1. ClassifyR
  2. Graph
Graph of ClassifyR
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  • e130926f (HEAD -> master, origin/master, origin/HEAD) Merge pull request <a href="#71">#71</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2023-02-27 16:02:45 +1100;
  • c1cc0b8f preformatted replaced by code to avoid LaTeX errors. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-27 16:00:51 +1100;
  • 334d70b8 Merge pull request <a href="#70">#70</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2023-02-21 09:56:45 +1100;
  • baba87c0 - Fixed a couple of variables mistakes in prepareData's list method. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-21 09:55:28 +1100;
  • 698b7d36 Add missing alias for precisionPathwaysPredict. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-20 19:35:43 +1100;
  • 9387b3a7 - Made precision pathway evaluation functions generics. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-20 17:25:02 +1100;
  • 9cf4407c - Added prediction function for precusion pathway. - Added calcCostsAndPerformance, summary, bubblePlot, flowchart, and strataPlot evaluation functions for precision pathways. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-20 17:10:15 +1100;
  • 6fc05f09 Merge pull request <a href="#69">#69</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2023-02-16 14:22:53 +1100;
  • 897aceec - Elastic net GLM and ordinary GLM wrappers now automatically determine sample weights to give better performance on unbalanced classification tasks. - precisionPathwaysTrain function implemented. Prediction companion function to do in the near future. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-16 14:20:54 +1100;
  • 31a54d04 - Fixed bugs introduced during today's coding. - selectionMethod should be none and not NULL if to be skipped. Easier to use with naming than NULL. - elasticNetGLM made robust against choosing lambda values which cause zero features to be chosen. - elasticNetFeatures corrected to map indices back from one-hot encoding to original features. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-16 00:00:02 +1100;
  • 6c8638d8 Saving in-progess and untested changes. - useFeatures replaced by clinicalPredictors. Filtering of variables only really needed for clinical data so this simplifies the user experienece. - precisionPathyTrain function added and partially implemented. - prepareData topNvariance is now applied per-assay and has safeguards for assays with less than topNvariance features. - crossValidate S4 method signature simplification (i.e. MultiAssayExperimentOrList). by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-15 17:25:05 +1100;
  • 82808adc Merge pull request <a href="#68">#68</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2023-02-13 16:02:31 +1100;
  • ca9ffe90 - measurements subsetting in crossValidate robustified so that it doesn't cause havoc when an assay has only one feature. - Ellis' bracketing in rankingDifferentMeans fixed. - CSS now correctly applied to articles, not just the vignettes. - Pkgdown style now uses Bootstrap 5 for better layouts. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-13 16:00:11 +1100;
  • d42901e3 Merge pull request <a href="#67">#67</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2023-02-10 15:50:28 +1100;
  • 3edfe44c presets HTML article showing models which have tuning parameters set by default for crossValidate and all parameters which can be edited is added. - extraParams now allows removal of a parameter if the element value of the named list of is NULL. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-10 15:48:48 +1100;
  • 5b3d1d05 Merge pull request <a href="#66">#66</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2023-02-10 13:12:46 +1100;
  • 4cad80c2 - extraParams parameter of crossValidate allows any parameter in a predefined parameter set (in simpleParams.R) to be overwritten or unused ones to be set by the user. - .permutations private utility function which allows any position(s) to be fixed to a certain value. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-10 13:10:18 +1100;
  • 04d9a3ef (origin/RELEASE_3_16, RELEASE_3_16) Added Makevars to specify C++ compiler version to use. by Dario Strbenac <dario@maths.usyd.edu.au> 2023-02-03 21:20:20 +1100;
  • 7a654407 fix documentation issues causeing warnig by Nick <nickrrrr@gmail.com> 2023-02-02 10:24:44 +1100;
  • 1806ef1e Update Roxy version by Nick <nickrrrr@gmail.com> 2023-02-02 09:45:09 +1100;
  • cb13ad97 Merge pull request <a href="#63">#63</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-12-13 10:58:25 +1100;
  • 7c9958d3 Corrected version number. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-12-13 10:57:52 +1100;
  • b1591aba Merge pull request <a href="#62">#62</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-12-13 10:56:48 +1100;
  • 1fbdd461 - Minor modifications to package imports to avoid notes and warnings. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-12-13 10:55:11 +1100;
  • ad22f2a5 - selectionMethod and classifer now automatically chosen. Were already documented to be, but overlooked for code implementation. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-12-08 20:44:46 +1100;
  • b056adee Merge pull request <a href="#60">#60</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-12-08 20:35:26 +1100;
  • c6ea2926 - randomSelection function added. - crissCrossValidate and crissCrossPlot contributions by Harry Robertson added and harmonised to ClassifyR code style. - selectionMethod and classifier defaults become "auto" for crossValidate. Previously only documented but not implemented in code. - predict method for standalone use now finds the correct prediction method for each trained model. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-12-08 17:15:07 +1100;
  • 735bbf5f - Closing bracket in if check corrected. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-29 14:00:08 +1100;
  • a5eafb95 Merge pull request <a href="#57">#57</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-11-29 13:58:20 +1100;
