Merge pull request #231 from SimonGoring/master

Submitted 1.7.4 version for CRAN.

Author: SimonGoring

.Rbuildignore

@@ -1,3 +1,4 @@
+^CRAN-RELEASE$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^.*\.yml

CRAN-RELEASE

@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2019-01-03.
+Once it is accepted, delete this file and tag the release (commit 8a3aa68e0b).

man/compile_downloads.Rd

@@ -0,0 +1,28 @@
+Package: neotoma
+Type: Package
+Title: Access to the Neotoma Paleoecological Database Through R
+Version: 1.7.4
+Date: 2019-01-03
+Encoding: UTF-8
+Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek
+    [ctb], Karthik Ram [aut], Luke Sosalla [ctb]
+Authors@R: c(person(given = c("Simon", "J."), family = "Goring",
+    role = c("aut", "cre"), email = "goring@wisc.edu"),
+    person(given = c("Gavin", "L."), family = "Simpson", role = "aut"),
+    person(given = c("Jeremiah", "P."), family = "Marsicek", role = "ctb"),
+    person(given = "Karthik", family = "Ram", role = "aut"),
+    person(given = "Luke", family = "Sosalla", role = "ctb"))
+Maintainer: Simon J. Goring <goring@wisc.edu>
+Description: Access paleoecological datasets from the Neotoma Paleoecological
+    Database using the published API (<http://api.neotomadb.org/>).  The functions
+    in this package access various pre-built API functions and attempt to return
+    the results from Neotoma in a usable format for researchers and the public.
+License: MIT + file LICENSE
+URL: https://github.com/ropensci/neotoma
+BugReports: https://github.com/ropensci/neotoma/issues
+Depends: R (>= 2.10)
+Imports: plyr, reshape2, jsonlite, httr, xml2, analogue, leaflet, dplyr
+Suggests: testthat, knitr
+RoxygenNote: 6.1.1
+NeedsCompilation: no
+Packaged: 2019-01-03 23:57:10 UTC; simon

man/get_dataset.integer.Rd

@@ -0,0 +1,2 @@
+YEAR: 2016
+COPYRIGHT HOLDER: Simon Goring

man/get_dataset.numeric.Rd

@@ -0,0 +1,125 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method(Stratiplot,download)
+S3method(Stratiplot,download_list)
+S3method(ages,download)
+S3method(ages,download_list)
+S3method(bind,default)
+S3method(browse,dataset)
+S3method(browse,dataset_list)
+S3method(browse,default)
+S3method(browse,download)
+S3method(browse,download_list)
+S3method(counts,download)
+S3method(counts,download_list)
+S3method(depths,default)
+S3method(depths,download)
+S3method(depths,download_list)
+S3method(get_chroncontrol,dataset)
+S3method(get_chroncontrol,dataset_list)
+S3method(get_chroncontrol,default)
+S3method(get_chroncontrol,download)
+S3method(get_chroncontrol,download_list)
+S3method(get_closest,dataset)
+S3method(get_closest,default)
+S3method(get_closest,download)
+S3method(get_closest,site)
+S3method(get_dataset,default)
+S3method(get_dataset,download)
+S3method(get_dataset,download_list)
+S3method(get_dataset,geochronologic)
+S3method(get_dataset,geochronologic_list)
+S3method(get_dataset,integer)
+S3method(get_dataset,numeric)
+S3method(get_dataset,site)
+S3method(get_download,dataset)
+S3method(get_download,dataset_list)
+S3method(get_download,default)
+S3method(get_download,site)
+S3method(get_geochron,dataset)
+S3method(get_geochron,dataset_list)
+S3method(get_geochron,default)
+S3method(get_geochron,site)
+S3method(get_publication,dataset)
+S3method(get_publication,dataset_list)
+S3method(get_publication,default)
+S3method(get_publication,download)
+S3method(get_publication,download_list)
+S3method(get_site,dataset)
+S3method(get_site,dataset_list)
+S3method(get_site,default)
+S3method(get_site,download)
+S3method(get_site,download_list)
+S3method(get_site,geochronologic)
+S3method(get_site,geochronologic_list)
+S3method(get_site,integer)
+S3method(get_site,numeric)
+S3method(plot,dataset)
+S3method(plot,dataset_list)
+S3method(plot,download)
+S3method(plot,download_list)
+S3method(plot,site)
+S3method(plot_leaflet,dataset)
+S3method(plot_leaflet,dataset_list)
+S3method(plot_leaflet,download)
+S3method(plot_leaflet,download_list)
+S3method(print,chroncontrol)
+S3method(print,dataset)
+S3method(print,dataset_list)
+S3method(print,download)
+S3method(print,download_list)
+S3method(print,geochronologic)
+S3method(print,geochronologic_list)
+S3method(print,site)
+S3method(taxa,download)
+S3method(taxa,download_list)
+export(ages)
+export(bind)
+export(browse)
+export(compile_downloads)
+export(compile_taxa)
+export(counts)
+export(depths)
+export(get_chroncontrol)
+export(get_closest)
+export(get_contact)
+export(get_dataset)
+export(get_download)
+export(get_geochron)
+export(get_publication)
+export(get_site)
+export(get_table)
+export(get_taxa)
+export(param_check)
+export(plot_leaflet)
+export(read.tilia)
+export(read_bacon)
+export(taxa)
+export(write_agefile)
+importFrom(analogue,Stratiplot)
+importFrom(analogue,tran)
+importFrom(dplyr,bind_rows)
+importFrom(graphics,legend)
+importFrom(graphics,par)
+importFrom(graphics,plot)
+importFrom(graphics,points)
+importFrom(httr,GET)
+importFrom(httr,content)
+importFrom(jsonlite,fromJSON)
+importFrom(leaflet,addCircleMarkers)
+importFrom(leaflet,addProviderTiles)
+importFrom(leaflet,leaflet)
+importFrom(leaflet,markerClusterOptions)
+importFrom(leaflet,markerOptions)
+importFrom(plyr,ldply)
+importFrom(stats,aggregate)
+importFrom(stats,na.omit)
+importFrom(utils,browseURL)
+importFrom(utils,write.csv)
+importFrom(utils,write.table)
+importFrom(xml2,as_list)
+importFrom(xml2,read_xml)
+importFrom(xml2,xml_attr)
+importFrom(xml2,xml_find_all)
+importFrom(xml2,xml_find_one)
+importFrom(xml2,xml_text)

