SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2018-03-14T08:52:39Zhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/49Adjust prediction function2018-03-14T08:52:39ZJakob WirbelAdjust prediction function### Summary
For proper hold-out testing, it would make sense for the `predict` function to be able to be given a new, unrelated dataset.
- [x] make option argument in predict function (another `siamcat` object)
- [x] if no hold-out dat...### Summary
For proper hold-out testing, it would make sense for the `predict` function to be able to be given a new, unrelated dataset.
- [x] make option argument in predict function (another `siamcat` object)
- [x] if no hold-out data are given, perform the function at it is now
- [x] if hold-out data are given, perform data sanity checks
- [x] apply model on hold-out data and return predictions
### Question
Should the function for the hold-out prediction return only the prediction matrix or a modified `siamcat` object?
### Affected functions/datasets/objects
- `make.predictions`
/cc @zychJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/48buggy test2018-02-27T13:01:33ZKonrad Zychbuggy testSummary
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/cc @zychSummary
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/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/47Bug reporting with issue system2018-02-27T16:40:53ZKonrad ZychBug reporting with issue systemLet's see if this works!Let's see if this works!Ece KartalEce Kartalhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/46Prepare description templates for contributors2018-02-27T13:14:17ZKonrad ZychPrepare description templates for contributors- [ ] bug report
- [ ] feature request
- [ ] will to contribute
- [ ] ...- [ ] bug report
- [ ] feature request
- [ ] will to contribute
- [ ] ...Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/45Bug in the interpretor.model.plot with heatmap.type="fc"2018-02-26T14:39:40ZKonrad ZychBug in the interpretor.model.plot with heatmap.type="fc"```
+++ preparing heatmap
NaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaN...```
+++ preparing heatmap
NaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs produced+++ plotting model properties
Layout height values: 0.1, 0.64, 0.26
+++ plotting titles
+++ plotting legend
Error in seq.default(round(min(img.data, na.rm = TRUE), digits = 1), round(max(img.data, :
'from' must be a finite number
```https://git.embl.de/grp-zeller/SIAMCAT/-/issues/44Evolve to tidyverse2018-02-26T06:18:25ZKonrad ZychEvolve to tidyverse- [ ] elapsed time formatted with lubridate
- [x] documentation website with pkgdown
- [ ] ...- [ ] elapsed time formatted with lubridate
- [x] documentation website with pkgdown
- [ ] ...https://git.embl.de/grp-zeller/SIAMCAT/-/issues/43Start using gitLab and issues system properly2018-04-17T09:40:13ZKonrad ZychStart using gitLab and issues system properly- [x] add, commit and push are your friends
- [ ] issues - make an issue for every problem/ bug you find, for every feature you are developing etc - make it verbose and easy to track for us
- [ ] be a pro and use Markdown and quick actio...- [x] add, commit and push are your friends
- [ ] issues - make an issue for every problem/ bug you find, for every feature you are developing etc - make it verbose and easy to track for us
- [ ] be a pro and use Markdown and quick actions (e.g. `/estimate` and `/spend`)
- [x] question authorityMorgan EssexMorgan Essexhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/41Homogenous names2018-03-28T20:55:25ZKonrad ZychHomogenous names- [ ] class-siamcat slots are all using _ (data_split, otu_table)
- [ ] functions are using action.subject (split.data, plot.model.interpretation)
- [ ] SIAMCAT/R files names match name of the (main) function they contain
- [ ] plot. fun...- [ ] class-siamcat slots are all using _ (data_split, otu_table)
- [ ] functions are using action.subject (split.data, plot.model.interpretation)
- [ ] SIAMCAT/R files names match name of the (main) function they contain
- [ ] plot. functions are reserved namesBioconductor submissionKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/40Better association testing module2018-04-19T08:56:59ZKonrad ZychBetter association testing module- [x] implement blocking for wilcoxon tests
- [ ] anything for e.g. fold change, prevalence shift, etc?
- [x] implement anova on ranks
- [ ] heatmap for anova
- [ ] other visualization for differential abundance methods- [x] implement blocking for wilcoxon tests
- [ ] anything for e.g. fold change, prevalence shift, etc?
