Merge pull request #178 from kristenpeach/master

Updates to improve pkgdown website

Author: jeanetteclark

.Rbuildignore

@@ -7,3 +7,5 @@
 ^\.travis\.yml$
 ^LICENSE$
 ^MAINTENANCE\.md$
+^_pkgdown\.yml$
+^pkgdown$

DESCRIPTION

@@ -10,7 +10,8 @@ Authors@R: c(
   person("Emily", "O'Dean", email = "[email protected]", role = "ctb"),
   person("Robyn", "Thiessen-Bock", email = "[email protected]", role = "ctb"),
   person("Derek", "Strong", email = "[email protected]", role = "ctb"),
-  person("Rachel", "Sun", email = "[email protected]", role = "ctb")
+  person("Rachel", "Sun", email = "[email protected]", role = "ctb"),
+  person("Jasmine", "Lai", email = "[email protected]", role = "ctb")
   )
 Description: A set of utilities for working with the Arctic Data Center 
   (https://arcticdata.io).

R/eml.R

@@ -1,6 +1,6 @@
 # Helper functions for creating EML metadata
 
-#' Create EML entity with physical section from a DataONE PID
+#' Create EML entity with physical section from any DataONE PID
 #'
 #' @param mn (MNode) Member Node where the PID is associated with an object.
 #' @param pid (character) The PID of the object to create the sub-tree for.
@@ -74,7 +74,7 @@ pid_to_eml_entity <- function(mn,
 
 #' Create an EML physical object from system metadata
 #'
-#' This function creates a pre-canned EML physical object from what's in the
+#' This function creates an EML physical object based on what's in the
 #' System Metadata of an object. Note that it sets an Online Distribution URL
 #' of the DataONE v2 resolve service for the PID.
 #'
@@ -276,7 +276,7 @@ eml_party <- function(type="associatedParty",
 }
 
 
-#' Create an EML creator
+#' Create an EML creator.
 #'
 #' See [eml_party()] for details.
 #'
@@ -298,7 +298,7 @@ eml_creator <- function(...) {
 }
 
 
-#' Create an EML contact
+#' Create an EML contact. Contact information is passed on to [eml_party()]
 #'
 #' See [eml_party()] for details.
 #'

R/helpers.R

@@ -64,7 +64,7 @@ create_dummy_metadata <- function(mn, data_pids = NULL) {
 
 #' Create a test object
 #'
-#' Create a test data object.
+#' Create a test data object. Make sure the member node you use is not a production node.
 #'
 #' @param mn (MNode) The Member Node.
 #'
@@ -121,7 +121,7 @@ create_dummy_object <- function(mn) {
 
 #' Create a test package
 #'
-#' Create a test data package.
+#' Create a full test data package with data objects and 1 metadata object. Size = the number of data objects you want in the dummy package + 1 metadata object.
 #'
 #' @param mn (MNode) The Member Node.
 #' @param size (numeric) The number of files in the package, including the metadata file.
@@ -195,7 +195,7 @@ create_dummy_package <- function(mn, size = 2) {
 
 #' Create a test parent package
 #'
-#' Create a test parent data package.
+#' Create a test parent data package. Make sure the node is not a production node.
 #'
 #' @param mn (MNode) The Member Node.
 #' @param children (character) Child package (resource maps) PIDs.
@@ -324,7 +324,7 @@ create_dummy_enumeratedDomain_dataframe <- function(factors) {
 
 #' Create dummy package with fuller metadata
 #'
-#' Creates a fuller package than [create_dummy_package()]
+#' Creates a more complete package than [create_dummy_package()]
 #' but is otherwise based on the same concept. This dummy
 #' package includes multiple data objects, responsible parties,
 #' geographic locations, method steps, etc.
@@ -579,7 +579,7 @@ list_submissions <- function(mn, from = Sys.Date(), to = Sys.Date(), formatType
 
 #' Read a shapefile from a pid
 #'
-#' Read a shapefile from a pid that points to the zipped directory of the shapefile and associated files
+#' Read a shapefile 'sf' from a pid that points to the zipped directory of the shapefile and associated files
 #' on a given member node.
 #'
 #' @param mn (MNode) A DataOne Member Node
@@ -626,7 +626,7 @@ read_zip_shapefile <- function(mn, pid){
 
 #' Recovers failed submissions
 #'
-#' Recovers failed submissions and write the new, valid EML to a given path
+#' Recovers failed submissions and writes the new, valid EML to a given path
 #'
 #' @param node (MNode) The Member Node to publish the object to.
 #' @param pid The PID of the EML metadata document to be recovered.

