spell check and update WORDLIST

DESCRIPTION

@@ -27,10 +27,10 @@ Authors@R:
               email = "jmtaylor@fredhutch.org"),
       person(given = "Kara", family = "Woo",
               role = "rev",
-              comment = "Kara reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/230>"),
+              comment = "Kara reviewed the package for rOpenSci, see <https://github.com/ropensci/onboarding/issues/230>"),
       person(given = "William", family = "Landau",
               role = "rev",
-      comment = "William reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/230>"))
+      comment = "William reviewed the package for rOpenSci, see <https://github.com/ropensci/onboarding/issues/230>"))
 Version: 0.15.9.9000
 Description: A framework to help construct R data packages in a 
   reproducible manner. Potentially time consuming processing of 

NEWS.md

@@ -61,13 +61,13 @@
 * Data objects are incrementally stored during the build process, into the render_root directory specified in the datapackager.yml config file.
 
 # DataPackageR 0.15.3
-* conditional tests when pandoc is missing (ropensci/DataPackager/issues/46)
-* add use_data_object and use_processing_script (ropensci/DataPackager/issues/44)
-* allow datapackage_skeleton to be called without files or data objects for interactive construction. (ropensci/DataPackager/issues/44)
+* conditional tests when pandoc is missing (ropensci/DataPackageR/issues/46)
+* add use_data_object and use_processing_script (ropensci/DataPackageR/issues/44)
+* allow datapackage_skeleton to be called without files or data objects for interactive construction. (ropensci/DataPackageR/issues/44)
 
 # DataPackageR 0.15.2
-* Add  pandoc to SystemRequirements (ropensci/DataPackager/issues/46)
-* Add use_raw_dataset() method (and tests) to add data sets to inst/extdata. interactively. (ropensci/DataPackager/issues/44)
+* Add  pandoc to SystemRequirements (ropensci/DataPackageR/issues/46)
+* Add use_raw_dataset() method (and tests) to add data sets to inst/extdata. interactively. (ropensci/DataPackageR/issues/44)
 
 # DataPackageR 0.15.1.9000
 * Development version
@@ -81,7 +81,7 @@
 
 # DataPackageR 0.14.9
 
-- Moving towards ropensci compliance
+- Moving towards rOpenSci compliance
 - NEWS.md updated with description of changes to data sets when version is bumped (or new package is created).
 - Output of "next steps" for user when package is built
 - New `document()` function to rebuild docs from `documentation.R` in `data-raw` without rebuilding the whole package.

R/DataPackageR-package.R

@@ -108,12 +108,12 @@ NULL
 #'   \code{package_build()}. See the example above and the
 #'   \href{https://ropensci.org/blog/2018/09/18/datapackager/}{rOpenSci blog
 #'   post} for more details on how to set this to FALSE, which will never prompt
-#'   user for a NEWS update. FALSE is also the setting used for DataPackageR's
-#'   internal tests.
+#'   user for a NEWS update. FALSE is also the setting used for DataPackageR
+#'   internal package tests.
 #'
 #' - \code{DataPackageR_verbose}: Default upon package load is TRUE. FALSE suppresses
-#'   all console output and is currently only used for DataPackageR's automated
-#'   unit tests.
+#'   all console output and is currently only used for automated
+#'   unit tests of the DataPackageR package.
 #'
 #' - \code{DataPackageR_packagebuilding}: Default upon package load is FALSE. This
 #'   option is used internally for package operations and changing it is not

R/digests.R

@@ -31,7 +31,7 @@
 
 .compare_digests <- function(old_digest, new_digest) {
   # Returns FALSE when any exisiting data has is changed, new data is added, or data is removed, else return TRUE.
-  # Use .mutlilog_warn when there is a change and multilog_debug when new data is added.
+  # Use .multilog_warn when there is a change and multilog_debug when new data is added.
 
   existed <- names(new_digest)[names(new_digest) %in% names(old_digest)]
   added <- setdiff(names(new_digest), existed)

README.Rmd

@@ -58,7 +58,7 @@ You have diverse raw data sets that you need to preprocess and tidy in order to:
 
 - **Collaboration.**
 
-  A data set packaged in R is easy to distribute and share amongst collaborators, and is easy to install and use.
+  A data set packaged in R is easy to distribute and share among collaborators, and is easy to install and use.
   All the hard work you've put into documenting and standardizing the tidy data set comes right along with the data package.
 
 - **Documentation.**
@@ -75,7 +75,7 @@ You have diverse raw data sets that you need to preprocess and tidy in order to:
 
 - **Package size limits.**
 
-  R packages have a 10MB size limit, at least on [CRAN](https://cran.r-project.org/web/packages/policies.html). BioConductor [ExperimentHub](http://contributions.bioconductor.org/data.html#data) may be able to support larger data packages.
+  R packages have a 10MB size limit, at least on [CRAN](https://cran.r-project.org/web/packages/policies.html). Bioconductor [ExperimentHub](http://contributions.bioconductor.org/data.html#data) may be able to support larger data packages.
 
