ids_apply.RdAdds labels to rows of all individual spectra in collections.
Such labels are required for subsequent processing functions that aggregate
spectral collections by group, for example colmean_group_apply().
It can also be used to initialize a single spectral collection with labels
when inputting a single matrix, data frame or data.table.
ids_apply(X, dt_prep_sets = NULL, vec_row, vec_id, vec_group)matrix, data.frame or data.table for which label rows
are to be applied.
A standardized data.table, i.e. returned from specprepper::*_apply()
function. Contains labelled sets of preprocessed spectra:
This argument allows to chain preprocessing in sequential manner, and i.e. apply variable
Savitzky-Golay smoothers with a single function application.
atomic vector with row labels; need to have same length
as nrow(X) or rows in all spc_proc list-column data.table's.
atomic vector with id labels, needs to have same length
as nrow(X) or rows in all spc_proc list-column data.table's. id_vec
typically represents the smallest hiararchical unit in the measurement
design, e.g., a replicate spectrum measured.
atomic vector with group labels; needs to have same length
as nrow(X) or rows in all spc_proc list-column data.table's. id_group
typically represents the group to aggregate by in specific methods applied
later. Currently, this is colmean_group_apply() that takes grouped means
of spectra or collections of spectra.
If X is specified:
A one-row "data.table" with the following columns
prep_set: "init_ids",
prep_label: "prep_label"
prep_params: list-column of length 1 with "data.table" containing
init_ids = NA
id_labels: list-column (repeated across rows) with "data.table"
containing columns with labels: row (from vec_row),
id (from vec_id), and group (from vec_group).
If dt_prep_sets is specified:
A "data.table" with as many rows as spectral collections. A spectral
collection typically represents an outcome of one or more specific
preprocessing with methods and possibly associated parameters used.
Specifically, it augments the input dt_prep_sets and outputs the
following (list-)columns:
prep_set: appends "-init_ids to the input string that states what
the main preprocessings done in previous steps.
prep_label: appends "-init_ids to the input string that states what
was done with abbreviations of methods in previous steps.
prep_params: augments each data.table element in the list-column with
a new non-specific column init_ids = NA (indicating a new label
column but no direct effect on the processed spectra).
id_labels: new list-column that contains a set of labels that applies
for all spectral collections nested within respective rows of the
dt_prep_sets input. Each data.table in the list contains the label
columns row (from vec_row),id (from vec_id), and group
(from vec_group).
spec_prep: unmodified list-column with sets of already prepared,
processed spectra. Each element is a data.table which rows corresponds
to the row labels in id_labels.