Testing a hypothesis – non-stationary or time-reversible¶
We evaluate whether the GTR model is sufficient for a data set, compared with the GN (non-stationary general nucleotide model).
result
is a hypothesis_result
object. The repr()
displays the likelihood ratio test statistic, degrees of freedom and associated p-value>
In this case, we accept the null given the p-value is > 0.05. We still use this object to demonstrate the properties of a hypothesis_result
.
hypothesis_result
has attributes and keys¶
Accessing the test statistics¶
The null hypothesis¶
This model is accessed via the null
attribute.
The alternate hypothesis¶
Saving hypothesis results¶
You are advised to save these results as json using the standard json writer, or the db writer.
This following would write the result into a tinydb
.
from cogent3.app.io import write_db
writer = write_db("path/to/myresults.tinydb", create=True, if_exists="overwrite")
writer(result)