   Sharing large volumes of raw data in an R package format is still not ideal, and there are public biological data repositories better suited for raw data: e.g.,  [GEO](https://www.ncbi.nlm.nih.gov/geo/), [SRA](https://www.ncbi.nlm.nih.gov/sra), [ImmPort](https://www.immport.org/), [ImmuneSpace](https://immunespace.org/), [FlowRepository](http://flowrepository.org/).
 
@@ -131,7 +131,7 @@ There are a number of tools out there that address similar and complementary pro
 - **rrrpkg**
   [github repo](https://github.com/ropensci/rrrpkg)
 
-  A document from ropensci describing using an R package as a research compendium. Based on ideas originally introduced by Robert Gentleman and Duncan Temple Lang (Gentleman and Lang (2004)<!--@Gentleman2004-oj-->)
+  A document from rOpenSci describing using an R package as a research compendium. Based on ideas originally introduced by Robert Gentleman and Duncan Temple Lang (Gentleman and Lang (2004)<!--@Gentleman2004-oj-->)
 
 - **template**
   [github repo](https://github.com/ropensci/rrrpkg)
@@ -260,10 +260,10 @@ DataPackageR::project_data_path()
 
 ## Preprint and publication. <a id = "publication"></a>
 
-The publication describing the package, (Finak *et* *al.,* 2018)<!--@10.12688/gatesopenres.12832.2-->, is now available at   [Gates Open Research](https://gatesopenresearch.org/articles/2-31/v2) .
+The publication describing the package, (Finak *et al.*, 2018)<!--@10.12688/gatesopenres.12832.2-->, is now available at   [Gates Open Research](https://gatesopenresearch.org/articles/2-31/v2) .
 
 
-The preprint is on [biorxiv](https://doi.org/10.1101/342907).
+The preprint is on [bioRxiv](https://doi.org/10.1101/342907).
 
 
 ## Code of conduct 
@@ -276,7 +276,7 @@ Please note that this project is released with a [Contributor Code of Conduct](h
 1. Gentleman, Robert, and Duncan Temple Lang. 2004. “Statistical Analyses and Reproducible Research.” Bioconductor Project Working Papers, Bioconductor project working papers,. bepress.
 
 2. Finak G, Mayer B, Fulp W, et al. DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis. Gates Open Res 2018, 2:31
-(doi: 10.12688/gatesopenres.12832.1)
+(DOI: 10.12688/gatesopenres.12832.1)
 
 
 

README.md

@@ -58,7 +58,7 @@ purpose is to contain, access, and / or document data sets.
 
 - **Collaboration.**
 
-  A data set packaged in R is easy to distribute and share amongst
+  A data set packaged in R is easy to distribute and share among
   collaborators, and is easy to install and use. All the hard work
   you’ve put into documenting and standardizing the tidy data set comes
   right along with the data package.
@@ -84,7 +84,7 @@ purpose is to contain, access, and / or document data sets.
 
   R packages have a 10MB size limit, at least on
   [CRAN](https://cran.r-project.org/web/packages/policies.html).
-  BioConductor
+  Bioconductor
   [ExperimentHub](http://contributions.bioconductor.org/data.html#data)
   may be able to support larger data packages.
 
@@ -169,7 +169,7 @@ complementary problems:
 
 - **rrrpkg** [github repo](https://github.com/ropensci/rrrpkg)
 
