Merge pull request #195 from ropensci/joss-doi

fix doi and capitalisation in paper.bib

rOpensci acceptance edits, addresses #188 (#189)

* DESCRIPTION for rOpensci

* News out of README.md

* Create NEWS.md

* Links to ropensci in README.md

* ropensci in codemeta.json

* Create codemeta.json

* Addressed CRAN gotchas

See https://devguide.ropensci.org/building.html#crangotchas

* NEWS.md link from README

* reword code of conduct lines in README

As described in https://devguide.ropensci.org/collaboration.html

* Update CONTRIBUTING.md

* Removed duplicated development

Co-authored-by: Samuel Joseph Haynes <[email protected]>

Merge pull request #177 from ewallace/paper-v0.5

- affiliations, grant numbers, rOpenSci, in paper.md

This pull request only made minor changes to paper.md so I am approving.

New in README.md

stable version for rOpenSci submission

calculate_efficiency warning correct, fixes #80

Deltadeltacq 53 (#62)

* fix value_name in calculate_deltacq.R

* 96-well delta cq vignette draft

* simplify calculate_deltacq.R

* clarifications to ddcq vignette

* calculate_deltadeltacq_bytargetid runs

* Deltadeltacq 53 (#58)

* Fixes: #56 all variables are now explicitly defined

* Fixed bug in deltadeltaqc function so that sample_id rather than target_id is passed onto calculate_normvalue function

* calculate_deltacq documentation clarifications

* explanations in deltacq_96well_vignette.Rmd

* delta cq and vignette updates on README.md

* multiple ref genes for deltacq, addresses #52

* Comments on delta Cq vignette

Hi there,
I had a few minutes so I went through your new vignette. It's really good, clear and easy to understand! I like the simpler (but still real) data set. 

I made a bunch of changes throughout, I hope you don't mind. My philosophy is to make as many comments and changes as possible and then let the author decide which ones are valuable. Please don't take the volume of comments/changes as a criticism! A few notes below about my comments:   

Summary section: tried to simplify the technical details of the experiment a bit to make it more approachable to non-microbiologists. Sorry if I got anything wrong!

Throughout: shortened here and there by removing information I didn't think was critical

I added comments in some places inside `[]`

I mostly used "gene" instead of "target" because I think it's easier to understand, but qPCR users will probably be familiar with the word "target". Maybe just define it at the top.

* responded to @seaaan's vignette edits

* Comments on delta Cq vignette (#59)

Hi there,
I had a few minutes so I went through your new vignette. It's really good, clear and easy to understand! I like the simpler (but still real) data set. 

I made a bunch of changes throughout, I hope you don't mind. My philosophy is to make as many comments and changes as possible and then let the author decide which ones are valuable. Please don't take the volume of comments/changes as a criticism! A few notes below about my comments:   

Summary section: tried to simplify the technical details of the experiment a bit to make it more approachable to non-microbiologists. Sorry if I got anything wrong!

Throughout: shortened here and there by removing information I didn't think was critical

I added comments in some places inside `[]`

I mostly used "gene" instead of "target" because I think it's easier to understand, but qPCR users will probably be familiar with the word "target". Maybe just define it at the top.

* fixed col_types for doubles in read_lightcycler_1colour_cq

* fixed decimal places of deltacq_96well select data

Co-authored-by: Samuel Joseph Haynes <[email protected]>
Co-authored-by: Sean Hughes <[email protected]>

Repo status active at top