages in depends should be minimize, but these are needed

Sep 24 2020, 11:38 AM · challengeR (v1.0)
wiesenfa triaged T27774: wrong text in report on algorithm subsets as High priority.
Sep 24 2020, 11:32 AM · challengeR (v1.0)
wiesenfa created T27773: package dependencies.
Sep 24 2020, 11:21 AM · challengeR (v1.0)

Sep 11 2020

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

the first sentence refers to the fact that no missings have been found in the data set. would rephrasing to "0 missing cases entered in the data set have been found" help? the next sentence is about cases which have been inserted by the sanity check. Would adding "However, ..." in between help?
If you have any other suggestions, I would be happy to include them

Sep 11 2020, 11:42 AM · challengeR (v1.0)

Sep 7 2020

wiesenfa moved T27287: is warning given if na.treat unspecified in rank-first and obligatory otherwise from Backlog to Done on the challengeR (v1.0) board.
Sep 7 2020, 7:06 PM · challengeR (v1.0)
wiesenfa added a comment to T27456: Extraction of task subset from (bootstrap) ranking does not raise an error for invalid task name.

@eisenman I dont understand this task, could you give an example?

Sep 7 2020, 7:05 PM · challengeR (v1.0)
wiesenfa added a comment to T27287: is warning given if na.treat unspecified in rank-first and obligatory otherwise.

solved in T27338

Sep 7 2020, 7:03 PM · challengeR (v1.0)
wiesenfa created T27708: ggplot2 dendrogram .
Sep 7 2020, 7:01 PM · challengeR (v1.0)
wiesenfa added a comment to T27326: autolayout networks in multi task report ugly.

networks should be replaced by some ggplot2 implementation, see
https://journal.r-project.org/archive/2017/RJ-2017-023/RJ-2017-023.pdf

Sep 7 2020, 6:57 PM · challengeR