-  A document from ropensci describing using an R package as a research
+  A document from rOpenSci describing using an R package as a research
   compendium. Based on ideas originally introduced by Robert Gentleman
   and Duncan Temple Lang (Gentleman and Lang
   (2004)<!--@Gentleman2004-oj-->)
@@ -234,8 +234,8 @@ datapackage_skeleton(
   code_files = processing_code, 
   r_object_names = "cars_over_20", 
   path = tempdir()) 
-#> ✔ Creating 'C:/Users/dslager/AppData/Local/Temp/RtmpuqBumR/mtcars20/'
-#> ✔ Setting active project to 'C:/Users/dslager/AppData/Local/Temp/RtmpuqBumR/mtcars20'
+#> ✔ Creating 'C:/Users/dslager/AppData/Local/Temp/RtmpaIslsQ/mtcars20/'
+#> ✔ Setting active project to 'C:/Users/dslager/AppData/Local/Temp/RtmpaIslsQ/mtcars20'
 #> ✔ Creating 'R/'
 #> ✔ Writing 'DESCRIPTION'
 #> Package: mtcars20
@@ -251,7 +251,7 @@ datapackage_skeleton(
 #> RoxygenNote: 7.3.1
 #> ✔ Writing 'NAMESPACE'
 #> ✔ Setting active project to '<no active project>'
-#> ✔ Setting active project to 'C:/Users/dslager/AppData/Local/Temp/RtmpuqBumR/mtcars20'
+#> ✔ Setting active project to 'C:/Users/dslager/AppData/Local/Temp/RtmpaIslsQ/mtcars20'
 #> ✔ Added DataVersion string to 'DESCRIPTION'
 #> ✔ Creating 'data-raw/'
 #> ✔ Creating 'data/'
@@ -279,13 +279,13 @@ package_build(packageName = file.path(tempdir(),"mtcars20"))
 #> Writing 'mtcars20.Rd'
 #> Writing 'cars_over_20.Rd'
 #> ── R CMD build ─────────────────────────────────────────────────────────────────
-#>          checking for file 'C:\Users\dslager\AppData\Local\Temp\RtmpuqBumR\mtcars20/DESCRIPTION' ...  ✔  checking for file 'C:\Users\dslager\AppData\Local\Temp\RtmpuqBumR\mtcars20/DESCRIPTION' (341ms)
+#>          checking for file 'C:\Users\dslager\AppData\Local\Temp\RtmpaIslsQ\mtcars20/DESCRIPTION' ...  ✔  checking for file 'C:\Users\dslager\AppData\Local\Temp\RtmpaIslsQ\mtcars20/DESCRIPTION' (432ms)
 #>       ─  preparing 'mtcars20':
 #>    checking DESCRIPTION meta-information ...     checking DESCRIPTION meta-information ...   ✔  checking DESCRIPTION meta-information
 #>       ─  checking for LF line-endings in source and make files and shell scripts
 #>       ─  checking for empty or unneeded directories
 #>       ─  looking to see if a 'data/datalist' file should be added
-#>       ─  building 'mtcars20_1.0.tar.gz'
+#>   ─  building 'mtcars20_1.0.tar.gz'
 #>      
 #> Next Steps 
 #> 1. Update your package documentation. 
@@ -298,7 +298,7 @@ package_build(packageName = file.path(tempdir(),"mtcars20"))
 #>    - Set up a github repository for your pacakge. 
 #>    - Add the github repository as a remote of your local package repository. 
 #>    -  git push  your local repository to gitub.
-#> [1] "C:/Users/dslager/AppData/Local/Temp/RtmpuqBumR/mtcars20_1.0.tar.gz"
+#> [1] "C:/Users/dslager/AppData/Local/Temp/RtmpaIslsQ/mtcars20_1.0.tar.gz"
 
 # Update the autogenerated roxygen documentation in data-raw/documentation.R. 
 # edit(file.path(tempdir(),"mtcars20","R","mtcars20.R"))
@@ -377,11 +377,11 @@ DataPackageR::project_data_path()
 
 ## Preprint and publication. <a id = "publication"></a>
 
-The publication describing the package, (Finak *et* *al.,*
+The publication describing the package, (Finak *et al.*,
 2018)<!--@10.12688/gatesopenres.12832.2-->, is now available at [Gates
 Open Research](https://gatesopenresearch.org/articles/2-31/v2) .
 
-The preprint is on [biorxiv](https://doi.org/10.1101/342907).
+The preprint is on [bioRxiv](https://doi.org/10.1101/342907).
 
 ## Code of conduct
 
@@ -397,7 +397,7 @@ By participating in this project you agree to abide by its terms.
 
 2.  Finak G, Mayer B, Fulp W, et al. DataPackageR: Reproducible data
     preprocessing, standardization and sharing using R/Bioconductor for
-    collaborative data analysis. Gates Open Res 2018, 2:31 (doi:
+    collaborative data analysis. Gates Open Res 2018, 2:31 (DOI:
     10.12688/gatesopenres.12832.1)
 
 [![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)

inst/WORDLIST

@@ -1,46 +1,62 @@
-amongst
-autogenerated
 CMD
+Codecov
+Coopting
+DATADIGEST
+DOI
+DataONE
+DataVersion
+ExperimentHub
+FlowRepository
+Hadley
+ImmPort
+ImmuneSpace
+ORCID
+Pre
+Preprint
+README
+RMarkdown
+Rbuildignore
+Reproducibility
+Rmd
+SRA
+SystemRequirements
+Wickham's
+YAML
+al
+bepress
+bioRxiv
 config
 csv
-DATADIGEST
+datapack
 datapackage
 datapackager
-DataVersion
-Dont
+datastorr
+et
 extdata
-filesystem
-Finak
-fredhutch
-gfinak
+fst
+gatesopenres
 github
-graphicx
-Hadley
+gitignore
+https
 incrementing
-inputenc
-knitr
-maintinaing
+loc
 md
 mtcars
-mutli
 mydata
-objecs
-pacakge
-Pre
-procesing
-rda
-README
+onboarding
+pandoc
+pre
+preprint
+preprocess
+rOpenSci
+repo
 reproducibility
 reproducibly
 rmarkdown
-Rmd
-toc
-usepackage
+ropensci
+roxygen
+rrrpkg
 useR
-utf
-VignetteEngine
-VignetteIndexEntry
-Wickham's
+usethis
 yaml
-YAML
 yml