-
`load_pkg_metadata()` reads the metadata file from a previously
-downloaded package and loads a list of fields and their attributes into a
-dataframe.
+
`load_pkg_metadata()` is essentially a wrapper around `DPchecker::load_metadata` with the directory structure pre-set to work well the default location that `get_data_package` stores downloaded data packages. If you did not use the default settings for `get_data_package` (or downloaded a data package manually) you may find it easier to adjust the directory structure pointing to your data package and load the metadata using `DPchecker::load_metadata()`. Much like `load_metadata`, `load_pkg_metadata` requires that there be a single .xml file in the data package directory, that the metadata file name end in *_metadata.xml, and that the file contain schema-valid EML metadata.
-
load_pkg_metadata(holding_id, directory = here::here("data"))
+
load_pkg_metadata(holding_id, directory = "data")
@@ -68,11 +64,11 @@
Arguments
- holding_id
-is a 6-7 digit number corresponding to the holding ID of the data package zip file.
is a 6-7 digit number corresponding to the holding ID of the data package zip file. Your data should be in a directory that that has the holding ID as its name.
- directory
-String. Path to the data package
String. Path to the data package directory, defaults to "data".
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 80cfae3..40dc0fa 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -16,7 +16,9 @@
/reference/get_park_taxon_citations.html
/reference/get_park_taxon_refs.html
/reference/get_park_taxon_url.html
+/reference/get_refs_info.html
/reference/get_ref_info.html
+/reference/get_ref_list.html
/reference/get_unit_code.html
/reference/get_unit_code_info.html
/reference/get_unit_info.html
@@ -29,6 +31,7 @@
/reference/map_wkt.html
/reference/NPSutils-package.html
/reference/rm_local_packages.html
+/reference/summarize_packages.html
/reference/validate_data_package.html
diff --git a/man/get_ref_list.Rd b/man/get_ref_list.Rd
new file mode 100644
index 0000000..afc6288
--- /dev/null
+++ b/man/get_ref_list.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/meta_analyses.R
+\name{get_ref_list}
+\alias{get_ref_list}
+\title{Get a list of reference codes from DataStore}
+\usage{
+get_ref_list(
+ reference_type = "dataPackage",
+ no_of_entries = 500,
+ secure = FALSE
+)
+}
+\arguments{
+\item{reference_type}{String. The reference type to to query data store for. Defaults to data package ("dataPackage").}
+
+\item{no_of_entries}{Integer. The number of entries to return per page (where only one "page" of results is returned by default). Defaults to 500.}
+
+\item{secure}{Logical. Defaults to FALSE for external users. Setting secure = TRUE will, with the proper credentials, return DataStore references with visibility set to both Public and Restricted.}
+}
+\value{
+A List of reference IDs
+}
+\description{
+`get_ref_list` will return a list of the DataStore reference codes associated with a given reference type. Where "All" might be a bit generous: I would not expect more than the number given by "no_of_entries" as that is technically the number of entries per page and the function defaults to returning just one page (not entirely sure what a "page" is in this context).
+}
+\examples{
+\dontrun{
+get_ref_list()
+}
+}
diff --git a/man/get_refs_info.Rd b/man/get_refs_info.Rd
new file mode 100644
index 0000000..51f2672
--- /dev/null
+++ b/man/get_refs_info.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/meta_analyses.R
+\name{get_refs_info}
+\alias{get_refs_info}
+\title{Return Basic information about a list of DataStore References}
+\usage{
+get_refs_info(
+ reference_type = "dataPackage",
+ no_of_entries = 500,
+ secure = FALSE
+)
+}
+\arguments{
+\item{reference_type}{String. The reference type to to query data store for. Defaults to data package ("dataPackage").}
+
+\item{no_of_entries}{Integer. The number of entries to return per page (where only one "page" of results is returned by default). Defaults to 500.}
+
+\item{secure}{Logical. Defaults to FALSE for external users. Setting secure = TRUE will, with the proper credentials, return DataStore references with visibility set to both Public and Restricted.}
+}
+\value{
+a data frame
+}
+\description{
+The function will return a data frame containing information about a given number of references within a reference type. The data returned includes the reference ID (referenceId), the date the references was activated on DataStore (dateOfIssue), the references visibility (visibility), the number of files associated with the reference (fileCount), the access level of the files (fileAccess), the reference title (title), the abbreviated citation (citation), the URL for the DataStore reference (referenceUrl), the group-type for the reference (referenceGroupType), the type of reference (typeName), whether the reference has a DOI associated with it (isDOI), whether their is a newer version of the reference (newVersion) and what the most recent version of the reference is (mostRecentReference).
