qiime longitudinal linear-mixed-effects (version 2019.4)

--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]:

--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metric. [optional]:

--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: :

--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]:

--m-metadata-file [required]s

--m-metadata-file [required] 0

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'), 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