update function and argument names to snake-case (#15)

* add testthat for unit testing

* add testthat for unit testing

* update function names to tidyverse style guide: public functions in snake case. Private functions prefixed by .

* update function name and documentation conform to tidyverse snake case style guide

* remove old function name man files

* initial commit snake case function naming

* snake case function naming initial commit

* remove old function name man files

* initial commit snake case function names

* set_DOI to set_doi

* set_DOI to set_doi

* write.readMe to write_readme

* arguments to snake case

* arguments to snake case

* arguments to snake case

* set_DOI to set_doi

* delete man file for old read me function name

* write_readme initial commit

* Version to 0.0.1.1 - all function and argument names changed to snake case.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: EMLeditor
 Title: View and Edit EML
-Version: 0.0.1.0
+Version: 0.0.1.1
 Authors@R: 
     person("Robert", "Baker", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7591-5035"))
@@ -25,3 +25,6 @@ Imports:
     ISOcodes,
     crayon,
     dplyr
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

@@ -1,33 +1,29 @@
 # Generated by roxygen2: do not edit by hand
 
-export(get.CUI)
-export(get.DOI)
-export(get.DRRdoi)
-export(get.DSRefID)
-export(get.abstract)
-export(get.authorList)
-export(get.beginDate)
-export(get.citation)
-export(get.endDate)
-export(get.fileInfo)
-export(get.lit)
-export(get.parkUnits)
-export(get.producingUnits)
-export(get.title)
-export(get.unitPolygon)
-export(new.DOI)
-export(set.CUI)
-export(set.DOI)
-export(set.DRRdoi)
-export(set.NPSpublisher)
-export(set.abstract)
-export(set.forByNPS)
-export(set.language)
-export(set.lit)
-export(set.parkUnits)
-export(set.producingUnits)
-export(set.protocol)
-export(set.title)
-export(set.version)
-export(write.readMe)
+export(get_abstract)
+export(get_author_list)
+export(get_begin_date)
+export(get_citation)
+export(get_cui)
+export(get_doi)
+export(get_drr_doi)
+export(get_ds_id)
+export(get_end_date)
+export(get_file_info)
+export(get_lit)
+export(get_park_units)
+export(get_producing_units)
+export(get_title)
+export(new_doi)
+export(set_abstract)
+export(set_cui)
+export(set_doi)
+export(set_drr_doi)
+export(set_language)
+export(set_lit)
+export(set_park_units)
+export(set_producing_units)
+export(set_protocol)
+export(set_title)
+export(write_readme)
 importFrom(magrittr,"%>%")

R/utils.R

@@ -1,21 +1,20 @@
 #' inject NPS Publisher info into metadata
 #'
-#' @description injects static NPS-specific publisher info into eml documents. Calls the sub-function set.forOrByNPS, which adds an additionalMetadata element with for or by NPS = TRUE.
+#' @description .set_npspublisher injects static NPS-specific publisher info into eml documents. Calls the sub-function set.forOrByNPS, which adds an additionalMetadata element with for or by NPS = TRUE.
 #'
 #' @details checks to see if the publisher element exists, and if not injects NPS-specific info into EML such as publisher, publication location, and ROR id - the types of things that will be the same for all NPS data or non-data publications and do not require user input. This function will be embedded in all set. and write. class functions (and get. functions?).
 #'
-#' @param emlObject is an R object imported (typically from an EML-formatted .xml file) using EmL::read_eml(<filename>, from="xml").
+#' @param eml_object is an R object imported (typically from an EML-formatted .xml file) using EmL::read_eml(<filename>, from="xml").
 #'
-#' @return emlObject
-#' @export
+#' @return eml_object
 #'
 #' @examples
 #'  \dontrun{
-#' set.NPSpublisher(emlObject)
+#' .set_npspublisher(eml_object)
 #' }
-set.NPSpublisher<-function(emlObject){
+.set_npspublisher<-function(eml_object){
   #get existing publisher info for the data package:
-  publish<-emlObject$dataset$publisher
+  publish<-eml_object$dataset$publisher
 
   #create desired publisher info:
   pubset<- list(organizationName =
@@ -31,31 +30,30 @@ set.NPSpublisher<-function(emlObject){
 
   #if existing and desired publisher don't match, replace existing with desired.
   if(!identical(publish, pubset)){
-    emlObject$dataset$publisher<-pubset
+    eml_object$dataset$publisher<-pubset
   }
 
   #since the publisher is NPS, sets an additionalMetadata field for For or By NPS to TRUE.
-  emlObject<-set.forByNPS(emlObject)
+  eml_object<-.set_for_by_nps(eml_object)
 