  • 5b348ed4 - Closing bracket in if check corrected. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-29 13:57:19 +1100;
  • 88d9f5c8 Merge pull request <a href="#56">#56</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-11-27 21:52:50 +1100;
  • acc7fad1 - Random forest's survival mode now calculates risk values by multiplying sum of survival probabilities by negative one. - performancePlot and samplesMetricMap now use a variable named metric to consistently refer to the metric. - samplesMetricMap now has default value of auto for metric. Also, the metric will be calculated rather then stopping with an error, if the metric hasn't been calculated previously using calcCVperformance. - samplesMetricMap default metric is accuracy, to be consistent with performancePlot. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-27 21:50:16 +1100;
  • 0c8a3bbc - Random forest's survival mode now calculates risk values by multiplying sum of survival probabilities by negative one. - performancePlot and samplesMetricMap now use a variable named metric to consistently refer to the metric. - samplesMetricMap now has default value of "auto" for metric. Also, the metric will be calculated rather then stopping with an error, if the metric hasn't been calculated previously using calcCVperformance. - samplesMetricMap default metric is accuracy, to be consistent with performancePlot. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-27 21:45:33 +1100;
  • aca71775 - Synchronise random forest survival and performancePlot orderingList fixes. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-26 00:55:04 +1100;
  • cbf637e4 Merge pull request <a href="#55">#55</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-11-26 00:40:13 +1100;
  • b7f37b96 - performancePlot no longer ignores orderingList. - Default random forest function now seamlessly works when outcome is a Surv object so classifier doesn't need to be changed from default setting if input data is survival. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-25 22:40:05 +1100;
  • eb01a641 make makevars protable by Nick <nickrrrr@gmail.com> 2022-11-25 15:12:52 +1100;
  • b95f2200 remove Sint from C++ code by Nick <nickrrrr@gmail.com> 2022-11-25 15:12:43 +1100;
  • 1ffd6658 change to 2 workers by Nick <nickrrrr@gmail.com> 2022-11-25 14:47:05 +1100;
  • a1de49b8 change to 2 workers by Nick <nickrrrr@gmail.com> 2022-11-25 14:46:47 +1100;
  • 56367922 bump roxygen version by Nick <nickrrrr@gmail.com> 2022-11-25 14:46:27 +1100;
  • b0b2eb70 ignore compiled binaries by Nick <nickrrrr@gmail.com> 2022-11-24 11:44:32 +1100;
  • f62c2b4e add makevar indicating c++11 compilation by Nick <nickrrrr@gmail.com> 2022-11-24 11:28:27 +1100;
  • c2bb11be - .doSelection modified so that feature selection doesn't happen twice for selectMulti function. - selectMulti fixed so correct indices are returned relative to the whole training data table, not to an individual assay table. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-22 15:52:30 +1100;
  • 6f655e6c Increase version. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-22 15:45:52 +1100;
  • 24472cbe - .doSelection modified so that feature selection doesn't happen twice for selectMulti function. - selectMulti fixed so correct indices are returned relative to the whole training data table, not to an individual assay table. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-22 15:45:11 +1100;
  • c8dc5e11 - Roll-up of fixes from development branch over the past two weeks in preparation for workshop and software demonstration. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-17 21:45:05 +1100;
  • 1cd8cc5d Merge pull request <a href="#53">#53</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-11-17 20:43:39 +1100;
  • 2ad6f285 - Removed external documentation for internal utility functions. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-17 20:40:49 +1100;
  • e2dcdb98 - Corrected ranger random forest to do two model fits in each iteration; one for prediction and one for variable importance. Previously, a mode of model fitting which uses permuted features was being executed. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-17 16:55:04 +1100;
  • 10dff0ef - calcExternalPeformance factor,tabular for AUC. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-15 15:30:34 +1100;
  • 676432e6 Merge branch 'master' of https://github.com/SydneyBioX/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-14 13:00:29 +1100;
  • 24009d82 - Performance metrics article written. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-14 13:00:06 +1100;
  • 7675396c update website by Nick <nickrrrr@gmail.com> 2022-11-11 16:21:37 +1100;
  • 0ca7ee3c - Merge conflicts. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-11 16:14:00 +1100;
  • 53a43089 - Article for registering new function written. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-11 16:00:17 +1100;
  • 0cc77fa5 update website by Nick <nickrrrr@gmail.com> 2022-11-11 10:02:59 +1100;
  • fcd6c4c3 rebuild website by Nick <nickrrrr@gmail.com> 2022-11-11 09:29:46 +1100;
  • 9d2759c8 update to high res and transparent image by Nick <nickrrrr@gmail.com> 2022-11-11 09:28:55 +1100;
  • 7dd9b63f theme navbar by Nick <nickrrrr@gmail.com> 2022-11-11 09:28:30 +1100;
  • 6b14f443 change classifyR path by Nick <nickrrrr@gmail.com> 2022-11-11 09:28:07 +1100;
  • 22faa611 Add vscode by Nick <nickrrrr@gmail.com> 2022-11-11 09:17:23 +1100;
  • 0f8655da - Moved sticker image into man/figures folder, as is required by pkgdown. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-10 14:40:10 +1100;
  • e9ff57d6 - Added a basic Readme file with sticker. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-10 12:45:05 +1100;
  • 312e4763 - Get rid of forgotten debugging breakpoint from random forest survival function. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-09 21:55:04 +1100;
