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Dev #100

Merged
merged 106 commits into from
May 12, 2017
Merged

Dev #100

merged 106 commits into from
May 12, 2017

Commits on Mar 17, 2017

  1. some attempts at oop changes to core

    @paulhendricks
    paulhendricks committed Mar 17, 2017
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Commits on Mar 18, 2017

  1. mininimum proof of concept for s3 classes...easy_* functions create e… 

    …asy_* classes which when passed to replicate_* functions appropriately and flexibly dispatch to fit_model, predict_model, etc. functions depending on the class
    @paulhendricks
    paulhendricks committed Mar 18, 2017
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  2. demonstration of how easy it is to add a new algorithm like glinterne… 

    …t; the user is warned that glinternet is not complete but needs a couple of tweaks to adhere to best practices
    @paulhendricks
    paulhendricks committed Mar 18, 2017
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  3. changed python readme project status badge to wip

    @paulhendricks
    paulhendricks committed Mar 18, 2017
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  4. some documentation

    @paulhendricks
    paulhendricks committed Mar 18, 2017
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Commits on Mar 21, 2017

  1. some fixes; added glinternet, neural network, and deep neural network… 

    …; updated documentation and changed some unit tests; still need to add more unit tests
    @paulhendricks
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  2. added some unit tests

    @paulhendricks
    paulhendricks committed Mar 21, 2017
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Commits on Mar 30, 2017

  1. added a try catch to glinternet as it is unstable and fails occasionally

    @paulhendricks
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Commits on Apr 2, 2017

  1. hoping to kick off a build and pass this time

    @paulhendricks
    paulhendricks committed Apr 2, 2017
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  2. updated bibtex

    @paulhendricks
    paulhendricks committed Apr 2, 2017
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Commits on Apr 8, 2017

  1. updated badge for appveyor

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  2. loads ggplot2 upon startup

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  3. changed replicate to generate

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  4. fixed docs; fixed namespace on attach warning

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  5. added vignettes...starting to work on prostate and cocaine

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  6. Merge pull request #96 from CCS-Lab/experimental 

    merge experimental branch into dev
    @paulhendricks
    paulhendricks authored Apr 8, 2017
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  7. preliminary pass at vignettes

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  8. updated unit tests

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  9. changed logging level

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  10. commented out troubling lines

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  11. commented out binomial lines

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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  12. updated documentation

    @paulhendricks
    paulhendricks committed Apr 8, 2017
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Commits on Apr 9, 2017

  1. attempt at 100% code coverage

    @paulhendricks
    paulhendricks committed Apr 9, 2017
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  2. remove gaussian glmnet test case

    @paulhendricks
    paulhendricks committed Apr 9, 2017
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  3. try installing gcc

    @paulhendricks
    paulhendricks committed Apr 9, 2017
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Commits on Apr 11, 2017

  1. refactored easy_* functions into classes

    @paulhendricks
    paulhendricks committed Apr 11, 2017
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  2. updated unit tests

    @paulhendricks
    paulhendricks committed Apr 11, 2017
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  3. updated tests

    @paulhendricks
    paulhendricks committed Apr 11, 2017
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  4. removed glinternet test as it repeatedly fails

    @paulhendricks
    paulhendricks committed Apr 11, 2017
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  5. implemented predictions and metrics

    @paulhendricks
    paulhendricks committed Apr 11, 2017
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Commits on Apr 12, 2017

  1. added random_forest algorithm...still work in progress

    @paulhendricks
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  2. added support vector machine

    @paulhendricks
    paulhendricks committed Apr 12, 2017
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  3. some attempts at updating Python documentation

    @paulhendricks
    paulhendricks committed Apr 12, 2017
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Commits on Apr 14, 2017

  1. added some templates for unit testing

    @paulhendricks
    paulhendricks committed Apr 14, 2017
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Commits on Apr 19, 2017

  1. added documentation to utility functions

    @paulhendricks
    paulhendricks committed Apr 19, 2017
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  2. some housecleaning

    @paulhendricks
    paulhendricks committed Apr 19, 2017
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  3. updated documentation

    @paulhendricks
    paulhendricks committed Apr 19, 2017
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  4. added some placeholders for resampling

    @paulhendricks
    paulhendricks committed Apr 19, 2017
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  5. some placeholders to mirror r functions

    @paulhendricks
    paulhendricks committed Apr 19, 2017
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  6. some minor fixes to setters

    @paulhendricks
    paulhendricks committed Apr 19, 2017
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  7. some minor fixes to setters

    @paulhendricks
    paulhendricks committed Apr 19, 2017
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  8. some minor fixes to module docs

    @paulhendricks
    paulhendricks committed Apr 19, 2017
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Commits on Apr 21, 2017

  1. updated measure functions

    @paulhendricks
    paulhendricks committed Apr 21, 2017
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  2. some minor updates to core, glmnet, resample, and setters utilizing b… 

    …etter inheritance
    @paulhendricks
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  3. edited some setters functions

    @paulhendricks
    paulhendricks committed Apr 21, 2017
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  4. updated classes to mirror R code

    @paulhendricks
    paulhendricks committed Apr 21, 2017
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  5. quick changes for resampling

    @paulhendricks
    paulhendricks committed Apr 21, 2017
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  6. fixed tests; travis should build correctly

    @paulhendricks
    paulhendricks committed Apr 21, 2017
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  7. added support for custom model arguments

