SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2018-04-17T09:37:29Zhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/57Change how label object is build2018-04-17T09:37:29ZKonrad ZychChange how label object is build### Summary
We need to use a scenario where an user is using phyloseq to read the data in and then the label is rebuild whilst creating phyloseq-class object from metadata.
### Goals/sub-features
- [x] a parameter which specifies which...### Summary
We need to use a scenario where an user is using phyloseq to read the data in and then the label is rebuild whilst creating phyloseq-class object from metadata.
### Goals/sub-features
- [x] a parameter which specifies which column of metadata should be used to create label
- [x] update siamcat constructor function
/cc @zych @jawirbelKonrad ZychKonrad Zychhttps://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/54Unit testing2018-04-16T11:34:55ZKonrad ZychUnit testing### Summary
Add unit testing to SIAMCAT with [testthat](http://testthat.r-lib.org/index.html)
### Useful link
http://bioconductor.org/developers/how-to/unitTesting-guidelines/
/cc @zych### Summary
Add unit testing to SIAMCAT with [testthat](http://testthat.r-lib.org/index.html)
### Useful link
http://bioconductor.org/developers/how-to/unitTesting-guidelines/
/cc @zychKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/53Accessors for SIAMCAT-class2018-03-30T07:45:00ZKonrad ZychAccessors for SIAMCAT-class### Summary
All slots in the class should be accessible by an accessor function
/cc @zych### Summary
All slots in the class should be accessible by an accessor function
/cc @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/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
(Summarize the bug encountered concisely)
Relevant logs and/or screenshots
(Paste any relevant logs - please use code blocks (```) to format console output,
logs, and code as it's very hard to read otherwise.)
/cc @zychSummary
(Summarize the bug encountered concisely)
Relevant logs and/or screenshots
(Paste any relevant logs - please use code blocks (```) to format console output,
logs, and code as it's very hard to read otherwise.)
/cc @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/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/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/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/27Update galaxy interface2018-04-17T09:42:48ZKonrad ZychUpdate galaxy interface- [ ] incorporate latest version
- [ ] test
- [ ] :package: ship it- [ ] incorporate latest version
- [ ] test
- [ ] :package: ship itPublicationhttps://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/18Radical code clean-up fro metagenomics course2017-10-02T19:46:27ZKonrad ZychRadical code clean-up fro metagenomics course- [x] remove unused parameters
- [x] mlr only
- [x] add mlr-related parameters- [x] remove unused parameters
- [x] mlr only
- [x] add mlr-related parametersNijmegen conferenceKonrad ZychKonrad Zychhttps://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 Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/15Update how plm.predictor takes in the test data2017-10-02T11:04:33ZJakob WirbelUpdate how plm.predictor takes in the test dataCurrently, plm.predict takes a set of features and labels as test data.
But it would be better if it could, analogously to plm.trainer, take the list returned by data.splitter as inputCurrently, plm.predict takes a set of features and labels as test data.
But it would be better if it could, analogously to plm.trainer, take the list returned by data.splitter as inputNijmegen conferenceKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/14Update plm.trainer()2018-01-16T13:40:24ZJakob WirbelUpdate plm.trainer()- [x] implement modsel.criterion
- [x] implement model.type as parameter- [x] implement modsel.criterion
- [x] implement model.type as parameterBioconductor submissionKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/13Update how plm.trainer takes in the training instances2017-09-28T11:52:47ZJakob WirbelUpdate how plm.trainer takes in the training instancesCurrently, the training instance indices have to be supplied to plm.trainer as file. Should be adjusted so that the function does not read/write data to diskCurrently, the training instance indices have to be supplied to plm.trainer as file. Should be adjusted so that the function does not read/write data to diskNijmegen conferencehttps://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 Zych