README.md

@@ -11,16 +11,12 @@ Note: The package is intended to be used by NCEAS staff and may not make much se
 
 ## Installing
 
-We recommend installing from the latest [release](https://github.com/NCEAS/arcticdatautils/releases) (aka tag) instead of from `master`. Install the latest release with the [`remotes`](https://github.com/r-lib/remotes) package:
+To install the latest version of this package we recommend installing from Github:
 
 ```r
-remotes::install_github("nceas/arcticdatautils@*release")
-```
-
-If you're feeling adventurous, you can install from the bleeding edge:
 
-```r
 remotes::install_github("nceas/arcticdatautils")
+
 ```
 
 ## Contributing
@@ -64,3 +60,7 @@ If you *do* want to run integration tests
 options(dataone_test_token = "{YOUR_TOKEN_HERE}") # <- Modify this line
 devtools::test()
 ```
+
+<div>
+<p align="center"> <a href="https://www.nceas.ucsb.edu/"> <img  src="https://www.nceas.ucsb.edu/files/logos/NCEAS/NCEAS-full%20logo-4C.jpg" width="250px" align="center" /></a> <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png"  /> </p>
+</div>

_pkgdown.yml

@@ -2,3 +2,93 @@ navbar:
   right:
     - icon: fa-github
       href: https://github.com/NCEAS/arcticdatautils
+
+reference:
+- title: Access functions
+  desc: High-level utility functions for getting and setting access rules for DataONE objects
+  contents:
+  - set_rights_holder
+  - set_access
+  - remove_access
+  - set_rights_and_access
+  - set_public_read
+  - remove_public_read
+  - is_public_read
+
+- title: DataOne Functions
+  desc: Helper functions for the dataone package
+  contents:
+  - is_token_set
+  - get_token
+  - is_token_expired
+  - get_mn_base_url
+  - is_authorized
+
+- title: NetCDF Functions
+  desc: Get a data.frame of attributes from a NetCDF object
+  contents:
+  - get_ncdf4_attributes
+  - get_token
+  - is_token_expired
+  - get_mn_base_url
+  - is_authorized
+
+- title: Sysmeta Function
+  desc: Utility function for modifying System Metadata objects
+  contents:
+  - get_all_sysmeta
+
+
+- title: Package editing functions
+  desc: Functions for managing package contents
+  contents:
+  - publish_object
+  - update_object
+  - publish_update
+  - create_resource_map
+  - update_resource_map
+  - set_file_name
+  - reformat_file_name
+
+- title: Functions to help test a package
+  desc: Various helper functions for things like testing a package
+  contents:
+  - starts_with('create_')
+  - get_orcid_name
+  - get_orcid_email
+
+- title: EML Functions
+  desc: Helper functions for creating EML metadata
+  contents:
+  - starts_with('pid_')
+  - starts_with('eml_')
+  - sysmeta_to_eml_physical
+  - get_orcid_email
+  - set_abstract
+  - which_in_eml
+  - reorder_pids
+
+- title: Environment Functions
+  desc: Function related to loading configuriation based upon the environment
+  contents:
+  - starts_with('env_')
+
+- title: Format Functions
+  desc: Functions related to data object formats
+  contents:
+  - guess_format_id
+  - format_eml
+  - format_iso
+
+- title: QA Function
+  desc: Function related to metadata quality
+  contents:
+  - mdq_run
+
+
+
+
+
+
+
+

index.md

@@ -11,14 +11,15 @@ Note: The package is intended to be used by NCEAS staff and may not make much se
 
 ## Installing
 
-We recommend installing from the latest [release](https://github.com/NCEAS/arcticdatautils/releases) (aka tag) instead of from `master`. Install the latest release with the [`remotes`](https://github.com/r-lib/remotes) package:
 
-```r
-remotes::install_github("nceas/arcticdatautils@*release")
-```
-
-If you're feeling adventurous, you can install from the bleeding edge:
+To install the latest version of this package we recommend installing from Github:
 
 ```r
+
 remotes::install_github("nceas/arcticdatautils")
+
 ```
+
+<div>
+<p align="center"> <a href="https://www.nceas.ucsb.edu/"><img  src="https://www.nceas.ucsb.edu/files/logos/NCEAS/NCEAS-full%20logo-4C.jpg" width="250px" align="center" /></a> <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png"  /> </p>
+</div>