-  return(emlObject)
+  return(eml_object)
 }
 
 #' Add/update EMLeditor version
 #'
-#' @description set.version adds the current version of EMLeditor to the EML document.
+#' @description .set_version adds the current version of EMLeditor to the EML document.
 #'
-#' @details set.version adds the current version of EMLeditor to the metadata, specifically in the "additionalMetadata" element
+#' @details .set_version adds the current version of EMLeditor to the metadata, specifically in the "additionalMetadata" element
 #'
-#' @param emlObject is an R object imported (typically from an EML-formatted .xml file) using EML::read_eml(<filename>, from="xml").
+#' @param eml_object is an R object imported (typically from an EML-formatted .xml file) using EML::read_eml(<filename>, from="xml").
 #'
-#' @return emlObject
-#' @export
+#' @return eml_object
 #'
 #' @examples
 #'  \dontrun{
-#' set.version(emlObject)
+#' .set_version(eml_object)
 #' }
-set.version<-function(emlObject){
+.set_version<-function(eml_object){
   #get current EMLeditor package version:
   currentvers<-as.character(utils::packageVersion("EMLeditor"))
 
@@ -66,11 +64,11 @@ set.version<-function(emlObject){
                                    id="emlEditor")
 
   #access additionalMetadata elements:
-  addMeta<-EML::eml_get(emlObject, "additionalMetadata")
+  addMeta<-EML::eml_get(eml_object, "additionalMetadata")
 
   #if no additionalMetadata, add in EMLeditor and current version:
   if(sum(names(addMeta)!="@context")==0){
-    emlObject$additionalMetadata<-EMLed
+    eml_object$additionalMetadata<-EMLed
   }
 
   #if there are existing additionalMetadata elements:
@@ -96,34 +94,33 @@ set.version<-function(emlObject){
     #if no info on EMLeditor, add EMLeditor to additionalMetadata
     if(is.null(app)){
       if(x==1){
-        emlObject$additionalMetadata<-list(EMLed, emlObject$additionalMetadata)
+        eml_object$additionalMetadata<-list(EMLed, eml_object$additionalMetadata)
       }
       if(x>1){
-        emlObject$additionalMetadata[[x+1]]<-EMLed
+        eml_object$additionalMetadata[[x+1]]<-EMLed
       }
     }
   }
-  return(emlObject)
+  return(eml_object)
 }
 
 #' Get Park Unit Polygon
 #'
-#' @description get.unitPolygon gets the polygon for a given park unit.
+#' @description .get_unit_polygon gets the polygon for a given park unit.
 #'
 #' @details retrieves a geoJSON string for a polygon of a park unit from NPS Rest services. Note: This is not the official boundary (erm... ok then what is it?!?).
 #'
-#' @param Unit_Code a string (typically 4 characters) that is the park unit code.
+#' @param unit_code a string (typically 4 characters) that is the park unit code.
 #'
 #' @return a park polygon
-#' @export
 #'
 #' @examples
 #'  \dontrun{
-#' poly<-get.unitPolygon("BICY")
+#' poly<-.get_unit_polygon("BICY")
 #' }
-get.unitPolygon <- function(Unit_Code) {
+.get_unit_polygon <- function(unit_code) {
   # get geography from NPS Rest Services
-  UnitsURL <- paste0("https://irmaservices.nps.gov/v2/rest/unit/", Unit_Code, "/geography")
+  UnitsURL <- paste0("https://irmaservices.nps.gov/v2/rest/unit/", unit_code, "/geography")
   xml <- httr::content(httr::GET(UnitsURL))
 
   # Create spatial feature from polygon info returned from NPS
@@ -134,19 +131,17 @@ get.unitPolygon <- function(Unit_Code) {
 
 #' Set "For or By" NPS
 #'
-#' @description set.forByNPS adds an element to additionalMetadata with For or By NPS set to TRUE and a second element agencyOriginated set to "NPS" with the understanding that all data products created for or by the NPS have NPS as the originating agency.
+#' @description .set_for_by_nps adds an element to additionalMetadata with For or By NPS set to TRUE and a second element agencyOriginated set to "NPS" with the understanding that all data products created for or by the NPS have NPS as the originating agency.
 #'
-#' @param emlObject is an R object imported (typically from an EML-formatted .xml file) using EML::read_eml(<filename>, from="xml").
+#' @param eml_object is an R object imported (typically from an EML-formatted .xml file) using EML::read_eml(<filename>, from="xml").
 #'
-#' @return emlObject
-#'
-#' @export
+#' @return eml_object
 #'
 #' @examples
 #'  \dontrun{
-#' set.forByNPS(emlObject)
+#' .set_for_by_nps(eml_object)
 #' }
-set.forByNPS<-function(emlObject){
+.set_for_by_nps<-function(eml_object){
 
