SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2021-07-28T12:18:24Zhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/23Vignette2021-07-28T12:18:24ZKonrad ZychVignettewe need to write a full-Rmd vignette to acoompany the package on BioConductor (and also, because we want people to use the package) :smile: :smile_cat:we need to write a full-Rmd vignette to acoompany the package on BioConductor (and also, because we want people to use the package) :smile: :smile_cat:Bioconductor submissionhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/10Update normalize.feat()2020-03-20T14:39:42ZJakob WirbelUpdate normalize.feat()- [ ] Add default values for normalization parameters
- [ ] Update Documentation- [ ] Add default values for normalization parameters
- [ ] Update DocumentationNijmegen conferenceKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/2Update roxygen documentation2019-01-09T12:17:36ZKonrad ZychUpdate roxygen documentationBioconductor submissionJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/83Release 1.0.1 on bioconductor2018-07-23T13:58:14ZKonrad ZychRelease 1.0.1 on bioconductor### Summary
- [x] new vignettes
- [x] version bump
- [x] NEWS file
### NEWS file:
## Version 1.0.1
- updated function `create.label.from.metadata` to make it more flexible
- added `transpose` parameter to the `read.features` function
...### Summary
- [x] new vignettes
- [x] version bump
- [x] NEWS file
### NEWS file:
## Version 1.0.1
- updated function `create.label.from.metadata` to make it more flexible
- added `transpose` parameter to the `read.features` function
- added vignette describing holdout validation
- added vignette describing how to read in your data and process it with SIAMCAT
- added function `read.lefse` to read input files in LEfSe file format
- small bugfixes
/cc @zychBioconductor 1.0.1 releaseKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/76Vignette - holdout/frozen2018-05-23T13:51:17ZKonrad ZychVignette - holdout/frozen/cc @zych/cc @zychBioconductor 1.0.1 releaseJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/56Vignette - how to get your data into SIAMCAT2018-05-23T13:51:02ZKonrad ZychVignette - how to get your data into SIAMCAT### Summary
A vignette that shows crucial steps in reading in and preprocessing your data to use in SIAMCAT
### Goals/sub-features
- [x] loading different data types with phyloseq
- [x] reading SIAMCAT type text files
- [x] adding phyl...### Summary
A vignette that shows crucial steps in reading in and preprocessing your data to use in SIAMCAT
### Goals/sub-features
- [x] loading different data types with phyloseq
- [x] reading SIAMCAT type text files
- [x] adding phyloseq-class object to siamcat-class object
/cc @zychBioconductor 1.0.1 releaseKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/69Make use of DiagrammeR2018-05-23T13:50:47ZKonrad ZychMake use of DiagrammeRUse it to visualize workflows/data structure
/cc @zychUse it to visualize workflows/data structure
/cc @zychKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/80Vignette - troubleshooting2018-05-16T13:20:59ZJakob WirbelVignette - troubleshootingWhen the vignette is built by BioConductor, some graphics do not look nice, and some error messages should not be shown.
See also [here](https://bioconductor.org/packages/release/bioc/vignettes/SIAMCAT/inst/doc/SIAMCAT_vignette.html)...
...When the vignette is built by BioConductor, some graphics do not look nice, and some error messages should not be shown.
See also [here](https://bioconductor.org/packages/release/bioc/vignettes/SIAMCAT/inst/doc/SIAMCAT_vignette.html)...
minor tasks:
- [x] no error message for feature import
- [x] rename files to `feat.txt`, `label.txt`, `meta.txt`
- [x] fix graphic states
- [x] remove output for model training - `verbose=0`
- [x] fix the first section with the link to [EMBL microbiome tools](http://microbiome-tools.embl.de/)
- [x] remove confounder/association testing (maybe mention other vignettes?)https://git.embl.de/grp-zeller/SIAMCAT/-/issues/68Docs for internal functions2018-04-17T09:36:58ZKonrad ZychDocs for internal functions### Summary
We need to add docs for some of the internal functions.
We just need to be sure, but I think just `#' @keywords internal` should be enough. In that case some of those are safe already.
### Goals/sub-features
In `check_a...### Summary
We need to add docs for some of the internal functions.
We just need to be sure, but I think just `#' @keywords internal` should be enough. In that case some of those are safe already.
