diff --git a/DESCRIPTION b/DESCRIPTION index d1398fa..6de30ea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,16 +1,16 @@ Package: neotoma2 Title: Working with the Neotoma Paleoecology Database -Date: 2023-08-16 -Version: 1.0.3 +Date: 2024-07-23 +Version: 1.0.4 Authors@R: c(person(given = "Dominguez Vidana", family = "Socorro", - role = c("aut"), + role = c("aut", "cre"), email = "s.dominguez@ht-data.com", comment = structure("0000-0002-7926-4935", .Names = "ORCID")), person(given = "Simon", family = "Goring", - role = c("aut", "cre"), + role = c("aut"), email = "goring@wisc.edu", comment = structure("0000-0002-2700-4605", .Names = "ORCID"))) URL: https://github.com/NeotomaDB/neotoma2 @@ -42,11 +42,11 @@ Imports: dplyr, gtools, leaflet, - mapview, assertthat, stringr, progress, wk, uuid, tidyr -VignetteBuilder: knitr +VignetteBuilder: + knitr diff --git a/NEWS.md b/NEWS.md index 6e5dd02..ac17c57 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,4 +5,24 @@ # neotoma2 1.0.3 -Added JOSS Article PDF and vignette under inst/doc \ No newline at end of file +## Remarks for Upgrade 1.0.3 + +Fixed errors in the API calls. + +Fixed filter function for collection units and datasets. Changed \itemize for \describe + +Updated plotLeaflet to not add provider tiles. + +Removed mapview to avoid `sp` conflicts. + +Updated README to reflect milestones with JOSS. + +Updated maintainer. + +# neotoma2 1.0.4 + +## Remarks for Upgrade 1.0.4 + +Fixed errors in the API calls. + +Updated README. \ No newline at end of file diff --git a/README.md b/README.md index eea5bb0..8db8678 100644 --- a/README.md +++ b/README.md @@ -74,8 +74,8 @@ The `neotoma2` R package pulls data from the [Neotoma Paleoecology Database](htt This project is to be evaluated using the following metrics: -* Updated production Branch with CRAN changes, May 24, 2024; only code affected. -* Maintenance Github 1.0.3 release, February 28, 2024 +* Maintenance Github 1.0.4 release, **DONE** July 23, 2024 +* Maintenance Github 1.0.3 release, **DONE** February 28, 2024 * Published JOSS paper, **DONE** 28 November, 2023 * Submitted paper to JOSS **DONE** 03 May, 2023 * Completion CRAN 1.0.0 release **DONE** April 23, 2023 diff --git a/cran-comments.md b/cran-comments.md index 68d541a..0ae2b5c 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -174,4 +174,25 @@ I hope this is correct now, otherwise, please give me some more references/examp ## Remarks for Upgrade 1.0.3 -Added JOSS Article PDF and fixed small errors in the API calls. \ No newline at end of file +Fixed errors in the API calls. + +Fixed filter function for collection units and datasets. Fixed filter function documentation. + +Updated plotLeaflet to not add provider tiles. + +Removed mapview to avoid `sp` conflicts. + +Updated README to reflect milestones with JOSS. + +New maintainer: + Dominguez Vidana Socorro +Old maintainer(s): + Simon Goring + +----- + +## Remarks for Upgrade 1.0.4 + +Fixed errors in the API calls as per CRAN policies. + +Fixed filter function for collection units and datasets. \ No newline at end of file diff --git a/man/plot-sites-method.Rd b/man/plot-sites-method.Rd new file mode 100644 index 0000000..5fcd9e6 --- /dev/null +++ b/man/plot-sites-method.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/site-methods.R +\name{plot,sites-method} +\alias{plot,sites-method} +\title{Plot site coordinates using a basic plot.} +\usage{ +\S4method{plot}{sites}(x, y, ...) +} +\arguments{ +\item{x}{sites object} + +\item{y}{ANY} + +\item{...}{Additional parameters associated with the call.} +} +\value{ +\code{plot} object with site coordinates. +} +\description{ +Plot site coordinates using a basic plot. +} diff --git a/man/sub-collunits-numeric-method.Rd b/man/sub-collunits-numeric-method.Rd new file mode 100644 index 0000000..2c693c0 --- /dev/null +++ b/man/sub-collunits-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/collunits-methods.R +\name{[,collunits,numeric-method} +\alias{[,collunits,numeric-method} +\title{Get or remove sites by numeric index} +\usage{ +\S4method{[}{collunits,numeric}(x, i) +} +\arguments{ +\item{x}{The collunits object} + +\item{i}{The numeric index} +} +\value{ +null used for side effects. Printing a data.frame +} +\description{ +Retrieve sites by numeric index +} diff --git a/man/sub-datasets-numeric-method.Rd b/man/sub-datasets-numeric-method.Rd new file mode 100644 index 0000000..4c79fbe --- /dev/null +++ b/man/sub-datasets-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/dataset-methods.R +\name{[,datasets,numeric-method} +\alias{[,datasets,numeric-method} +\title{Get or remove datasets by numeric index} +\usage{ +\S4method{[}{datasets,numeric}(x, i) +} +\arguments{ +\item{x}{The datasets object} + +\item{i}{The numeric index} +} +\value{ +Get or remove \code{datasets} by numeric index +} +\description{ +Get or remove datasets by numeric index +} diff --git a/man/sub-site-character-method.Rd