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Multinomial and Cox redux; also fixing showarray error #50

Merged
merged 66 commits into from
Dec 5, 2020
Merged

Multinomial and Cox redux; also fixing showarray error #50

merged 66 commits into from
Dec 5, 2020

Commits on Jul 19, 2015

  1. add support for survival data

    @linxihui
    linxihui committed Jul 19, 2015
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Commits on Jul 20, 2015

  1. add CV for coxnet

    @linxihui
    linxihui committed Jul 20, 2015
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Commits on Jul 21, 2015

  1. add coxDeviance

    @linxihui
    linxihui committed Jul 21, 2015
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  2. support for multi-class classification

    @linxihui
    linxihui committed Jul 21, 2015
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  3. replace tab by spaces

    @linxihui
    linxihui committed Jul 21, 2015
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Commits on Jul 22, 2015

  1. define GLMNetPathMultinomial as output

    @linxihui
    linxihui committed Jul 22, 2015
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  2. add another method for coxnet

    @linxihui
    linxihui committed Jul 22, 2015
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Commits on Jul 25, 2015

  1. code clean up

    @linxihui
    linxihui committed Jul 25, 2015
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  2. add loss/deviance function

    @linxihui
    linxihui committed Jul 25, 2015
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  3. code clean up

    @linxihui
    linxihui committed Jul 25, 2015
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  4. Add export CoxNet; change coxDeviance to CoxDeviance

    @linxihui
    linxihui committed Jul 25, 2015
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  5. add export; change GLMNetPathMultinomial to LogNetPath

    @linxihui
    linxihui committed Jul 25, 2015
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  6. change GLMNetCrossValidation.path to Any; include Multinomial, CoxNet

    @linxihui
    linxihui committed Jul 25, 2015
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  7. big bug: x->X; mean/std does not reduce dim; add offsets to glmnetcv;… 

    … define StringVector
    @linxihui
    linxihui committed Jul 25, 2015
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  8. fixed bug: x->X; define StringVector; fixed bug in CoxDeviance

    @linxihui
    linxihui committed Jul 25, 2015
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  9. add offsets to glmnetcv

    @linxihui
    linxihui committed Jul 25, 2015
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  10. add predict function on GLMNetCrossValidation object; code clean up

    @linxihui
    linxihui committed Jul 25, 2015
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  11. add glmnet method on AbstractMatrix

    @linxihui
    linxihui committed Jul 25, 2015
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  12. fixed bug in glmnetcv: pass weights/offsets to glmnet

    @linxihui
    linxihui committed Jul 25, 2015
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  13. fixed bug in glmnetcv: pass weights/offsets to glmnet

    @linxihui
    linxihui committed Jul 25, 2015
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  14. fix bug in glmnetcv: no offsets for Normal family

    @linxihui
    linxihui committed Jul 25, 2015
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  15. add convenient function coef, lambdamin

    @linxihui
    linxihui committed Jul 25, 2015
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  16. add to predict: output type

    @linxihui
    linxihui committed Jul 25, 2015
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  17. update for new functionality; added multiclass example

    @linxihui
    linxihui committed Jul 25, 2015
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  18. in glmnetcv, change default weights from ones(legnth(y)) to ones(size… 

    …(X, 1)) as y can be matrix
    @linxihui
    linxihui committed Jul 25, 2015
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  19. add method glmentcv(Matrix, y::StringVector)

    @linxihui
    linxihui committed Jul 25, 2015
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  20. change outtype to be keyword parameter

    @linxihui
    linxihui committed Jul 25, 2015
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  21. fix typo

    @linxihui
    linxihui committed Jul 25, 2015
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Commits on Jul 26, 2015

  1. clean example

    @linxihui
    linxihui committed Jul 26, 2015
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Commits on Jul 27, 2015

  1. glmnetcv: fixed bug on offsets when binomial; test passed

    @linxihui
    linxihui committed Jul 27, 2015
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  2. glmnetcv: offsets issue for multivariate

