---
title: "Function List"
output:
   rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Function List}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```


* *ML algorithms*

    * **qeAdaBoost()**: Ada Boosting, wraps **Jousboost** pkg

    * **qeDeepnet()**: wraps **deepnet** pkg

    * **qeDT()**: decision trees, wraps **party** pkg

    * **qeGBoost()**: gradient boosting, wraps **gbm** pkg

    * **qeKNN()**: k-Nearest Neighbors, wraps **regtools** pkg; includes
      predictor importance settings; allows linear interpolation within
      a bin

    * **qeLASSO()**: LASSO and ridge regression, wraps **glmment** pkg

    * **qeLightGBoost()**: gradient boosting, wraps **lightgbm** pkg

    * **qeliquidSVM**: wraps liquidSVM pkg

    * **qeLin()**: wraps R's **lm()**

    * **qeLinKNN()**: first fits **qeLin()**, followed by k-NN on the
      residuals to correct deviations from linearity

    * **qeLogit()**: wraps R's **glm()**

    * **qeNCVregCV**: wraps **ncvreg** package, linear
      gen. linear regression regularized via SCAD etc.

    * **qeNeural()**: wraps **keras** package, including CNN

    * **qePolyLASSO()**: LASSO/ridge applied to polynomial regression;
      wraps **glmnet**, **polyreg** pkgs

    * **qePolyLin()**: polynomial regression on linear models;
      uses Moore-Penrose inverse if overfitting; wraps **polyreg** pkg

    * **qePolyLog()**: polynomial regression on logistic models;
      wraps **polyreg** pkg

    * **qeRF()**: random forests, wraps **randomforest** pkg

    * **qeRFgrf**: random forests, wraps **grf** pkg; allows linear
      interpolation within a bin

    * **qeRpart()**: decision trees, wraps **Rpart** pkg; colorful tree plot

    * **qeRFranger()**: random forests, wraps **ranger** pkg

    * **qeskRF()**: random forests, wraps Python **Scilearn** pkg

    * **qeskSVM()**: SVM, wraps Python **Scilearn** pkg

    * **qeSVM()**: SVM, wraps **e1071** pkg

    * **qeSVMliquid()**: SVM, wraps **liquid SVM** pkg

    * **qeXGBoost()** wraps the **xgboost** pkg

* *feature importance/selection* 

    * **qeFOCI(), qeFOCIrand()**: fully nonparametric method for feature
      selection

    * **qeLASSO()**:  for feature importance, apply **coef()** to return value

    * **qeLeaveOut1Var**:  fits full model, then with all features but
      1, for each feature, reporting difference in predictive power; use
      with any **qeML** predictive function

    * **qeRareLevels()**:  investigates whether rare levels of a feature
      that is an R factor should be included

    * **qeRFranger**:  **variable.importance** component of return value

* *model development*

    * **doubleD()**: computation and plotting for exploring Double Descent

    * **plotClassesUMAP()**: plot first two UMAP components,
      color-coding classes

    * **plotPairedResiduals()**: plot residuals against pairs of
      features

    * **qeCompare()**:  compare the accuracy various ML methods on a 
      given dataset

    * **qeFT()**:  automated grid hyperparameter search, *with
      Bonferroni-Dunn corrected standard errors*

    * **qePCA()**:  find principal components, number specified by user,
      then fit the resulting model, according to **qe*** function
      specified by user

    * **qeROC()**:  ROC computation and plotting, wraps **pROC** pkg

    * **qeUMAP()**:  same as **qePCA()** but using UMAP

    * **replicMeans()**: (from **regtools**, included in **qeML**)
      averages output, e.g. **testAcc**, over many holdout sets

* *application-specific functions (elementary)*
    
    * **qeText()**  text classification

    * **qeTS():**  time series
    
* *prediction with missing values*

    * **qeLinMV()**, **qeLogitMV()**, **qeKNNMV()**, 
      associated **predict()** generics for use with **toweranNA** pkg

* *utilities, exploratory tools*

    * **cartesianFactor()**:  with inputs of R factors of n1, n2...
      levels, creates a combined "superfactor" of n1*n2*... levels

    * **dataToTopLevels()**:  applies **factorToTopLevels()** to all
      fadtors in the given data frame

    * **factorToTopLevels()**:  removes rare levels from a factor

    * **levelCounts()**:  performs a census of levels for each R factor in
      the dataset

    * **newDFRow()**:  creates a new case to input to **predict()**

    * **qeParallel()**:  apply "Software Alchemy" to parallelize
      **qe** functions