Non-Negative Matrix Factorization Signal ExtractionSource:
step_nnmf creates a specification of a recipe step
that will convert numeric data into one or more non-negative
step_nnmf_sparse() instead of this step function.
A recipe object. The step will be added to the sequence of operations for this recipe.
One or more selector functions to choose variables for this step. See
selections()for more details.
For model terms created by this step, what analysis role should they be assigned? By default, the new columns created by this step from the original variables will be used as predictors in a model.
A logical to indicate if the quantities for preprocessing have been estimated.
The number of components to retain as new predictors. If
num_compis greater than the number of columns or the number of possible components, a smaller value will be used. If
num_comp = 0is set then no transformation is done and selected variables will stay unchanged.
A positive integer for the number of computations runs used to obtain a consensus projection.
A list of options to
nmf()in the NMF package by way of the
NNMF()function in the
dimRedpackage. Note that the arguments
ndimshould not be passed here, and that NMF's parallel processing is turned off in favor of resample-level parallelization.
NNMF()object is stored here once this preprocessing step has been trained by
A character string of variable names that will be populated elsewhere.
A character string that will be the prefix to the resulting new variables. See notes below.
An integer that will be used to set the seed in isolation when computing the factorization.
A logical to keep the original variables in the output. Defaults to
A logical. Should the step be skipped when the recipe is baked by
bake()? While all operations are baked when
prep()is run, some operations may not be able to be conducted on new data (e.g. processing the outcome variable(s)). Care should be taken when using
skip = TRUEas it may affect the computations for subsequent operations.
A character string that is unique to this step to identify it.
An updated version of
recipe with the new step added to the
sequence of any existing operations.
Non-negative matrix factorization computes latent components that have non-negative values and take into account that the original data have non-negative values.
num_comp controls the number of components that
will be retained (the original variables that are used to derive
the components are removed from the data). The new components
will have names that begin with
prefix and a sequence of
numbers. The variable names are padded with zeros. For example,
num < 10, their names will be
num = 101, the names would be
tidy() this step, a tibble with column
terms (the selectors or variables selected) and the number of
components is returned.
library(modeldata) data(biomass) # rec <- recipe(HHV ~ ., data = biomass) %>% # update_role(sample, new_role = "id var") %>% # update_role(dataset, new_role = "split variable") %>% # step_nnmf(all_numeric_predictors(), num_comp = 2, seed = 473, num_run = 2) %>% # prep(training = biomass) # # bake(rec, new_data = NULL) # # library(ggplot2) # bake(rec, new_data = NULL) %>% # ggplot(aes(x = NNMF2, y = NNMF1, col = HHV)) + geom_point()