Compute first distances or distance from baseline between sequential states
Calculates first distances between sequential states for samples collected
from individual subjects sampled repeatedly at two or more states. This
method is similar to the "first differences" method, except that it
requires a distance matrix as input and calculates first differences as
distances between successive states. Outputs a data series of first
distances for each individual subject at each sequential pair of states,
labeled by the SampleID of the second state (e.g., paired distances between
time 0 and time 1 would be labeled by the SampleIDs at time 1). This file
can be used as input to linear mixed effects models or other longitudinal
or diversity methods to compare changes in first distances across time or
among groups of subjects. Also supports distance from baseline (or other
static comparison state) by setting the "baseline" parameter.
Parameters
- distance_matrix : DistanceMatrix
- Matrix of distances between pairs of samples.
- metadata : Metadata
- Sample metadata file containing individual_id_column.
- state_column : Str
- Metadata column containing state (time) variable information.
- individual_id_column : Str
- Metadata column containing IDs for individual subjects.
- baseline : Float, optional
- A value listed in the state_column metadata column against which all
other states should be compared. Toggles calculation of static
distances instead of first distances (which are calculated if no value
is given for baseline). If a "baseline" value is provided, sample
distances at each state are compared against the baseline state,
instead of the previous state. Must be a value listed in the
state_column.
- replicate_handling : Str % Choices('error', 'random', 'drop'), optional
- Choose how replicate samples are handled. If replicates are detected,
"error" causes method to fail; "drop" will discard all replicated
samples; "random" chooses one representative at random from among
replicates.
Returns
- first_distances : SampleData[FirstDifferences]
- Series of first distances.