diff --git a/docs/usage.md b/docs/usage.md index 5481c420..99b6b517 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -176,12 +176,12 @@ posteriors_df.head() # Show the dataframe Since we are using a {ref}`sec_methods_discrete_time` method, each node (numbered column of the dataframe) is associated with a vector of probabilities that sum to one: each cell gives the probability that the time of the node -whose ID is given by the column header lies within the -timeslice specified by the `start_time` and `end_time` columns. +whose ID is given by the column header lies at the specific timepoint +given by the `time` column. For the continuous-time `variational_gamma` method, the posterior for each node is represented by the shape and rate parameter of the gamma approximation, -and the `start_time` and `end_time` entries may be ignored. +as described by the `parameter` column. (sec_usage_popsize)= @@ -193,6 +193,14 @@ over a number of contiguous time intervals. Functions of this sort are captured {class}`~demography.PopulationSizeHistory` class: see the {ref}`sec_variable_popsize` page for its use and interpretation. +If you don't have an established estimate for the effective population size of your data, +a rough approximation is to use the (sitewise) genetic diversity divided by +four-times the mutation rate: + +```{code-cell} ipython3 +print("A rough estimate of the effective population size is", sim_ts.diversity() / (4 * 1e-6)) +``` + (sec_usage_popsize_timescale)= ### Timescale adjustment