### Goals/sub-features
In `check_associations.r`:
- [x] associations.bean.plot
- [x] associations.box.plot
- [x] associations.quantile.box.plot
- [x] associations.quantile.rect.plot
- [x] associations.margins.plot
- [x] associations.aucs.plot
- [x] associations.fcs.plot
- [x] associations.pr.shift.plot
- [x] associations.pvals.plot
- [x] is.color
- [x] check.color.scheme
- [x] associations.labels.plot
- [x] analyse.binary.marker
- [x] change.transparency
- [x] quantiles.plot
- [x] create.tints
- [x] quantile.rect.plot
- [x] quantile.median.plot
In `evaluate_predictions.r`:
- [x] evaluate.classifier
- [x] evaluate.area.trapez
- [x] evaluate.get.pr
- [x] evaluate.calc.aupr
In `model_interpretation_plot.R`:
- [x] plot.feature.weights
- [x] plot.pred.and.meta
- [x] plot.proportion.of.weights
- [x] plot.percentage.of.features
- [x] plot.heatmap
- [x] prepare.heatmap.fc
- [x] prepare.heatmap.zscore
- [x] select.features
- [x] get.weights.matrix
In `plm_utils.R`:
- [x] train.plm
- [x] get.optimal.lambda.for.glmnet
- [x] get.parameters.from.param.set
In `siamcat_class_constructor.r`:
- [x] get.component.classes
- [x] is.component.class
In `train_model.r`:
- [x] measureAUPRC
/cc @zych @jawirbel Bioconductor review 1https://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/11Update documentation2018-03-30T07:45:18ZJakob WirbelUpdate documentationUpdate documentation in all the functions after the `siamcat-class` introduction
- [x] `add.meta.pred`
- [x] `check.associations`
- [x] `check.confounders`
- [x] `create.data.split`
- [x] `evaluate.predictions`
- [x] `filter.features`
-...Update documentation in all the functions after the `siamcat-class` introduction
- [x] `add.meta.pred`
- [x] `check.associations`
- [x] `check.confounders`
- [x] `create.data.split`
- [x] `evaluate.predictions`
- [x] `filter.features`
- [x] IO-utils functions
- [x] `make.predictions`
- [x] `model.evaluation.plot`
- [x] `model.interpretation.plot`
- [x] `normalize.features`
- [x] `select.samples`
- [ ] `siamcat.class` and accompanying functions
- [x] `train.model`
- [x] `validate.data`
Bioconductor submissionKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/52Bioconductor submission checklist2018-03-30T07:44:52ZKonrad ZychBioconductor submission checklist- [x] clone to GitHub/ check if it could be submitted from git.embl
- [x] R CMD check with no warnings and errors
- [x] R CMD BiocCheck with no warnings and errors
- [x] R CMD BiocCheck notes - careful with those
- [x] siamcat_example do...- [x] clone to GitHub/ check if it could be submitted from git.embl
- [x] R CMD check with no warnings and errors
- [x] R CMD BiocCheck with no warnings and errors
- [x] R CMD BiocCheck notes - careful with those
- [x] siamcat_example does not work with log.std normalization
- [x] replacing previous import ‘mlr::auc’ by ‘pROC::auc’ when loading ‘SIAMCAT -> importsFrom should solve it but seems not to work properly?
- [x] The result of R CMD build must be less than 4MB
- [x] R CMD check must complete within 5 minutes
- [x] Set Version: 0.99.0 in the DESCRIPTION
- [x] Include an inst/NEWS file for providing users with information on package updates
- [ ] NOTE: Consider shorter lines
- [ ] NOTE: Consider multiples of 4 spaces for line indentsBioconductor submission2018-03-29https://git.embl.de/grp-zeller/SIAMCAT/-/issues/26Pre-BioConductor code check and clean-up2018-03-28T20:56:05ZKonrad ZychPre-BioConductor code check and clean-upBioconductor submissionKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/8Update documentation for eval.result()2017-09-29T14:55:28ZJakob WirbelUpdate documentation for eval.result()Nijmegen conferenceJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/17Taking care of the utils.R2017-09-28T11:51:24ZKonrad ZychTaking care of the utils.R- [x] removing all the :poop: `make_xyz_options` functions from the utils file
- [x] removing all the :poop: `make_xyz_options` functions from the R_script file
- [x] renaming it to read_data.R
- [x] add some docs for the read functions ...- [x] removing all the :poop: `make_xyz_options` functions from the utils file
- [x] removing all the :poop: `make_xyz_options` functions from the R_script file
- [x] renaming it to read_data.R
- [x] add some docs for the read functions (see Georg's readme and copy from there about file formats). Do not spend too much time here, once the structure is done there will be aconstructor function that would not expose any of those to the user!Nijmegen conferenceJakob WirbelJakob Wirbel