Docstring:
Usage: qiime longitudinal linear-mixed-effects [OPTIONS]
Linear mixed effects models evaluate the contribution of exogenous
covariates "group_columns" and "random_effects" to a single dependent
variable, "metric". Perform LME and plot line plots of each group column. A
feature table artifact is required input, though whether "metric" is derived
from the feature table or metadata is optional.
Inputs:
--i-table ARTIFACT FeatureTable[RelativeFrequency]
Feature table containing metric. [optional]
Parameters:
--m-metadata-file METADATA...
(multiple arguments Sample metadata file containing
will be merged) individual-id-column. [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 Dependent variable column name. Must be a column
name located in the metadata or feature table files.
[optional]
--p-group-columns TEXT Comma-separated list (without spaces) of metadata
columns to use as independent covariates used to
determine mean structure of "metric". [optional]
--p-random-effects TEXT Comma-separated list (without spaces) of metadata
columns to use as independent covariates used to
determine the variance and covariance structure
(random effects) of "metric". To add a random slope,
the same value passed to "state-column" should be
passed here. A random intercept for each individual
is set by default and does not need to be passed
here. [optional]
--p-palette TEXT Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2',
'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c',
'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis')
Color palette to use for generating boxplots.
[default: 'Set1']
--p-lowess / --p-no-lowess
Estimate locally weighted scatterplot smoothing.
Note that this will eliminate confidence interval
plotting. [default: False]
--p-ci NUMBER Size of the confidence interval for the regression
Range(0, 100) estimate. [default: 95]
--p-formula TEXT R-style formula to use for model specification. A
formula must be used if the "metric" parameter is
None. Note that the metric and group columns
specified in the formula will override metric and
group columns that are passed separately as
parameters to this method. Formulae will be in the
format "a ~ b + c", where "a" is the metric
(dependent variable) and "b" and "c" are independent
covariates. Use "+" to add a variable; "+ a:b" to
add an interaction between variables a and b; "*" to
include a variable and all interactions; and "-" to
subtract a particular term (e.g., an interaction
term). See
https://patsy.readthedocs.io/en/latest/formulas.html
for full documentation of valid formula operators.
Always enclose formulae in quotes to avoid
unpleasant surprises. [optional]
Outputs:
--o-visualization VISUALIZATION
[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.visualizers import linear_mixed_effects
Docstring:
Linear mixed effects modeling
Linear mixed effects models evaluate the contribution of exogenous
covariates "group_columns" and "random_effects" to a single dependent
variable, "metric". Perform LME and plot line plots of each group column. A
feature table artifact is required input, though whether "metric" is
derived from the feature table or metadata is optional.
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, optional
Dependent variable column name. Must be a column name located in the
metadata or feature table files.
group_columns : Str, optional
Comma-separated list (without spaces) of metadata columns to use as
independent covariates used to determine mean structure of "metric".
random_effects : Str, optional
Comma-separated list (without spaces) of metadata columns to use as
independent covariates used to determine the variance and covariance
structure (random effects) of "metric". To add a random slope, the same
value passed to "state_column" should be passed here. A random
intercept for each individual is set by default and does not need to be
passed here.
table : FeatureTable[RelativeFrequency], optional
Feature table containing metric.
palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
Color palette to use for generating boxplots.
lowess : Bool, optional
Estimate locally weighted scatterplot smoothing. Note that this will
eliminate confidence interval plotting.
ci : Float % Range(0, 100), optional
Size of the confidence interval for the regression estimate.
formula : Str, optional
R-style formula to use for model specification. A formula must be used
if the "metric" parameter is None. Note that the metric and group
columns specified in the formula will override metric and group columns
that are passed separately as parameters to this method. Formulae will
be in the format "a ~ b + c", where "a" is the metric (dependent
variable) and "b" and "c" are independent covariates. Use "+" to add a
variable; "+ a:b" to add an interaction between variables a and b; "*"
to include a variable and all interactions; and "-" to subtract a
particular term (e.g., an interaction term). See
https://patsy.readthedocs.io/en/latest/formulas.html for full
documentation of valid formula operators. Always enclose formulae in
quotes to avoid unpleasant surprises.
Returns
-------
visualization : Visualization