man/get_site.numeric.Rd

@@ -0,0 +1,94 @@
+neotoma 1.7.4
+====================
+o Bug fix: `get_dataset(gpid=123) was returning an error, fix corrects the error to allow unassigned `x` variables.
+o Updated the allowable dataset types for searching to reflect the larger set of dataset types within Neotoma.
+
+neotoma 1.7.3
+====================
+o Added numeric/integer methods to the `get_site` and `get_dataset` functions so that a vector of dataset or siteids can be passed to improve more general workflow methods.
+
+neotoma 1.7.2
+====================
+o Bugfixes, added the `taxa` function to easily extract taxa from one or multiple download objects.
+
+neotoma 1.7.1
+====================
+o Bugfix for `compile_download`, single sample downloads were failing to compile properly.
+
+neotoma 1.7.0
+====================
+o Added `plot_leaflet` to allow interactive exploration of downloaded Neotoma data.  Integrates with the Neotoma Explorer.
+o Minor bugfix for `get_download` to allow records to be sent to Neotoma and to be filtered.
+
+neotoma 1.6.2
+====================
+o Bugfix in `get_chroncontrol`, `read.tilia` based on experience in extensive testing.  Improved the basic `plot` method based on tests against Tilia files in the Neotoma Holding Tank.
+o Built more robust interpolation in `read_bacon` so that age models without interpolated dates can still be imported.
+o `browse` now opens multiple datastes in the Neotoma Explorer at once.
+
+neotoma 1.6.1
+====================
+o Bugfix
+o New `Stratiplot` method, using the `analogue` package to plot dataset diagrams from `download` and `download_list` objects.
+o Bug fixes for `write_agefile`
+o New function `read_bacon` to read in and integrate Bacon chronologies into `download` objects.
+
+neotoma 1.6.0
+====================
+o Support for vector inputs in the `gpid` selection.
+o Added a `get_closest` function to find the closest datasets to a sample site.
+o Mostly clean-up of reported bugs by users.
+o Revised examples for faster check speed.
+
+neotoma 1.5.1
+====================
+o Fix for datasets with empty submission dates.
+o Some minor (non-functional) code cleaning.
+o Added extra tests.
+
+neotoma 1.5.0
+====================
+o More extensive testing to support multiple dataset types.  Water chemistry datasets still unsupported.
+o Function `read.tilia` added to read Tilia (http://tiliait.com) style XML files.
+o Moved to using `xml2`, `httr` and `jsonlite` to support parsing.
+
+neotoma 1.4.0
+====================
+o The few records without chronologies were causing errors when `get_download` was applied.
+o Added plot method.
+
+neotoma 1.3.3
+====================
+o Critical bug fix: `get_download` now correctly assigns the default chronology to `sample.meta`.  All other chronologies (including the default) are stored in the `chronologies` list for the `download`.
+o Bugfix for issue #187, empty `dataset_list`s now return a NULL value, rather than breaking the `print` method.
+
+neotoma 1.3.2
+====================
+o Bugfix for `get_download`, assignment to the `dataset.id` was incorrectly placed causing the columns to be out of place relative to the data.
+
+neotoma 1.3.1
+====================
+o Bugfix for `write_agefile`
+o Added a `browse` method for datasets, that will open a browser window for a specific dataset or download.
+o The deprecated `compile_list` function has now been removed.  Use `compile_taxa` instead.
+
+neotoma 1.3.0
+====================
+o Improved functionality of get_chroncontrol to allow it to deal with empty tables and work directly with download and download_list objects.
+
+neotoma 1.2-0
+====================
+o Added new datasettypes for records, including water chemistry, charcoal, XRD and others.
+
+neotoma 1.1-0
+====================
+o Publication of Goring, S., Dawson, A., Simpson, G. L., Ram, K., Graham, R. W., Grimm, E. C., & Williams, J. W.. (2015). neotoma: A Programmatic Interface to the Neotoma Paleoecological Database, 1(1), Art. 2. DOI: http://doi.org/10.5334/oq.ab
+
+neotoma 0.1
+====================
+o continued development of API implementation and working toward a common 
+  standard for data output.
+
+o Continued development of tests for the package.
+
+o Changed function names to singular.

