SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2020-01-31T14:43:09Zhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/107parameter for `evaluation.plot`2020-01-31T14:43:09ZJakob Wirbelparameter for `evaluation.plot`parameter to turn off ROC curves from individual cross-validation runsparameter to turn off ROC curves from individual cross-validation runsJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/106Feature request: warning if the species are too long to fit on the associatio...2019-11-01T11:35:46ZJakob WirbelFeature request: warning if the species are too long to fit on the association plotpretty well described in the title...pretty well described in the title...https://git.embl.de/grp-zeller/SIAMCAT/-/issues/101Feature request for check.associations2019-02-07T10:33:49ZKonrad ZychFeature request for check.associationsadd an option to use paired=TRUE in `wilcox.test`
add an option to use paired=TRUE in `wilcox.test`
https://git.embl.de/grp-zeller/SIAMCAT/-/issues/97feature_weights/weight_matrix compute on the fly2018-09-07T11:33:41ZJakob Wirbelfeature_weights/weight_matrix compute on the fly### Summary
Instead of saving feature_weights/weight_matrix in the object, make the accessor functions compute them on the fly
### Affected functions/datasets/objects
`train.model`
`accessors`
/cc @zych### Summary
Instead of saving feature_weights/weight_matrix in the object, make the accessor functions compute them on the fly
### Affected functions/datasets/objects
`train.model`
`accessors`
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/96on which type of features should the function work?2018-10-01T19:17:21ZJakob Wirbelon which type of features should the function work?### Summary
Include a parameter, on which type of features the function should work (i.e. original, filtered, normalized). Make smart defaults to keep the current workflow unaffected
### Affected functions/datasets/objects
- [x] `fil...### Summary
Include a parameter, on which type of features the function should work (i.e. original, filtered, normalized). Make smart defaults to keep the current workflow unaffected
### Affected functions/datasets/objects
- [x] `filter.features`
- [x] `normalize.features`
- [x] `check.associations`
- [x] `train.model`
- [x] `make.predictions`
- [x] `model.interpretation.plot`
- [x] `add.meta.pred`
- [x] `summarize.features`
/cc @zych @jawirbel https://git.embl.de/grp-zeller/SIAMCAT/-/issues/95remove meta-column after construction the label in the constructor function2018-09-21T08:57:59ZJakob Wirbelremove meta-column after construction the label in the constructor function### Summary
throw out the column with the label (for plotting reasons later)
only in the constructor function, not the `create.label` function
### Affected functions/datasets/objects
`siamcat-constructor`
/cc @zych### Summary
throw out the column with the label (for plotting reasons later)
only in the constructor function, not the `create.label` function
### Affected functions/datasets/objects
`siamcat-constructor`
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/94Store feature weights in SIAMCAT2018-08-16T14:13:31ZJakob WirbelStore feature weights in SIAMCAT## Summary
Store mean/median feature weights in the slot for the models (for easier access, e.g. in `model.interpretation.plot`) and make them accessible by `model_weights(siamcat)` (or sth similar?)
## Affected functions/datasets/obj...## Summary
Store mean/median feature weights in the slot for the models (for easier access, e.g. in `model.interpretation.plot`) and make them accessible by `model_weights(siamcat)` (or sth similar?)
## Affected functions/datasets/objects
- `train.model`
- `model.interpretation.plot`
- `siamcat` Class
- `show` function
- accessors
- definition
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/93Create tax table from appropriate feature names2018-08-13T06:57:52ZJakob WirbelCreate tax table from appropriate feature names## Summary
Create a tax table automatically from feature names that contain this information, i.e. k__;p__;g__ and so on
## Affected functions/datasets/objects
`summarize.features`
/cc @zych## Summary
Create a tax table automatically from feature names that contain this information, i.e. k__;p__;g__ and so on
## Affected functions/datasets/objects
`summarize.features`
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/92easier label import2018-08-09T13:50:31ZJakob Wirbeleasier label importmake it possible to give a vector as label into the construction functionmake it possible to give a vector as label into the construction functionhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/89fix constructor function2018-08-01T14:16:46ZJakob Wirbelfix constructor function- [x] use named arguments
- [x] perform some checks on features/labels/metadata
- [x] call data validator at the end of the constructor
- [x] SIAMCAT without the label (or NaN label)- [x] use named arguments
- [x] perform some checks on features/labels/metadata
- [x] call data validator at the end of the constructor
- [x] SIAMCAT without the label (or NaN label)Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/84Fix progressbars2019-10-14T09:28:42ZJakob WirbelFix progressbars### Summary
The messages following the progress bars are usually printed in the same line. Should be fixed. Also, progressbars should not appear in the vignette.
Example:
```{r}
+ finished filter.features in 0.038 s
|================...### Summary
The messages following the progress bars are usually printed in the same line. Should be fixed. Also, progressbars should not appear in the vignette.
Example:
```{r}
+ finished filter.features in 0.038 s
|===============================================================================================| 100%Trained lasso models successfully.
```
Proposed fix:
does not appear in `evaluate.predictions`, which also shows a progressbar from the `pROC` package. maybe we can try to do the progressbars in the same way...
### Affected Functions
- [ ] `make.predictions`
- [ ] `train.model`
- [ ] `check.associations`
/cc @zychKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/81add a license2018-05-16T13:31:57ZToby Hodgesadd a license### Summary
I noticed that the SIAMCAT repo doesn't include a license. I believe that that means that no-one is allowed to copy it and use it (e.g. https://www.infoworld.com/article/2615869/open-source-software/github-needs-to-take-open...### Summary
I noticed that the SIAMCAT repo doesn't include a license. I believe that that means that no-one is allowed to copy it and use it (e.g. https://www.infoworld.com/article/2615869/open-source-software/github-needs-to-take-open-source-seriously.html). It would be a good idea to discuss and agree upon an appropriate license (perhaps CC-BY?).
### Affected functions/datasets/objects
Without a license, users are likely to be either, (unintentionally) copying and using SIAMCAT in breach of copyright, or afraid to use the tool without knowing what restrictions may be enforced in future.
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/67Return results from check associations2018-08-09T13:53:09ZJakob WirbelReturn results from check associations### Summary
Return results of `check.associations` as a matrix/dataframe -> add it to `siamcat@assoc`
### Affected functions/datasets/objects
`check.associations`,
`siamcat-class`
/cc @zych @jawirbel### Summary
Return results of `check.associations` as a matrix/dataframe -> add it to `siamcat@assoc`
### Affected functions/datasets/objects
`check.associations`,
`siamcat-class`
/cc @zych @jawirbelhttps://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 Wirbel