rtimicropem

[maelle]

Summary

• What does this package do? (explain in 50 words or less):

This package aims at supporting the analysis of PM2.5 measures made with RTI MicroPEM. RTI MicroPEM are personal monitoring devices (PM2.5 and PM10) developped by RTI international.

• Paste the full DESCRIPTION file inside a code block below:

Package: rtimicropem
Type: Package
Title: Supports the Analysis of RTI MicroPEM Output Files
Version: 1.3
Authors@R: c(person("Maëlle", "Salmon", email = "maelle.salmon@yahoo.se", role = c("aut", "cre")),
             person("Zheng", "Zhou", comment = "Department of Environmental Health Sciences Mailman School of Public Health at Columbia University, New York, USA", role = c("aut")),
             person(family = "ERC Grant Agreement number 336167 - the CHAI Project", role = c("fnd")),
             person("Carles", "Milà", role = c("ctb")),
             person("Sreekanth", "Vakacherla", role = c("ctb")),
             person("Cathryn", "Tonne", role = c("ctb")),
             person("Julian", "Marshall", role = c("ctb")))
Description: Supports the input and reproducible analysis of RTI MicroPEM output files.
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests: testthat,
    rmarkdown,
    xtable,
    shiny
Imports: lubridate,
   ggplot2,
   dplyr (>= 0.4.3),
   rbokeh,
    R6,
   changepoint,
   tibble,
    tidyr,
    lazyeval,
    readr,
    pathological,
    stringr,
    knitr,
    methods
Depends: R (>= 3.3.1)
VignetteBuilder: knitr
URL: http://github.com/masalmon/rtimicropem
BugReports: http://github.com/masalmon/rtimicropem/issues
Encoding: UTF-8

• URL for the package (the development repository, not a stylized html page):

https://github.com/masalmon/rtimicropem

• Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

[e.g., "data extraction, because the package parses a scientific data file format"]

This package fits in the data extraction category because it allows to transform files produced by the RTI MicroPEM, which are scientific devices, into data.frames.

• Who is the target audience?

Scientists using RTI MicroPEMs for collecting personal PM2.5 data.

• Are there other R packages that accomplish the same thing? If so, how does
  yours differ or meet our criteria for best-in-category?

Not to my knowledge.

Requirements

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage, using services such as Travis CI, Coeveralls and/or CodeCov.
• I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Publication options

• Do you intend for this package to go on CRAN?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • The package contains a paper.md with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)

Detail

• Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

• Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:

• If this is a resubmission following rejection, please explain the change in circumstances:

• If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:

[sckott]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Thanks for your submission @maelle !

Currently seeking reviewers. It's a good fit and not overlapping.

• goodpractice::gp() output is below. Looks quite clean.

It is good practice to

  ✖ write unit tests for all functions, and all package code
    in general. 92% of code lines are covered by test cases.

    R/clean_measures.R:56:NA
    R/clean_measures.R:74:NA
    R/clean_measures.R:75:NA
    R/clean_measures.R:76:NA
    R/clean_measures.R:77:NA
    ... and 26 more lines

  ✖ avoid long code lines, it is bad for readability. Also,
    many people prefer editor windows that are about 80 characters
    wide. Try make your lines shorter than 80 characters

    inst/shiny-examples/myapp/server.R:50:1
    inst/shiny-examples/myapp/ui.R:42:1
    R/identify_lags.R:20:1
    R/identify_lags.R:25:1
    R/micropem_class.R:236:1

  ✖ not import packages as a whole, as this can cause name
    clashes between the imported packages. Instead, import only the
    specific functions you need.
  ✖ fix this R CMD check NOTE: Namespace in Imports field not
    imported from: ‘R6’ All declared Imports should be used.

---

Reviewers: @LucyMcGowan @karawoo
Due date: 2017-07-14

[maelle]

Thanks a lot @sckott , will take a look in particular at the Imports soon.

[maelle]

@sckott The package no longer imports ggplot2 as a whole but I don't understand where the R CMD check NOTE comes from.

fix this R CMD check NOTE: Namespace in Imports field not imported from: ‘R6’ All declared Imports should be used.

In micropem-class.R I actually import R6::R6Class 🤔

[sckott]

Right - i get that error sometimes too and doesn’t seem to make sense - will look into that warning message in general cause I'd like to know

[sckott]

@maelle do you have a travis or other build to reference with that note?

[maelle]

Will check tomorrow, Thanks!

[sckott]

ok, thanks