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smathot committed Jan 23, 2023
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64 changes: 32 additions & 32 deletions readme.md
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Expand Up @@ -52,7 +52,7 @@ This packages also provides a function (`plot()`) to visualize time-series data

### When to use `lmer_permutation_test()`?

`lmer_permutation_test()` implements a fairly standard cluster-based permutation test, which differs from most other implementations in that it relies on linear mixed-effects modeling to calculate the test statistics. Therefore, this function tends to be extremely computationally intensive. Its main advantage of `find()` is that it is also valid for data with multiple components, such as event-related potentials (ERPs).
`lmer_permutation_test()` implements a fairly standard cluster-based permutation test, which differs from most other implementations in that it relies on linear mixed-effects modeling to calculate the test statistics. Therefore, this function tends to be extremely computationally intensive, but should also be more sensitive than cluster-based permutation tests that are based on average data. Its main advantage as compared to `lmer_crossvalidation_test()` is that it is also valid for data with multiple components, such as event-related potentials (ERPs).


## Installation
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## Function reference

## <span style="color:purple">time\_series\_test.find</span>_(dm, formula, groups, re\_formula=None, winlen=1, split=4, split\_method='interleaved', samples\_fe=True, samples\_re=True, localizer\_re=False, fit\_method=None, suppress\_convergence\_warnings=False, fit\_kwargs=None, \*\*kwargs)_
## <span style="color:purple">time\_series\_test.lmer\_crossvalidation\_test</span>_(dm, formula, groups, re\_formula=None, winlen=1, split=4, split\_method='interleaved', samples\_fe=True, samples\_re=True, localizer\_re=False, fit\_method=None, suppress\_convergence\_warnings=False, fit\_kwargs=None, \*\*kwargs)_

Conducts a single linear mixed effects model to a time series, where the
to-be-tested samples are determined through crossvalidation.
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A dict where keys are effect labels, and values are named tuples
of `model`, `samples`, `p`, and `z`.

## <span style="color:purple">time\_series\_test.lmer\_series</span>_(dm, formula, winlen=1, fit\_kwargs={}, \*\*kwargs)_

Performs a sample-by-sample linear-mixed-effects analysis. See `lmer_crossvalidation()`
for an explanation of the arguments.

### Parameters

* **dm: DataMatrix**

* **formula: str**

* **winlen: int, optional**

* **fit\_kwargs: dict, optional**

* **\*\*kwargs: dict, optional**

### Returns

* **_DataMatrix_**

A DataMatrix with one row per effect, including the intercept, and
three series columns with the same depth as the dependent measure
specified in the formula:

- `est`: the slope
- `p`: the p value
- `z`: the z value
- `se`: the standard error

## <span style="color:purple">time\_series\_test.lmer\_permutation\_test</span>_(dm, formula, groups, re\_formula=None, winlen=1, suppress\_convergence\_warnings=False, fit\_kwargs={}, iterations=1000, cluster\_p\_threshold=0.05, \*\*kwargs)_

Performs a cluster-based permutation test based on sample-by-sample
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(start, end, z-sum, hit proportion) tuples. The p-value is
1 - hit proportion.

## <span style="color:purple">time\_series\_test.lmer\_series</span>_(dm, formula, winlen=1, fit\_kwargs={}, \*\*kwargs)_

Performs a sample-by-sample linear-mixed-effects analysis. See `lmer_crossvalidation()`
for an explanation of the arguments.

### Parameters

* **dm: DataMatrix**

* **formula: str**

* **winlen: int, optional**

* **fit\_kwargs: dict, optional**

* **\*\*kwargs: dict, optional**

### Returns

* **_DataMatrix_**

A DataMatrix with one row per effect, including the intercept, and
three series columns with the same depth as the dependent measure
specified in the formula:

- `est`: the slope
- `p`: the p value
- `z`: the z value
- `se`: the standard error

## <span style="color:purple">time\_series\_test.plot</span>_(dm, dv, hue\_factor, results=None, linestyle\_factor=None, hues=None, linestyles=None, alpha\_level=0.05, annotate\_intercept=False, annotation\_hues=None, annotation\_linestyle=':', legend\_kwargs=None, annotation\_legend\_kwargs=None)_

Visualizes a time series, where the signal is plotted as a function of
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2 changes: 1 addition & 1 deletion time_series_test.py
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import re
from collections import namedtuple

__version__ = '0.9.1'
__version__ = '0.9.2'
DEFAULT_HUE_COLORMAP = 'Dark2'
DEFAULT_ANNOTATION_COLORMAP = 'brg'
DEEP_ORANGE = ['#bf360c', '#e64a19', '#ff5722', '#ff8a65', '#ffccbc']
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