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rtemis (version 0.79)

s.GAM.formula: Generalized Additive Model (GAM) C, R

Description

Trains a GAM using mgcv::gam and validates it. Input will be used to create a formula of the form: $$y = s(x_{1}, k = gam.k) + s(x_{2}, k = gam.k) + ... + s(x_{n}, k = gam.k)$$

Usage

# S3 method for formula
s.GAM(formula, data, data.test = NULL, x.name = NULL,
  y.name = NULL, k = 6, interactions = TRUE, family = gaussian(),
  weights = NULL, method = "REML", select = FALSE, verbose = TRUE,
  print.plot = TRUE, plot.fitted = NULL, plot.predicted = NULL,
  plot.theme = getOption("rt.fit.theme", "lightgrid"),
  na.action = na.exclude, question = NULL, n.cores = rtCores,
  outdir = NULL, save.mod = ifelse(!is.null(outdir), TRUE, FALSE), ...)

Arguments

x.name

Character: Name for feature set

y.name

Character: Name for outcome

k

Integer. Number of bases for smoothing spline

interactions

Logical: If TRUE, include all pairwise interactions. formula = y ~.*.

family

Error distribution and link function. See stats::family

weights

Numeric vector: Weights for cases. For classification, weights takes precedence over ipw, therefore set weights = NULL if using ipw. Note: If weight are provided, ipw is not used. Leave NULL if setting ipw = TRUE. Default = NULL

verbose

Logical: If TRUE, print summary to screen.

print.plot

Logical: if TRUE, produce plot using mplot3 Takes precedence over plot.fitted and plot.predicted

plot.fitted

Logical: if TRUE, plot True (y) vs Fitted

plot.predicted

Logical: if TRUE, plot True (y.test) vs Predicted. Requires x.test and y.test

plot.theme

String: "zero", "dark", "box", "darkbox"

na.action

How to handle missing values. See ?na.fail

question

String: the question you are attempting to answer with this model, in plain language.

outdir

Path to output directory. If defined, will save Predicted vs. True plot, if available, as well as full model output, if save.mod is TRUE

save.mod

Logical. If TRUE, save all output as RDS file in outdir save.mod is TRUE by default if an outdir is defined. If set to TRUE, and no outdir is defined, outdir defaults to paste0("./s.", mod.name)

...

Additional arguments to be passed to mgcv::gam

covariates

Factors to be included as covariates in model building

covariates.test

Factors to be included as covariates in model validation

Value

rtMod

Details

s.GAM.default is the preferred way to train GAMs

See Also

elevate for external cross-validation

Other Supervised Learning: s.ADABOOST, s.ADDTREE, s.BART, s.BAYESGLM, s.BRUTO, s.C50, s.CART, s.CTREE, s.DA, s.ET, s.EVTREE, s.GAM.default, s.GAMSEL, s.GAM, s.GBM3, s.GBM, s.GLMNET, s.GLM, s.GLS, s.H2ODL, s.H2OGBM, s.H2ORF, s.IRF, s.KNN, s.LDA, s.LM, s.MARS, s.MLRF, s.MXN, s.NBAYES, s.NLA, s.NLS, s.NW, s.POLYMARS, s.PPR, s.PPTREE, s.QDA, s.QRNN, s.RANGER, s.RFSRC, s.RF, s.SGD, s.SPLS, s.SVM, s.TFN, s.XGBLIN, s.XGB