   #set up additionalMetadata elements for EMLeditor:
   forby<-list(metadata=list(agencyOriginated=list(
@@ -155,12 +150,12 @@ set.forByNPS<-function(emlObject){
                             id="agencyOriginated"))
 
   #access additionalMetadata elements:
-  addMeta<-EML::eml_get(emlObject, "additionalMetadata")
+  addMeta<-EML::eml_get(eml_object, "additionalMetadata")
   addMeta<-within(addMeta, rm('@context'))
 
   #if no additionalMetadata, add in EMLeditor and current version:
   if(length(names(addMeta))==0){
-    emlObject$additionalMetadata<-forby
+    eml_object$additionalMetadata<-forby
   }
 
   #if there are existing additionalMetadata elements:
@@ -178,12 +173,12 @@ set.forByNPS<-function(emlObject){
     #if no info on ForOrByNPS, add ForOrByNPS to additionalMetadata
     if(is.null(For_or_by_NPS)){
       if(x==1){
-        emlObject$additionalMetadata<-list(forby, emlObject$additionalMetadata)
+        eml_object$additionalMetadata<-list(forby, eml_object$additionalMetadata)
       }
       if(x>1){
-        emlObject$additionalMetadata[[x+1]]<-forby
+        eml_object$additionalMetadata[[x+1]]<-forby
       }
     }
   }
-  return(emlObject)
+  return(eml_object)
 }

R/writeReadMe.R

@@ -1,33 +1,33 @@
 #' Writes a README file
 #'
-#' @description write.readMe writes a readme file based on the current metadata
+#' @description write_readme writes a readme file based on the current metadata
 #'
-#' @details write.readMe writes a mock-up of the readme file that will eventually be automatically generated by DataStore. This file is for error checking purposes only. If something looks off, you can go back and fix your metadata to correct it but you should not upload this readme file with your data package.
+#' @details write_readme writes a mock-up of the readme file that will eventually be automatically generated by DataStore. This file is for error checking purposes only. If something looks off, you can go back and fix your metadata to correct it but you should not upload this readme file with your data package.
 #'
-#' @param emlObject is an R object imported (typically from an EML-formatted .xml file) using EML::read_eml(<filename>, from="xml").
+#' @param eml_object is an R object imported (typically from an EML-formatted .xml file) using EML::read_eml(<filename>, from="xml").
 #' @param outfile is the name of the file you want to write, typically *.txt.
 #'
 #' @return a character sting in readable format (saved to the given outfile)
 #' @export
 #'
 #' @examples
 #'  \dontrun{
-#' write.readMe(emlObject, "TestReadMe.txt")
+#' write_readme(eml_object, "TestReadMe.txt")
 #' }
-write.readMe<-function(emlObject, outfile){
+write_readme<-function(eml_object, outfile){
 
   #get components:
-  Ref<-get.DSRefID(emlObject) #Data Store Ref. ID
-  doi<-get.DOI(emlObject) #DOI
-  title<-get.title(emlObject) #title
-  abstract<-get.abstract(emlObject) #abstract
-  fileInfo<-get.fileInfo(emlObject) #names, sizes, descriptions
-  start<-get.beginDate(emlObject) #content start date
-  end<-get.endDate(emlObject) #content end date
-  units<-get.parkUnits(emlObject) #park units where data were collected
-  CUI<-get.CUI(emlObject) #controlled unclassified information status
-  DRRdoi<-get.DRRdoi(emlObject) #DOI of accompanying DRR
-  citation<-get.citation(emlObject) #citation
+  Ref<-get_ds_id(eml_object) #Data Store Ref. ID
+  doi<-get_doi(eml_object) #DOI
+  title<-get_title(eml_object) #title
+  abstract<-get_abstract(eml_object) #abstract
+  fileInfo<-get_file_info(eml_object) #names, sizes, descriptions
+  start<-get_begin_date(eml_object) #content start date
+  end<-get_end_date(eml_object) #content end date
+  units<-get_park_units(eml_object) #park units where data were collected
+  CUI<-get_cui(eml_object) #controlled unclassified information status
+  DRRdoi<-get_drr_doi(eml_object) #DOI of accompanying DRR
+  citation<-get_citation(eml_object) #citation
 
   #Write to the components to the text file specified in "outfile".
   cat(paste0("ReadMe file for DataStore reference# ", Ref), file=outfile, sep="\n")