Docstring:
Usage: qiime longitudinal first-differences [OPTIONS]
Calculates first differences in "metric" between sequential states for
samples collected from individual subjects sampled repeatedly at two or more
states. First differences can be performed on a metadata column (including
artifacts that can be input as metadata) or a feature in a feature table.
Outputs a data series of first differences for each individual subject at
each sequential pair of states, labeled by the SampleID of the second state
(e.g., paired differences 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 differences across time or among groups of subjects. Also supports
differences from baseline (or other static comparison state) by setting the
"baseline" parameter.
Inputs:
--i-table ARTIFACT FeatureTable[RelativeFrequency]
Feature table to optionally use for computing first
differences. [optional]
Parameters:
--m-metadata-file METADATA...
(multiple Sample metadata file containing
arguments will be individual-id-column.
merged) [required]
--p-state-column TEXT Metadata column containing state (time) variable
information. [required]
--p-individual-id-column TEXT
Metadata column containing IDs for individual
subjects. [required]
--p-metric TEXT Numerical metadata or artifact column to test.
[required]
--p-replicate-handling TEXT Choices('error', 'random', 'drop')
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. [default: 'error']
--p-baseline NUMBER A value listed in the state-column metadata column
against which all other states should be compared.
Toggles calculation of static differences instead of
first differences (which are calculated if no value
is given for baseline). If a "baseline" value is
provided, sample differences at each state are
compared against the baseline state, instead of the
previous state. Must be a value listed in the
state-column. [optional]
Outputs:
--o-first-differences ARTIFACT SampleData[FirstDifferences]
Series of first differences. [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible to
all nodes in the cluster.
--help Show this message and exit.
Import:
from qiime2.plugins.longitudinal.methods import first_differences
Docstring:
Compute first differences or difference from baseline between sequential
states
Calculates first differences in "metric" between sequential states for
samples collected from individual subjects sampled repeatedly at two or
more states. First differences can be performed on a metadata column
(including artifacts that can be input as metadata) or a feature in a
feature table. Outputs a data series of first differences for each
individual subject at each sequential pair of states, labeled by the
SampleID of the second state (e.g., paired differences 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 differences across time or among groups
of subjects. Also supports differences from baseline (or other static
comparison state) by setting the "baseline" parameter.
Parameters
----------
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.
metric : Str
Numerical metadata or artifact column to test.
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.
baseline : Float, optional
A value listed in the state_column metadata column against which all
other states should be compared. Toggles calculation of static
differences instead of first differences (which are calculated if no
value is given for baseline). If a "baseline" value is provided, sample
differences at each state are compared against the baseline state,
instead of the previous state. Must be a value listed in the
state_column.
table : FeatureTable[RelativeFrequency], optional
Feature table to optionally use for computing first differences.
Returns
-------
first_differences : SampleData[FirstDifferences]
Series of first differences.
