# first-differences: Compute first differences or difference from baseline between sequential states¶

#### 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:
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).
--examples             Show usage examples and exit.
--citations            Show citations and exit.
--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
----------
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.