    @paulhendricks
    paulhendricks committed Apr 21, 2017
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  8. updated examples to be a little more robust

    @paulhendricks
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  9. updated tests and documentation

    @paulhendricks
    paulhendricks committed Apr 21, 2017
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Commits on Apr 22, 2017

  1. added a resampling function

    @paulhendricks
    paulhendricks committed Apr 22, 2017
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  2. added a resampling function

    @paulhendricks
    paulhendricks committed Apr 22, 2017
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  3. conciseness

    @paulhendricks
    paulhendricks committed Apr 22, 2017
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  4. updated core plots for predictions and metrics, implemented generate … 

    …method for variable importances, and implemented plot for variable importances
    @paulhendricks
    paulhendricks committed Apr 22, 2017
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  5. added plot of coefficients for penalized linear models

    @paulhendricks
    paulhendricks committed Apr 22, 2017
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Commits on Apr 23, 2017

  1. some updates to the way plotting works

    @paulhendricks
    paulhendricks committed Apr 23, 2017
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  2. removed plotting for now...can't get it to work as a first class object

    @paulhendricks
    paulhendricks committed Apr 23, 2017
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  3. updated requirements.txt for travis

    @paulhendricks
    paulhendricks committed Apr 23, 2017
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  4. updated some unit tests for setters

    @paulhendricks
    paulhendricks committed Apr 23, 2017
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  5. fixed bug; results should be on par with R for glmnet

    @paulhendricks
    paulhendricks committed Apr 23, 2017
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  6. fixed edge where no model arguments are passed in

    @paulhendricks
    paulhendricks committed Apr 23, 2017
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  7. updated some docs

    @paulhendricks
    paulhendricks committed Apr 23, 2017
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  8. updated examples

    @paulhendricks
    paulhendricks committed Apr 23, 2017
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  9. updated run test script

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    paulhendricks committed Apr 23, 2017
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Commits on Apr 24, 2017

  1. Update README.md

    @youngahn
    youngahn authored Apr 24, 2017
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  2. Update README.Rmd

    @youngahn
    youngahn authored Apr 24, 2017
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Commits on Apr 29, 2017

  1. changed names of classes to mirror R naming conventions

    @paulhendricks
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  2. Merge remote-tracking branch 'origin/dev' into dev

    @paulhendricks
    paulhendricks committed Apr 29, 2017
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  3. set default gaussian measure to correlation score

    @paulhendricks
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  4. updated examples to be one liners

    @paulhendricks
    paulhendricks committed Apr 29, 2017
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  5. added easy_avNNet

    @paulhendricks
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  6. updated the way that plots show so that they have better default scales

    @paulhendricks
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  7. modified predictions so they use preprocessed data instead of data th… 

    …at hasnt bene preprocessed
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  8. setting the random state before each "generation" should result in th… 

    …e metric resulting from the generation of the predictions being very similar to the first value resulting from the generation of the metrics
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  9. removed '_mean' from predictions and metrics

    @paulhendricks
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  10. added a scratch file for plotting binomial predictions

    @paulhendricks
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  11. updated plots, measures, and core analysis

    @paulhendricks
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  12. updated plots and some documentation; vignettes need work

    @paulhendricks
    paulhendricks committed Apr 29, 2017
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  13. style setting for ggplot

    @paulhendricks
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Commits on Apr 30, 2017

  1. fixed a bug surrounding probas in the case of binomial for random forest

    @paulhendricks
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  2. some minor changes to plotting

    @paulhendricks
    paulhendricks committed Apr 30, 2017
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  3. updates to documentation

    @paulhendricks
    paulhendricks committed Apr 30, 2017
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  4. minor fix to measure

    @paulhendricks
    paulhendricks committed Apr 30, 2017
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  5. documentation

    @paulhendricks
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  6. updated tests

    @paulhendricks
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  7. updated random forest to handle regression case

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Commits on May 6, 2017

  1. fixed algorithm 4; and in the process of changing all the names in core

    @paulhendricks
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  2. some placeholders for python code

    @paulhendricks
    paulhendricks committed May 6, 2017
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  3. updated docs

    @paulhendricks
    paulhendricks committed May 6, 2017
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  4. updated some r code

    @paulhendricks
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Commits on May 8, 2017

  1. updated R code with changes from metrics to model_performance everywhere

    @paulhendricks
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  2. one additional change from metric to_model performance

    @paulhendricks
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  3. modified python code so references to metric point to model_performance

    @paulhendricks
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  4. implemented coefficients function for glmnet

    @paulhendricks
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  5. removed debug line

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Commits on May 11, 2017

  1. modified random forest and svm to produce probabilities

    @paulhendricks
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  2. slight change to neural network predict to be consistent with probabi… 

    …lities
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  3. Sort beta coefficients and variable importances as defaults

    @youngahn
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Commits on May 12, 2017

  1. updated plotting functions

    @paulhendricks
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  2. Merge remote-tracking branch 'origin/dev' into dev

    @paulhendricks
    paulhendricks committed May 12, 2017
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  3. updated travis script

    @paulhendricks
    paulhendricks committed May 12, 2017
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  4. some minor changes...

    @paulhendricks
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  5. got plotting functions working

    @paulhendricks
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  6. updated tests for setters

    @paulhendricks
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  7. updated documenation for easy_avNNet

    @paulhendricks
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