Inf in afb stats

[robynstuart]

spacing_stats_mean is Infinity in https://github.com/fpsim/fpsim/blob/main/tests/baseline.json

This file is generated when update_baselines is run, but the issue seems to be arising somewhere in the extract_birth_spacing method (https://github.com/fpsim/fpsim/blob/main/fpsim/experiment.py#L312)

[pausz]

@robynstuart Related issue - i can have a look this week cause i know you're super busy
#286

[emilydriano]

I will also take a look at this, as I modified the extract_birth_spacing function for the autocalibration PR

[robynstuart]

@pausz @emilydriano thank you both! I got started with some fixes here: #304

[emilydriano]

@robynstuart @pausz @MObrien-IDM I think the inf we're seeing in the data portion is because the afb.table.csv country data contains many values of 'Inf' in the afb column, which are currently included in the extraction of the ranked afb values (so end up in the 75th percentile). Prior to the autocalibration PR I made (where we saw this baseline affected), both the afb and spacing data were pulled from Senegal's 'BirthSpacing.obj' file...but with standardizing Senegal data to match that of Kenya (and other locations), we changed the data to pull from afb.table.csv and birth_spacing_dhs.csv. My guess is that the data in BirthSpacing.obj didn't have these inf values whereas the data in afb.table.csv does (hence baseline changed in this regard). I'm not sure why this file contains Inf values (missing data perhaps?) but I can exclude these rows if that's preferable.

[MObrien-IDM]

@emilydriano - Okay thanks for looking into this - Let's take a look at the underlying data, but we definitely don't want the Inf included.

[emilydriano]

Opened this issue which addresses the root cause of the issue above