stan-dev/bayesplot

mcmc_pairs bivariate off-diagonal plot axis incorrect.

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#132 opened on Dec 17, 2017

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Description

Data file: https://drive.google.com/open?id=1pnAUDCz9uscccSaUISodF9cqGF23uNzU

Off-diagonal bivariate scatter plot axes are out of line

My understanding from the documentation is that half the chains are used for each of the off-diagonal plots. In this example case (see posterior data file linked above) the chains have not converged and so the lower off-diagonal plot seems to be using chains that only sampled from one mode, using default condition I think this should be correct. I believe the x-axis should be inline with the above univariate marginal plot and the y-axis inline scaled as the x-axis of the upper off-diagonal bivariate plot?

load(file = "posterior.arr.RData")
mcmc_pairs(posterior, pars = c("u","v"))

mcmc_pairs_joint_samples_missing_data

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Research direction
Inspect the mcmc pairs function in the bayesplot package to understand how off diagonal plot axes are set. Check if the axis limits are correctly inherited from the respective marginal plots. The issue likely lies in the axis scaling logic for the off diagonal panels.
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