+}
+\examples{
+\dontrun{
+get_ref_info()
+}
+
+}
diff --git a/man/load_data_package_deprecated.Rd b/man/load_data_package_deprecated.Rd
index 55fefad..9ba20ec 100644
--- a/man/load_data_package_deprecated.Rd
+++ b/man/load_data_package_deprecated.Rd
@@ -20,6 +20,6 @@ a list of one or more tibbles contained within the data package to the global en
}
\examples{
\dontrun{
-load_data_package(2272461)
+load_data_package_deprecated(2272461)
}
}
diff --git a/man/load_pkg_metadata.Rd b/man/load_pkg_metadata.Rd
index 0d9c4a4..b8da639 100644
--- a/man/load_pkg_metadata.Rd
+++ b/man/load_pkg_metadata.Rd
@@ -2,23 +2,20 @@
% Please edit documentation in R/load_pgk_metadata.R
\name{load_pkg_metadata}
\alias{load_pkg_metadata}
-\title{Read contents of data package file and construct a data frame based on the
-metadata file summarizing the fields and their types/definitions.}
+\title{Loads EML-formatted metadata into R for inspection and/or editing}
\usage{
-load_pkg_metadata(holding_id, directory = here::here("data"))
+load_pkg_metadata(holding_id, directory = "data")
}
\arguments{
-\item{holding_id}{is a 6-7 digit number corresponding to the holding ID of the data package zip file.}
+\item{holding_id}{is a 6-7 digit number corresponding to the holding ID of the data package zip file. Your data should be in a directory that that has the holding ID as its name.}
-\item{directory}{String. Path to the data package}
+\item{directory}{String. Path to the data package directory, defaults to "data".}
}
\value{
one data frame to the global environment.
}
\description{
-`load_pkg_metadata()` reads the metadata file from a previously
-downloaded package and loads a list of fields and their attributes into a
-dataframe.
+`load_pkg_metadata()` is essentially a wrapper around `DPchecker::load_metadata` with the directory structure pre-set to work well the default location that `get_data_package` stores downloaded data packages. If you did not use the default settings for `get_data_package` (or downloaded a data package manually) you may find it easier to adjust the directory structure pointing to your data package and load the metadata using `DPchecker::load_metadata()`. Much like `load_metadata`, `load_pkg_metadata` requires that there be a single .xml file in the data package directory, that the metadata file name end in *_metadata.xml, and that the file contain schema-valid EML metadata.
}
\examples{
\dontrun{
diff --git a/man/summarize_packages.Rd b/man/summarize_packages.Rd
new file mode 100644
index 0000000..3063592
--- /dev/null
+++ b/man/summarize_packages.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/meta_analyses.R
+\name{summarize_packages}
+\alias{summarize_packages}
+\title{Collect summary statistics on data packages}
+\usage{
+summarize_packages(ref_list, secure = TRUE, check_metadata = FALSE)
+}
+\arguments{
+\item{ref_list}{list or string of data package reference IDs from DataStore (potentially generated via `get_references_list`.}
+
+\item{secure}{logical. Defaults to TRUE to access secure DataStore server and restricted data packages. Set to FALSE to to access only public references.}
+
+\item{check_metadata}{Logical. Defaults to FALSE. In this case, metadata will not be checked or loaded. Any load errors will occur due to problems with .csv files (for instance if they don't exist). To test whether the metadata meets minimal requirements (is schema-valid), set check_metadata = TRUE.}
+}
+\value{
+data frame
+}
+\description{
+Given a list of data package references from DataStore the function will download the indicated data packages (using creating the folders /data/reference for each data package; see `get_data_packages` for details), load them into R, and then collect some summary statistics on the data packages.
+}
+\details{
+If a data package fails to download (or load) into R, the function will return NAs instead of summary data about the data package as well as a message about the package status ("Loads", "Error") in the dataframe that the function returns. The function will ignore files that fall outside the data package specifications (one or more .csv files and a single .xml file ending in *_metadata.xml).
+
+When `check_metadata` is set to the default `FALSE`, the function will attempt to and load any .csv, regardless of the contents. Data packages with restricted access can produce false positives if you do not have the appropriate permissions to download the data as the function will still download the files, but they will be populated with unhelpful hmtl rather than the intended data. Functions that fail to load into R likely violate the data package specifications in some fundamental way (e.g. .CSV file instead of .csv or no .csv files at all).
+
+When `check_metadata` is set to `TRUE`, additional checks and tests are run on the data package and load errors may occur for all of the above reasons and also if there are multiple .xml files, if the metadata file name does not end in "*_metadata.xml", if there is no metadata file, or if the metadata file is EML schema-invalid.
+
+If you have access to restricted DataStore references (e.g. in an NPS office or logged in to an NPS VPN), you can set secure = TRUE. This will give you access to restricted (internal to NPS) references but if a reference is restricted to a named list of individuals you must be on that named list to access the reference.
+}
+\examples{
+\dontrun{
+x <- get_ref_list()
+get_ref_info(x[[1]])
+}
+}