Updated package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: neotoma2
 Title: Working with the Neotoma Paleoecology Database
-Date: 2024-02-16
+Date: 2024-02-27
 Version: 1.0.3
 Authors@R:
     c(person(given = "Dominguez Vidana",
@@ -48,4 +48,4 @@ Imports:
     wk,
     uuid,
     tidyr
-VignetteBuilder: knitr
+VignetteBuilder: knitr

R/filter.R

@@ -5,42 +5,40 @@ utils::globalVariables(c("elev", "notes"))
 #' is a nested object (it contains collection units, datasets, samples, etc.)
 #' the degree to which filtering occurs depends on the amount of data contained
 #' within the sites object. Filtering parameters include:
-#' \itemize{
-#'  \item{"siteid"}{A numeric site identifier from the Neotoma Database}
-#'  \item{"sitename"}{The character string sitename.}
-#'  \item{"lat"}{A numeric latitude value.}
-#'  \item{"long"}{A numeric longitude value.}
-#'  \item{"altitude"}{The elevation of the site. Note that some sites do not
+#'  * `siteid` A numeric site identifier from the Neotoma Database.
+#'  * `sitename` The character string sitename.
+#'  * `lat` A numeric latitude value.
+#'  * `long` A numeric longitude value.
+#'  * `altitude` The elevation of the site. Note that some sites do not
 #'   include elevation information. For these an NA value appears, and they
-#'   would be removed when using an elevation filter.}
-#'  \item{"datasetid"}{A numeric datasetid from Neotoma.}
-#'  \item{"database"}{A character string naming the constituent database
-#'   from which the dataset is drawn.}
-#'  \item{"datasettype"}{A character string representing one of the many
-#'   dataset types within Neotoma.}
-#'  \item{"age_range_old"}{A dataset-level parameter indicating the oldest
-#'   date covered by the dataset chronology.}
-#'  \item{"age_range_young"}{A dataset-level parameter indicating the youngest
-#'   date covered by the dataset chronology.}
-#'  \item{"notes"}{Free-form dataset notes provided by the dataset PI(s),
-#'   analysts or data stewards.}
-#'  \item{"collectionunitid"}{A numeric collection unit identifier from
-#'   Neotoma.}
-#'  \item{"handle"}{A character string identifying the collection unit. These
-#'   are often shorter form names (originally a default 8 character length).}
-#'  \item{"collectionunitname"}{A character string identifying the collection
-#'   unit name.}
-#'  \item{"colldate"}{The date on which the collection unit was sampled. Many
-#'   of these are empty.}
-#'  \item{"location"}{A free-form character string indicating the location of
-#'   the collection unit within the site.}
-#'  \item{"waterdepth"}{A numeric depth at which the core was obtained.}
-#'  \item{"collunittype"}{A character string for the collection unit type.}
-#'  \item{"collectiondevice"}{A fixed vocabulary term for the collection
-#'   device.}
-#'  \item{"depositionalenvironment"}{A fixed vocabulary name for the
-#'   depositional environment.}
-#'}
+#'   would be removed when using an elevation filter.
+#'  * `datasetid` A numeric datasetid from Neotoma.
+#'  * `database` A character string naming the constituent database
+#'   from which the dataset is drawn.
+#'  * `datasettype` A character string representing one of the many
+#'   dataset types within Neotoma.
+#'  * `age_range_old` A dataset-level parameter indicating the oldest
+#'   date covered by the dataset chronology.
+#'  * `age_range_young` A dataset-level parameter indicating the youngest
+#'   date covered by the dataset chronology.
+#'  * `notes` Free-form dataset notes provided by the dataset PI(s),
+#'   analysts or data stewards.
+#'  * `collectionunitid` A numeric collection unit identifier from
+#'   Neotoma.
+#'  * `handle` A character string identifying the collection unit. These
+#'   are often shorter form names (originally a default 8 character length).
+#'  * `collectionunitname` A character string identifying the collection
+#'   unit name.
+#'  * `colldate` The date on which the collection unit was sampled. Many
+#'   of these are empty.
+#'  * `location` A free-form character string indicating the location of
+#'   the collection unit within the site.
+#'  * `waterdepth` A numeric depth at which the core was obtained.
+#'  * `collunittype` A character string for the collection unit type.
+#'  * `collectiondevice` A fixed vocabulary term for the collection
+#'   device.
+#'  * `depositionalenvironment` A fixed vocabulary name for the
+#'   depositional environment.
 #' @import sf
 #' @import dplyr
 #' @importFrom purrr map
@@ -59,42 +57,40 @@ filter <- function(x, ...) {
 #' is a nested object (it contains collection units, datasets, samples, etc.)
 #' the degree to which filtering occurs depends on the amount of data contained
 #' within the sites object. Filtering parameters include:
-#' \itemize{
-#'  \item{"siteid"}{A numeric site identifier from the Neotoma Database}
-#'  \item{"sitename"}{The character string sitename.}
-#'  \item{"lat"}{A numeric latitude value.}
-#'  \item{"long"}{A numeric longitude value.}
-#'  \item{"altitude"}{The elevation of the site. Note that some sites do not
+#'  * `siteid` A numeric site identifier from the Neotoma Database.