neotoma.Rcheck/00_pkg_src/neotoma/DESCRIPTION

@@ -0,0 +1,75 @@
+#' @title Palaeoecological stratigraphic diagrams
+#' @description Draws paleoecological diagrams from a \code{download} object.  Allows control of variable type (using the \code{tran} function from the \code{analogue} package), and taxonomic grouping.
+#' @param x A \code{download} object.
+#' @param yaxis One of the columns in \code{sample.meta}, including \code{depth}, \code{age}, \code{age.younger}, or \code{age.older}, default \code{age}.
+#' @param method An option for axis transformation using \code{tran} from the \code{analogue} package.  \code{"none"} by default.
+#' @param group An ecological group from the taxon table.  
+#' @param ... variables to be passed to \code{Stratiplot}.
+#' @details A wrapper for the \code{analogue} package's \code{Stratiplot} function.  Allowing the user to plot a stratigraphic diagram directly from a \code{download} object.
+#' @return A \code{trellis} object.
+#' @examples
+#' \dontrun{
+#' lake_o_dl <- get_download(15925)
+#' Stratiplot(lake_o_dl[[1]])
+#' }
+#' @importFrom analogue Stratiplot tran
+#'@export
+#'
+Stratiplot.download <- function(x, yaxis = "age", method = "none", group = NULL, ...) {
+  counts <- counts(x)
+  
+  if (!yaxis %in% c("depth", "age.older", "age.younger", "age")) {
+    stop("You must provide a suitable variable name for the y axis.")
+  }
+  
+  if (!"sample.meta" %in% names(x) | all(is.na(x$sample.meta[,yaxis]))) {
+    stop("This download has no suitable chronological or depth information.")
+  }
+  
+  if (!is.null(group)) {
+    taxa <- x$taxon.list$taxon.name[x$taxon.list$ecological.group %in% group]
+  } else {
+    taxa <- x$taxon.list$taxon.name[!x$taxon.list$ecological.group %in% "LABO" ]
+    
+  }
+  
+  y <- x$sample.meta[,yaxis]
+  
+  counts <- analogue::tran(counts[,taxa], method = method)
+  
+  analogue::Stratiplot(counts, y, ...)
+  
+}
+
+#' @title Palaeoecological stratigraphic diagrams
+#' @description Draws paleoecological diagrams from a \code{download_list} object.  Allows control of variable type (using the \code{tran} function from the \code{analogue} package), and taxonomic grouping.  
+#' This function only works for \code{download_list} objects that contain a single object.
+#' @param x A \code{download_list} object.
+#' @param yaxis One of the columns in \code{sample.meta}, including \code{depth}, \code{age}, \code{age.younger}, or \code{age.older}, default \code{age}.
+#' @param method An option for axis transformation using \code{tran} from the \code{analogue} package.  \code{"none"} by default.
+#' @param group An ecological group from the taxon table.  
+#' @param ... variables to be passed to \code{Stratiplot}.
+#' @details A wrapper for the \code{analogue} package's \code{Stratiplot} function.  Allowing the user to plot a stratigraphic diagram directly from a \code{download} object.
+#' @return A \code{trellis} object.
+#' @examples
+#' \dontrun{
+#' lake_o_dl <- get_download(15925)
+#' # This works:
+#' Stratiplot(lake_o_dl)
+#' 
+#' lakes_o_nw <- get_download(get_site(sitename = "Lake B%"))
+#' # This Fails:
+#' # Stratiplot(lake_o_nw)
+#' 
+#' }
+#' @importFrom analogue Stratiplot tran
+#' @export
+#'
+Stratiplot.download_list <- function(x, yaxis = "age", method = "none", group = NULL, ...) {
+  if (length(x) == 1) {
+    Stratiplot(x[[1]], yaxis = "age", method = "none", group = NULL, ...)
+  } else {
+    stop("You must select a single `download` object to plot.")
+  }
+    
+}