    @linxihui
    linxihui committed Jul 27, 2015
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Commits on Jul 30, 2015

  1. add plot functions to visualize shrinkage path

    @linxihui
    linxihui committed Jul 30, 2015
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Commits on Aug 1, 2015

  1. add plotting example

    @linxihui
    linxihui committed Aug 1, 2015
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  2. add Gadfly to dependency

    @linxihui
    linxihui committed Aug 1, 2015
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  3. add test for multinomial and survival outcome

    @linxihui
    linxihui committed Aug 1, 2015
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  4. fixed bug in predict, ccall; add offsets to predict, loss and cv

    @linxihui
    linxihui committed Aug 1, 2015
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  5. add keyword argument offset to predict, loss, glmnetcv; include plot.jl

    @linxihui
    linxihui committed Aug 1, 2015
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  6. add integerity checking on x, y; re-indent

    @linxihui
    linxihui committed Aug 1, 2015
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  7. fixed bug in predict, ccall; add offsets to predict, loss and cv

    @linxihui
    linxihui committed Aug 1, 2015
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  8. re-indent

    @linxihui
    linxihui committed Aug 1, 2015
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  9. import Gadfly function

    @linxihui
    linxihui committed Aug 1, 2015
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  10. replace DataFrames.rep by repmat

    @linxihui
    linxihui committed Aug 1, 2015
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  11. load DataFrames

    @linxihui
    linxihui committed Aug 1, 2015
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  12. explicitly import predict from DataFrame, which solves that problem t… 

    …hat predict cannot be found when DataFrame is loaded after GLMNet
    @linxihui
    linxihui committed Aug 1, 2015
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  13. add coef method for Multinomial

    @linxihui
    linxihui committed Aug 1, 2015
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  14. more tests

    @linxihui
    linxihui committed Aug 1, 2015
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  15. fix bug, clean up, better test coverage

    @linxihui
    linxihui committed Aug 1, 2015
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  16. update examples

    @linxihui
    linxihui committed Aug 1, 2015
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  17. update examples

    @linxihui
    linxihui committed Aug 1, 2015
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  18. update examples

    @linxihui
    linxihui committed Aug 1, 2015
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  19. replaced PNG by SVG images

    @linxihui
    linxihui committed Aug 1, 2015
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  20. change links to svg images

    @linxihui
    linxihui committed Aug 1, 2015
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Commits on Dec 1, 2020

  1. Merge remote-tracking branch 'MultinomialCox/master' into HEAD

    dsweber2 committed Dec 1, 2020
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Commits on Dec 2, 2020

  1. modernizing and dropping gadfly dependencies.

    dsweber2 committed Dec 2, 2020
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  2. showarray isn't defined

    dsweber2 committed Dec 2, 2020
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  3. @testsets are nice

    dsweber2 committed Dec 2, 2020
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Commits on Dec 4, 2020

  1. readme update

    dsweber2 committed Dec 4, 2020
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  2. tweaking glmnetcv for cox to allow determined rng

    dsweber2 committed Dec 4, 2020
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  3. bye bye plots

    dsweber2 committed Dec 4, 2020
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  4. bug when using CategoricalArrays for Multinomial

    dsweber2 committed Dec 4, 2020
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  5. parameteric types are nice (just GLMNetPath now)

    dsweber2 committed Dec 4, 2020
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  6. this conversion breaks Multinomial regression

    dsweber2 committed Dec 4, 2020
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  7. fixing CategoricalArray dependency, revert JuliaStats#18

    dsweber2 committed Dec 4, 2020
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Commits on Dec 5, 2020

  1. Merge commit '456b9aeabe9e07ea72452461232a162df1f41837' into multinom… 

    …ialCox
    dsweber2 committed Dec 5, 2020
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  2. same error, but in the cox version

    dsweber2 committed Dec 5, 2020
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  3. also in Multinomial, add CategoricalArrays in tests

    dsweber2 committed Dec 5, 2020
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