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Graph ofClassifyR

cb13ad97 (HEAD -> master, origin/master, origin/HEAD) 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 (origin/RELEASE_3_16, RELEASE_3_16) - 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;
fbb1890e - Minor fixes to standalone train and predict functions for list of inputs. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-14 17:45:03 +1100;
ea07063f - Typo in train.DataFrame variable fixed. - .predict for DLDA made renamed to DLDA to enable easy dispatch by predict method. - randomForest wrapper now uses ranger as the underlying package instead of randomForest. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-14 11:30:12 +1100;
ed2b7cb5 - Extreme gradient boosting wrapper added in interfaceXGB.R. - crossValidate gains performanceType parameter that defaults to "auto" which chooses depending on classification or survival task or can be set to any user-specified performance metric. - SelectParams default performanceType is now balanced accuracy, for consistency with other functions. - Vignette text updated to refer to balanced accuracy and to add k-NN and XGB classifiers to classifier table. - NEWS file updated for upcoming Bioconductor release. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-10-13 00:05:23 +1100;
d440f597 Merge branch 'master' of https://github.com/DarioS/ClassifyR by Dario Strbenac <dario@maths.usyd.edu.au> 2022-09-28 22:16:03 +1000;
5188314b Merge pull request <a href="#43">#43</a> from SydneyBioX/master by Dario Strbenac <dario.strbenac@sydney.edu.au> 2022-09-28 22:15:37 +1000;
4c577191 - Tweaks to colCoxTests documentation to fix the last couple of warnings. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-09-28 22:10:03 +1000;
39f5da2e - crossValidate works with selectionMehod being none. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-09-27 11:26:02 +1000;
879f435d - plotFeatureClasses now works if classes is column name of data frame. - prepareData warning for variable name conversion for modelling. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-09-27 10:50:16 +1000;
9e6f6d8b - Fixed a couple of variable name typos. - Previous commit did not do variable name extraction correctly when getFeatures was not being used. Now it is done correctly regardless whether the variables are extracted from trained model (possibly already subsetted) or from feature selection (corresponding to original set of features). by Dario Strbenac <dario@maths.usyd.edu.au> 2022-09-21 17:00:05 +1000;
989c4fce - finalModel accessor added for getting final model properly. - Conversion back into selected features' original names fixed if feature selection does subsetting after the features are selected. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-09-15 14:30:03 +1000;
b226d9f2 - Provide a convenience S4 method for ClassifyResult input object for ROCplot, so that users don't need to put their result into a list, like performancePlot, rankingPlot, selectionPlot already provide. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-09-13 12:00:04 +1000;
48a84871 - Accessors for metadata columns changed to be robust in situtations when the column doesn't exist by using $column rather than [, "column"] access style. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-09-12 15:00:05 +1000;
e163e636 Update interfacePrevalidation.R by Ellis Patrick <ellis.patrick@sydney.edu.au> 2022-09-07 21:55:12 +1000;
d390d04d Update interfacePrevalidation.R by Ellis Patrick <ellis.patrick@sydney.edu.au> 2022-09-07 15:37:55 +1000;
9e25457a Update rankingCoxPH.R by Ellis Patrick <ellis.patrick@sydney.edu.au> 2022-09-07 13:08:03 +1000;
2ac7f667 Update runTest.R by Ellis Patrick <ellis.patrick@sydney.edu.au> 2022-09-07 12:45:27 +1000;
78a4c924 - Restored utilities.R. by Dario Strbenac <dario@maths.usyd.edu.au> 2022-09-07 10:48:49 +1000;
1ab4106c Allow mix of categorical and numeric variables in coxPH by Ellis Patrick <epatrick87@gmail.com> 2022-09-07 09:36:21 +1000;
265ed7a5 export colCoxTests by Ellis Patrick <epatrick87@gmail.com> 2022-09-07 08:57:36 +1000;
1e6d5e5e Update crossValidate.R by Ellis Patrick <ellis.patrick@sydney.edu.au> 2022-09-06 08:40:24 +1000;