S3 methods for mdm objects — mdm_methods • metabodeconplus

WARNING: These methods are experimental and must not be used in production. Their API is very likely to change in non-backwards-compatible ways over the next few weeks.

S3 methods for objects of class mdm and summary.mdm.

predict.mdm() predicts probabilities, classes, link scores, or all three from an mdm object. When newdata is a spectra object, the spectra are deconvoluted, aligned and snapped to the references stored in the model before prediction. When newdata is a numeric matrix, it is used directly as the feature matrix.

print.mdm() prints a compact model summary.

coef.mdm() returns lasso coefficients (or ranger importance).

plot.mdm() plots the lasso path (or ranger importance bars).

summary.mdm() builds a compact summary list.

print.summary.mdm() prints formatted output for summary.mdm objects.

Usage

# S3 method for class 'mdm'
predict(
  object,
  newdata,
  type = c("all", "prob", "class", "link"),
  nworkers = 1,
  verbosity = 1,
  ...
)

# S3 method for class 'mdm'
print(x, ...)

# S3 method for class 'mdm'
coef(object, ...)

# S3 method for class 'mdm'
plot(x, ...)

# S3 method for class 'mdm'
summary(object, ...)

# S3 method for class 'summary.mdm'
print(x, ...)

Arguments

object, x: A fitted mdm object (for predict, coef, summary, print and plot) or a summary.mdm object (for print.summary.mdm).
newdata: Spectra object or numeric feature matrix.
type: Prediction type, one of "all", "prob", "class", "link".
nworkers: Number of workers to deconvolute and align newdata.
verbosity: Integer verbosity level.
...: Passed to underlying methods where applicable.

Value

predict: numeric vector of probabilities, classes, and/or link scores.
print: invisibly returns x.
coef: coefficient object from glmnet (or ranger importance).
plot: invisibly returns NULL.
summary: object of class summary.mdm.
print.summary.mdm: invisibly returns x.