- [x] implement anova on ranks
- [ ] heatmap for anova
- [ ] other visualization for differential abundance methodsMorgan EssexMorgan Essexhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/39Easier parameters for data.splitter2018-05-23T13:52:39ZKonrad ZychEasier parameters for data.splitter- [ ] CV/holdout parameter
- [ ] num.folds -> cv.folds
- [ ] num.resample -> cv.resample- [ ] CV/holdout parameter
- [ ] num.folds -> cv.folds
- [ ] num.resample -> cv.resampleKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/38Updating R_script2018-02-15T16:15:59ZKonrad ZychUpdating R_scriptTO match the siamcat data structure workflow.TO match the siamcat data structure workflow.Version 0.4.0Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/36beeswarm plot for association testing2018-02-07T16:08:21ZJakob Wirbelbeeswarm plot for association testing- [ ] make function to plot data with the `beeswarm` package
- [ ] add `swarm` or `bee` as possible values for `plot.type`- [ ] make function to plot data with the `beeswarm` package
- [ ] add `swarm` or `bee` as possible values for `plot.type`Jakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/35update names of features only for `mlr` interface2018-03-30T18:00:25ZJakob Wirbelupdate names of features only for `mlr` interfacethe names that are created by `make.names()` can be very confusing to read, since e.g.
`Dialister mOTU [0012]` turns into `Dialister.mOTU..0012.`
which is not nice as labels for plots.
I therefore propose to use the native names thro...the names that are created by `make.names()` can be very confusing to read, since e.g.
`Dialister mOTU [0012]` turns into `Dialister.mOTU..0012.`
which is not nice as labels for plots.
I therefore propose to use the native names throughout all functions of the package and to update the names just before the data are given to `mlr` and update them again once they need to be extracted out of the model.Jakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/34make output of functions optional2018-01-31T17:11:00ZJakob Wirbelmake output of functions optionalSome functions produce a lot of output that -while useful for debugging and sanity-checking- can get quite annoying when using an established workflow, e.g. `data.splitter`, `make_predictions`, etc.
I propose to provide an argument (sth...Some functions produce a lot of output that -while useful for debugging and sanity-checking- can get quite annoying when using an established workflow, e.g. `data.splitter`, `make_predictions`, etc.
I propose to provide an argument (sth like `verbose=TRUE`) that can control if the output should be printed or not.https://git.embl.de/grp-zeller/SIAMCAT/-/issues/33Enable frozen normalization with set of parameters2018-01-16T08:24:18ZJakob WirbelEnable frozen normalization with set of parameters - [x] set list of `par` as parameter for normalization
- [x] check in function if frozen or _de novo_ normalization should be performed
- [x] check in function if all parameters for normalzation method have been supplied
- [x] awesom... - [x] set list of `par` as parameter for normalization
- [x] check in function if frozen or _de novo_ normalization should be performed
- [x] check in function if all parameters for normalzation method have been supplied
- [x] awesome multi-purpose function :+1_tone1: :grin:Jakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/32removing srcdir from R_script2018-01-16T13:39:42ZKonrad Zychremoving srcdir from R_scriptVersion 0.3.0Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/31Formating the author list in a machine-readable format2018-03-30T11:49:14ZKonrad ZychFormating the author list in a machine-readable formatAlready started:
- [x] adding ORCID for all the authors
- [x] making sure that all the fields are filled for all the authorsAlready started:
- [x] adding ORCID for all the authors
- [x] making sure that all the fields are filled for all the authorsBioconductor submissionKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/30Data validator2018-07-24T12:36:37ZKonrad ZychData validator- [ ] more flexible about the input- [ ] more flexible about the inputPublicationhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/28Implement custom model performance measure2017-12-20T13:41:26ZJakob WirbelImplement custom model performance measurehttps://mlr-org.github.io/mlr-tutorial/release/html/create_measure/index.html
- [x] implement `modsel.crit` to feed into the mlr model selection
- [x] F1 measure
- [x] Area under PRC
- [x] look also at minimum number of coefficientshttps://mlr-org.github.io/mlr-tutorial/release/html/create_measure/index.html
- [x] implement `modsel.crit` to feed into the mlr model selection
- [x] F1 measure
- [x] Area under PRC
- [x] look also at minimum number of coefficientsVersion 0.3.0https://git.embl.de/grp-zeller/SIAMCAT/-/issues/27Update galaxy interface2018-04-17T09:42:48ZKonrad ZychUpdate galaxy interface- [ ] incorporate latest version
- [ ] test
- [ ] :package: ship it- [ ] incorporate latest version
- [ ] test
- [ ] :package: ship itPublication