  • d3fc5481 - classifier and selectionMethod parameters of crossValidate set to "auto" by default. Different algorithms chosen depending on whether input data has cateogrical or survival outcome. - rfsrcTrainInterface corrected to extract the time and event columns in the correct order. - DESCRIPTION file updated to have Authors@R instead of Author and Maintainer fields for compatibility with pkgdown. - Description of prepareData input data filtering added to introduction vignette. - Placeholders added for performance evaluation, multi-view methods and registration of new functions articles. - Restored parallel processing in runTests which was inadvertently commented-out during recent testing. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-09 15:30:08 +1100;
  • feae6e87 - Initial progress creating website with articles for package. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-08 17:00:07 +1100;
  • 728aa1bd - ROCplot auto comparison choice now chooses most variable characteristic. - samplesMetricMap comparison default is now auto, in line with other plotting functions. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-04 13:35:05 +1100;
  • 34234a0c - Original variable names subsetting fixed when mcols only has feature column. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-03 14:45:03 +1100;
  • 21eba8cd - First try of pkgdown and website-only articles. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-11-03 12:20:32 +1100;
  • 592291a1 bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:10:05 -0400;
  • 9a59c525 bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:10:05 -0400;
  • d16b4c56 Merge branch 'master' of https://github.com/DarioS/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-25 10:32:06 +1100;
  • 43b1c426 Merge pull request <a href="#51">#51</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-10-25 10:32:01 +1100;
  • 3cd9ae72 - XGBoost wrapper now keeps a record of features for both survival and classification tasks. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-25 10:30:15 +1100;
  • 27ae9c17 Merge branch 'master' of https://github.com/DarioS/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-25 09:37:09 +1100;
  • f16c5341 Merge pull request <a href="#50">#50</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-10-25 09:36:18 +1100;
  • 82e856be - Fixed XGBoost for survival task to not specify any num_class parameter not even NULL value. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-25 09:35:10 +1100;
  • 6c9189b7 Merge branch 'master' of https://github.com/DarioS/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-24 21:21:25 +1100;
  • f9876801 Merge pull request <a href="#49">#49</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-10-24 21:21:11 +1100;
  • 17aa3388 - Prepended S4Vectors:: to mcols calls where necessary for it to work on Windows when multiple cores are used. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-24 21:20:07 +1100;
  • 86847171 Merge branch 'master' of https://github.com/DarioS/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-24 12:46:20 +1100;
  • cd006de0 Merge pull request <a href="#48">#48</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-10-24 12:46:12 +1100;
  • 6c5cbf89 - Updated developer names. - Result object creation fixed when a subset of cross-validations have an error. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-24 12:45:06 +1100;
  • c5d0ae49 Merge branch 'master' of https://github.com/DarioS/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-20 22:01:30 +1100;
  • 4c617e50 Merge pull request <a href="#47">#47</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-10-20 22:01:00 +1100;
  • 2c9da159 Remaining classifiers which don't name predictions have been made to name them. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-20 22:00:04 +1100;
  • 216b01c0 Merge branch 'master' of https://github.com/DarioS/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-20 21:20:42 +1100;
  • 45839def Merge pull request <a href="#46">#46</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-10-20 21:20:24 +1100;
  • 406234df - Changed mention of randomForest to ranger. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-20 18:00:21 +1100;
  • 855c728d - For each predict wrapper, the row names of the scores table or the names of the class vector now have sample IDs to make the output compatible with prevalidation. - XGBoost prediction function ensures that order of variables of test data table is the same as the variables used in model fitting. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-19 22:30:03 +1100;
  • ddfecae4 - XGBoost scores columns have class labels now. - nFeatures cleaning now only done once in crossValidate and not unnecessarily doubled in CV (it changes vector into list). by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-19 12:30:03 +1100;
  • 72e13321 Merge branch 'master' of https://github.com/DarioS/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-18 13:08:33 +1100;
  • 5daec252 Merge pull request <a href="#45">#45</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-10-18 13:08:20 +1100;
  • 875fbef3 - Import ranger package in DESCRIPTION. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-18 13:07:22 +1100;
  • 47a5f9f3 - Corrected prepareData when useFeatures is "all". - runTests outcome variable has0 name same for all methods to fix the generic dispatching. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-18 12:45:10 +1100;
  • 4503a484 - Minor fixes. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-17 14:30:05 +1100;
  • 4c68df87 Merge branch 'master' of https://github.com/DarioS/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-16 21:26:31 +1100;
  • 18b11799 Merge pull request <a href="#44">#44</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-10-16 21:25:33 +1100;
  • 12751f58 - Random survival forest now has ranking and feature selection extractor function rfsrcFeatures. - Ranger random forest simple parameter set now has num.trees range to optimise, analogous to ntree in other packages. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-14 21:00:04 +1100;