reconverse / outbreaks Goto Github PK

I've been transcribing the daily WHO Situation Reports for the current COVID-19 outbreak (https://github.com/eebrown/data2019nCoV). I think your R package outbreaks could be a good home for the data eventually. I'd be happy to add it, possibly after the outbreak has started to settle and the data isn't updated so frequently?

These data come from an outbreak of norovirus in summer 2001 in a primary school and nursery in Derbyshire, England, and were analysed by O'Neill and Marks (2005). As described in the paper, out of a total of 492 children in the school, 186 were absent from school with gastrointestinal symptoms. The school was cleaned on days 13 and 14, and on days 20 and 21, both of which were weekends, and the school was shut on days 18 and 19. Following the second cleaning, there were no further absences, although three children reported symptoms on day 22, the last day of the outbreak.

The raw data were kindly provided by Philip O'Neill, and can be found here.

It is in the format:
Class, 1st day absent, start of illness, end of illness, day of vomiting in school

There are 15 classes in the school.

@sdwfrost Just to check: are you okay with moving this project to github.com/reconhub/incidence?

I'm already hating myself for this, but as snake_case has become the standard in other RECON packages it would make sense to renamed our datasets and variables within datasets. Probably best done before too many packages depend on outbreaks too.

Make sure to increment the version number to reflect new features (middle number), pass the check, and submit to CRAN. There is a new dataset in there we are using in packages under development.

The version on CRAN still is using dots in names. We need to release the current one otherwise packages depending on this will break further down the line (thinking about first release of epicontacts for instance).

Cases of ZIKV for San Andres (n=928) and Girardot (n=1936) in Colombia in 2015/2016 are given in Rojas et al. (2016) and can be extracted from the figures:

Additional information is available in the paper.

I would imagine CC-BY or CC0, but this should be checked for each dataset. More info on licences on:
https://creativecommons.org/

@sdwfrost any preferences / strong feelings?

The package is used for examples throughout other RECON packages, so we need to get it on CRAN before making any other release (incidence is ready to go).

We need to go through our own guidelines:
http://www.repidemicsconsortium.org/resources/guidelines/

But most of it will be made easier as there's no code in this package.

@finlaycampbell lemme know if you have questions at any point; we also now have a slack for RECONHUB - I just invited you:
https://reconhub.slack.com/messages/general/

in the DESCRIPTION file, since we added the MERS data to the package from epicontacts

Somebody just pointed these data to me:
https://www.pnas.org/content/113/16/4488/tab-figures-data

Would be worth including in the package! @finlaycampbell could you have a look?

For instance:

> names(ebola_sim$linelist)
[1] "case.id"                 "generation"             
[3] "date.of.infection"       "date.of.onset"          
[5] "date.of.hospitalisation" "date.of.outcome"        
[7] "outcome"                 "gender"                 
[9] "hospital"               

We will need to coordinate the release of the next version with a new one of incidence, as it will otherwise break compatibility.

@finlaycampbell is now maintainer ;)
Need to update:

• DESCRIPTION file
• README.Rmd (and indirectly README.md)

Along the lines of incidence, but for data (lists of 0 and 1?)

@sbfnk has generously put the data used in his paper on comparative dynamics of dengue and zika online in a GitHub repo. I've included the raw data in this repository. Additional information on denominators can be found in the paper.

see the 'incidence' package for an example

in fact, it has been added:
http://www.repidemicsconsortium.org/outbreaks/

New data submission is manual so far. It may be useful to have a function of the type:
submit.data(foo)
where foo is a new dataset, which would generate:

• foo.RData: a compressed R object to be added to data/ (best compression possible by default)
• foo.R: a template of roxygen2 documentation for dataset foo

Optionally, the user could be prompted to populate some fields (provided as arguments defaulting to NULL).

Given that the version on CRAN is almost two years old, maybe it's time to submit the update with the two new(ish) data sets?

As of 0722bb3 I get:

> check()
Updating outbreaks documentation
Loading outbreaks
Invalid DESCRIPTION:
Malformed maintainer field.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

Setting env vars ---------------------------------------------------------------
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building outbreaks -------------------------------------------------------------
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD build '/home/thibaut/dev/RECON/outbreaks' --no-resave-data  \
  --no-manual 

* checking for file ‘/home/thibaut/dev/RECON/outbreaks/DESCRIPTION’ ... OK
* preparing ‘outbreaks’:
* checking DESCRIPTION meta-information ... ERROR
Malformed maintainer field.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

Error: Command failed (1)

@finlaycampbell make sure to run devtools::check() whenever you push to a master branch of a functional package. This one is probably a typo but it prevents the package from being installed.

> install()
Installing outbreaks
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/home/thibaut/dev/RECON/outbreaks'  \
  --library='/home/thibaut/R/x86_64-pc-linux-gnu-library/3.3' --install-tests 

* installing *source* package ‘outbreaks’ ...
Error : Invalid DESCRIPTION file

Malformed maintainer field.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

ERROR: installing package DESCRIPTION failed for package ‘outbreaks’
* removing ‘/home/thibaut/R/x86_64-pc-linux-gnu-library/3.3/outbreaks’
* restoring previous ‘/home/thibaut/R/x86_64-pc-linux-gnu-library/3.3/outbreaks’
Error: Command failed (1)