+#'  * `sitename` The character string sitename.
+#'  * `lat` A numeric latitude value.
+#'  * `long` A numeric longitude value.
+#'  * `altitude` The elevation of the site. Note that some sites do not
 #'   include elevation information. For these an NA value appears, and they
-#'   would be removed when using an elevation filter.}
-#'  \item{"datasetid"}{A numeric datasetid from Neotoma.}
-#'  \item{"database"}{A character string naming the constituent database
-#'   from which the dataset is drawn.}
-#'  \item{"datasettype"}{A character string representing one of the many
-#'   dataset types within Neotoma.}
-#'  \item{"age_range_old"}{A dataset-level parameter indicating the oldest
-#'   date covered by the dataset chronology.}
-#'  \item{"age_range_young"}{A dataset-level parameter indicating the youngest
-#'   date covered by the dataset chronology.}
-#'  \item{"notes"}{Free-form dataset notes provided by the dataset PI(s),
-#'   analysts or data stewards.}
-#'  \item{"collectionunitid"}{A numeric collection unit identifier from
-#'   Neotoma.}
-#'  \item{"handle"}{A character string identifying the collection unit. These
-#'   are often shorter form names (originally a default 8 character length).}
-#'  \item{"collectionunitname"}{A character string identifying the collection
-#'   unit name.}
-#'  \item{"colldate"}{The date on which the collection unit was sampled. Many
-#'   of these are empty.}
-#'  \item{"location"}{A free-form character string indicating the location of
-#'   the collection unit within the site.}
-#'  \item{"waterdepth"}{A numeric depth at which the core was obtained.}
-#'  \item{"collunittype"}{A character string for the collection unit type.}
-#'  \item{"collectiondevice"}{A fixed vocabulary term for the collection
-#'   device.}
-#'  \item{"depositionalenvironment"}{A fixed vocabulary name for the
-#'   depositional environment.}
-#'   }
+#'   would be removed when using an elevation filter.
+#'  * `datasetid` A numeric datasetid from Neotoma.
+#'  * `database` A character string naming the constituent database
+#'   from which the dataset is drawn.
+#'  * `datasettype` A character string representing one of the many
+#'   dataset types within Neotoma.
+#'  * `age_range_old` A dataset-level parameter indicating the oldest
+#'   date covered by the dataset chronology.
+#'  * `age_range_young` A dataset-level parameter indicating the youngest
+#'   date covered by the dataset chronology.
+#'  * `notes` Free-form dataset notes provided by the dataset PI(s),
+#'   analysts or data stewards.
+#'  * `collectionunitid` A numeric collection unit identifier from
+#'   Neotoma.
+#'  * `handle` A character string identifying the collection unit. These
+#'   are often shorter form names (originally a default 8 character length).
+#'  * `collectionunitname` A character string identifying the collection
+#'   unit name.
+#'  * `colldate` The date on which the collection unit was sampled. Many
+#'   of these are empty.
+#'  * `location` A free-form character string indicating the location of
+#'   the collection unit within the site.
+#'  * `waterdepth` A numeric depth at which the core was obtained.
+#'  * `collunittype` A character string for the collection unit type.
+#'  * `collectiondevice` A fixed vocabulary term for the collection
+#'   device.
+#'  * `depositionalenvironment` A fixed vocabulary name for the
+#'   depositional environment.
 #' @import sf
 #' @import dplyr
 #' @importFrom purrr map

R/get_sites.R

@@ -55,50 +55,47 @@ parse_site <- function(result) {
 #' ([api.neotomadb.org](https://api.neotomadb.org)) call for `sites`.
 #' The call itself uses a SQL query which accepts any one of the following
 #' parameters:
-#' \itemize{
-#'  \item{`siteid`}{The unique site ID (integer) in Neotoma. Can be passed as a
-#' vector of site IDs.}
-#'  \item{sitename}{The site name, or approximate match using the % wildcard.}
-#'  \item{database}{The constituent database for the record. See
-#' `get_table("constituentdatabases")`}
-#'  \item{altmin}{The minimum altitude range for site elevation (in meters).}
-#'  \item{altmax}{The maximum altitude range for site elevation (in meters).}
-#'  \item{datasetid}{The unique dataset ID (integer) in Neotoma. Can be passed
-#' as a vector of dataset IDs.}
-#'  \item{datasettype}{Neotoma contains data for a number of datasettypes.
+#'  * `siteid`  The unique site ID (integer) in Neotoma. Can be passed as a
+#' vector of site IDs.
+#'  * `sitename`  The site name, or approximate match using the % wildcard.
+#'  * `database`  The constituent database for the record. See `get_table("constituentdatabases")`
+#'  * `altmin`  The minimum altitude range for site elevation (in meters).
+#'  * `altmax`  The maximum altitude range for site elevation (in meters).
+#'  * `datasetid`  The unique dataset ID (integer) in Neotoma. Can be passed
+#' as a vector of dataset IDs.
+#'  * `datasettype`  Neotoma contains data for a number of datasettypes.
