mrc-ide / specio

:rainbow: Spectrum IO for EPP model for HIV epidemic estimates

specio

specio handles reading and parsing data from Spectrum PJNZ file into an R consumable format for use in the Estimation and Projection Package (EPP) for estimating and projecting HIV prevalence.

Usage

As well as the functions required for EPP specio also provides 2 more general functions for extracting population data and PLHIV data from the PJNZ file. These are extract_population and extract_hiv_population. See website reference for usage and examples.

Installation

To install internally released version via drat:

# install.packages("drat") # (if needed)
drat:::add("mrc-ide")
install.packages("specio")

specio's Issues

Include iso3 in all functions

When looping over all Spectrum files with e.g. specio::read_total_pop, the output dataframes do not contain any information on which country they are extracted from. Requesting an iso3 column included in all extract functions which would align behaviour with naomi::extract_pjnz_naomi

No "get_dp_data" function

Good afternoon!

I am trying to read into the .DP files from the spectrum projection files however the package "specio" does not seem to include "get_dp_data" even though it has been listed in the vignettes: https://github.com/mrc-ide/specio/blob/0bed6f1a52dff6ff5d8122ecee51900808cbf457/R/read_hivproj_param.R.

I was wondering why this might be, and if there are better ways to read in .DP files?

Kind regards
Salome

Issue locating "Results" data

Hello!

I only recently started to work with Spectrum so apologies for a possibly simple question:

• I have been able to successfully read in .DP files, however I am unable to locate data which I can see are available in "Results--> PMTCT--> PMTCT Summary" tab of the spectrum application. I was wondering how these (or other PMTCT) data can be located? I have gone through https://github.com/mrc-ide/eppasm/blob/47561e6ef41b593d67c26f871729eecc310dc86b/R/read-spectrum-files.R#L31 and https://mrc-ide.github.io/specio/articles/pjnz.html links.
• in .DP files, is it possible to identify what value levels (e.g. which age groups) the data points represent, when no descriptor details are available in "Notes" or "Description"? E.g. in the case of <CD4Distribution15_49 MV2> Or this can be done only manually by looking at the spectrum application?
  Thank you in advance!

Unable to read in files (read_hiv_pop() issue?)

Hi,

I've been trying to use the read_hiv_pop() command, so I tried to run the example code: The pjnz_path points to the right file, but trying to run read_hiv_pop() results in the following error – not sure if this the place to get help but it was the best way I could think of!

(Also, trying to use the ausrail file and read that into read_hiv_pop() gave me the same error.)

Thanks in advance!