artpoon/iupmbayes

Bayesian estimation of infectious units per million (IUPM) from viral outgrowth assay-based sequence data

iupmbayes's Issues

Data parsing issue

The data.pars function currently produces the following error if run on the packaged data:

Error in $<-.data.frame(*tmp*, "Variant", value = integer(0)) :
replacement has 0 rows, data has 180

This is due to a difference between the heading labels in the data file and those hard code in the script, specifically:
Variant # or Variant index vs. Variant and,
Presence of variant vs. Presence of Variant

This error can be fixed by:

1. Fixing the documentation and the packaged data to match the script.
2. Mapping the documented heading to those required by editing the script.
   a. Just fixing these two issues. (opting for this one)
   b. Build a more elaborate heading mapping function.

Variant label isn't consistent with Variant Column

Default parameter settings fail

When running the Metropolis-Hastings sampling the code fails with the following error:

Error in mh(data, max.steps = 1e+05, skip.console = 1000, skip.log = 100) :
(list) object cannot be coerced to type 'integer'

The issue is in determining the number of variants per region here:

m <- lapply(data, function(sub) ncol(sub$wells)) and,
regions <- names(m)

The first level of this list is the Patient ID so above code returns NULL.

Fixing code to:

m <- lapply(data[[1]], function(sub) ncol(sub$wells))