 #'  This returns a subset of data types. For a complete list of available 
-#'  datasettypes, run `neotoma2::get_table('datasettypes')`}
-#'  \item{doi}{The dataset DOI for a dataset contained within a site. Can be
-#' passed as a vector of DOIs.}
-#'  \item{gpid}{The geopolitical name or identifier containing a site. Can be
-#' passed as a vector of names.}
-#'  \item{keywords}{Keywords for samples within a set of sites. For example
-#' "modern" indicates a sample within the record uses the keyword "modern".}
-#'  \item{contacts}{Contact names or IDs associated with a site.}
-#'  \item{ageyoung}{A minimum spanning age for the record, in years before
-#' radiocarbon present (1950).}
-#'  \item{ageold}{A maximum spanning age for the record, in years before
-#' radiocarbon present (1950).}
-#'  \item{ageof}{An age which must be contained within the range of sample ages
-#' for a site.}
-#'  \item{taxa}{The names of taxa which must be present within samples in a
-#' record.}
-#'  \item{all_data}{The API only downloads the first 25 records of the query. 
-#'  For the complete records, use `all_data=TRUE`}
+#'  datasettypes, run `neotoma2::get_table('datasettypes')`
+#'  * `doi`  The dataset DOI for a dataset contained within a site. Can be
+#' passed as a vector of DOIs.
+#'  * `gpid`  The geopolitical name or identifier containing a site. Can be
+#' passed as a vector of names.
+#'  * `keywords`  Keywords for samples within a set of sites. For example
+#' "modern" indicates a sample within the record uses the keyword "modern".
+#'  * `contacts`  Contact names or IDs associated with a site.
+#'  * `ageyoung`  A minimum spanning age for the record, in years before
+#' radiocarbon present (1950).
+#'  * `ageold`  A maximum spanning age for the record, in years before
+#' radiocarbon present (1950).
+#'  * `ageof`  An age which must be contained within the range of sample ages
+#' for a site.
+#'  * `taxa`  The names of taxa which must be present within samples in a
+#' record.
+#'  * `all_data`  The API only downloads the first 25 records of the query. 
+#'  For the complete records, use `all_data=TRUE`
 #' This call will then return a data object that contains site metadata for one
 #' or more sites, along with limited metadata describing the collection units
 #' and datasets located at that site.
-#' }
 #' @returns The function returns either a single item of class `"try-error"`
 #' describing the reason for failure (either misdefined parameters or an error
 #' from the Neotoma API), or a table of sites, with rows corresponding to the
 #' number of individual sites returned by the Neotoma API.
 #' Each "site" object contains 6 parameters that can be accessed as well:
 #' siteid, sitename, location, altitude, description,
 #' limited collection units information.
-#'  *  `loc` An `sf` object that describes site's location.
-#'  *  `description`
-#'  *  `collunits` limited information on collunits
+#'  * `loc` An `sf` object that describes site's location.
+#'  * `description`
+#'  * `collunits` limited information on collunits
 #' @examples
 #' \donttest{
 #' ## Find all sites with a min altitude of 12m and a max altitude of 25m
@@ -108,7 +105,6 @@ parse_site <- function(result) {
 #' sites_2500 <- get_sites(altmin=2500, all_data = TRUE)
 #' ## To find all sites that contain the string "Alex%"
 #' alex_sites <- get_sites(sitename="Alex%")
-#'
 #' ## To find sites in Brazil (again with default 25 records)
 #' brazil <- '{"type": "Polygon",
 #' "coordinates": [[
@@ -154,10 +150,8 @@ get_sites <- function(x = NA, ...) {
 #' Each "site" object contains 6 parameters that can be accessed as well:
 #' siteid, sitename, location, altitude, description,
 #' limited collection units information.
-#' \describe{
-#'  \item{loc}{ An `sf` object that describes site's location.}
-#'  \item{collunits}{ limited information on collunits}
-#'  }
+#'  * `loc` An `sf` object that describes site's location.
+#'  * `collunits` limited information on collunits
 #' @export
 get_sites.default <- function(...) { # nolint
   oo <- options(scipen = 9999999)
@@ -229,8 +223,8 @@ get_sites.default <- function(...) { # nolint
 #' Each "site" object contains 6 parameters that can be accessed as well:
 #' siteid, sitename, location, altitude, description,
 #' limited collection units information.
-#'  *  `loc` An `sf` object that describes site's location.
-#'  *  `collunits` limited information on collunits
+#'  * `loc` An `sf` object that describes site's location.
+#'  * `collunits` limited information on collunits
 #' @examples {
 #' ## Find all sites by numeric siteid:
 #' sites <- get_sites(seq(1,3))
@@ -270,10 +264,8 @@ get_sites.numeric <- function(x, ...) {
 #' Each "site" object contains 6 parameters that can be accessed as well:
 #' siteid, sitename, location, altitude, description,
 #' limited collection units information.
-#' \itemize{
-#'  \item{loc}{ An `sf` object that describes site's location.}
-#'  \item{collunits}{ limited information on collunits}
-#'  }
+#'  * `loc` An `sf` object that describes site's location.
+#'  * `collunits` limited information on collunits
 #' @export
 get_sites.sites <- function(x, ...) {