SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2018-02-12T14:14:57Zhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/20Log R-script run into Rmd file2018-02-12T14:14:57ZKonrad ZychLog R-script run into Rmd fileThe log of R-script flavor execution should land in one neat R markdown file :ok_hand_tone1:
- [ ] each file starts with ##heading with name of the function\
- [ ] ###heading: paramaters of the run
- [ ] all the parameters of the run are...The log of R-script flavor execution should land in one neat R markdown file :ok_hand_tone1:
- [ ] each file starts with ##heading with name of the function\
- [ ] ###heading: paramaters of the run
- [ ] all the parameters of the run are saved :floppy_disk: there
- [ ] ###heading: results of the run
- [ ] all the verbose results of the run
- [ ] (optional): parameter for the user to choose screen/RmdPublicationKonrad ZychKonrad Zychhttps://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/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/104include feature weights in the models slot of the siamcat object?2019-09-17T14:15:25ZJakob Wirbelinclude feature weights in the models slot of the siamcat object?include the feature weights and weights table in different slots in the models slot of the siamcat object for easier access
for models trained on gene group abundance data, the retrieval of feature weights takes forever and could be spe...include the feature weights and weights table in different slots in the models slot of the siamcat object for easier access
for models trained on gene group abundance data, the retrieval of feature weights takes forever and could be sped up by saving the tables directlyJakob WirbelJakob Wirbel