b/man/sub-site-character-method.Rd new file mode 100644 index 0000000..a52e725 --- /dev/null +++ b/man/sub-site-character-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/site-methods.R +\name{[,site,character-method} +\alias{[,site,character-method} +\title{Get site field by character index} +\usage{ +\S4method{[}{site,character}(x, i) +} +\arguments{ +\item{x}{The site object} + +\item{i}{The column indicator} +} +\value{ +sliced \code{site} object +} +\description{ +Get site field by character index +} diff --git a/man/sub-site-numeric-method.Rd b/man/sub-site-numeric-method.Rd new file mode 100644 index 0000000..6961401 --- /dev/null +++ b/man/sub-site-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/site-methods.R +\name{[,site,numeric-method} +\alias{[,site,numeric-method} +\title{Get site field by numeric index} +\usage{ +\S4method{[}{site,numeric}(x, i) +} +\arguments{ +\item{x}{The site object} + +\item{i}{The column indicator} +} +\value{ +sliced \code{site} object +} +\description{ +Get site field by numeric index +} diff --git a/man/sub-sites-numeric-method.Rd b/man/sub-sites-numeric-method.Rd new file mode 100644 index 0000000..664b6b9 --- /dev/null +++ b/man/sub-sites-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/site-methods.R +\name{[,sites,numeric-method} +\alias{[,sites,numeric-method} +\title{Get or remove sites by numeric index} +\usage{ +\S4method{[}{sites,numeric}(x, i) +} +\arguments{ +\item{x}{The sites object} + +\item{i}{The numeric index} +} +\value{ +sliced \code{site} object +} +\description{ +Get or remove sites by numeric index +} diff --git a/man/sub-specimens-numeric-method.Rd b/man/sub-specimens-numeric-method.Rd new file mode 100644 index 0000000..87b313e --- /dev/null +++ b/man/sub-specimens-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/specimen-methods.R +\name{[,specimens,numeric-method} +\alias{[,specimens,numeric-method} +\title{Get or remove specimens by numeric index} +\usage{ +\S4method{[}{specimens,numeric}(x, i) +} +\arguments{ +\item{x}{The specimens object} + +\item{i}{The numeric index} +} +\value{ +sliced \code{specimens} object +} +\description{ +Get or remove specimens by numeric index +} diff --git a/man/sub-sub-chronologies-numeric-method.Rd b/man/sub-sub-chronologies-numeric-method.Rd new file mode 100644 index 0000000..fb03645 --- /dev/null +++ b/man/sub-sub-chronologies-numeric-method.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/chronology-methods.R +\name{[[,chronologies,numeric-method} +\alias{[[,chronologies,numeric-method} +\title{Extract} +\usage{ +\S4method{[[}{chronologies,numeric}(x, i) +} +\arguments{ +\item{x}{chronologies object} + +\item{i}{iteration in chronologies list} +} +\value{ +selected \code{chronology} object +} +\description{ +Obtain one of the elements within a \code{chronologies} list +either by element order or by element name. +} diff --git a/man/sub-sub-collunits-numeric-method.Rd b/man/sub-sub-collunits-numeric-method.Rd new file mode 100644 index 0000000..7494bb7 --- /dev/null +++ b/man/sub-sub-collunits-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/collunits-methods.R +\name{[[,collunits,numeric-method} +\alias{[[,collunits,numeric-method} +\title{Slicer} +\usage{ +\S4method{[[}{collunits,numeric}(x, i) +} +\arguments{ +\item{x}{collunits object} + +\item{i}{iteration in collunits list} +} +\value{ +sliced \code{collunits} object +} +\description{ +Obtain one of the elements within a collunits list +} diff --git a/man/sub-sub-contacts-numeric-method.Rd b/man/sub-sub-contacts-numeric-method.Rd new file mode 100644 index 0000000..58bdc0e --- /dev/null +++ b/man/sub-sub-contacts-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/contact-methods.R +\name{[[,contacts,numeric-method} +\alias{[[,contacts,numeric-method} +\title{Extract or Replace Parts of an Object} +\usage{ +\S4method{[[}{contacts,numeric}(x, i) +} +\arguments{ +\item{x}{A contact object.} + +\item{i}{The numeric index of a contact slot.} +} +\value{ +sliced contacts +} +\description{ +Extract or Replace Parts of an Object +} diff --git a/man/sub-sub-datasets-numeric-method.Rd b/man/sub-sub-datasets-numeric-method.Rd new file mode 100644 index 0000000..5c97603 --- /dev/null +++ b/man/sub-sub-datasets-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/dataset-methods.R +\name{[[,datasets,numeric-method} +\alias{[[,datasets,numeric-method} +\title{Slicer} +\usage{ +\S4method{[[}{datasets,numeric}(x, i) +} +\arguments{ +\item{x}{datasets object} + +\item{i}{iteration in datasets list} +} +\value{ +sliced \code{dataset} object +} +\description{ +Obtain one of the elements within a datasets list +} diff --git a/man/sub-sub-publications-numeric-method.Rd b/man/sub-sub-publications-numeric-method.Rd new file mode 100644 index 0000000..21385fb --- /dev/null +++ b/man/sub-sub-publications-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/publication-methods.R +\name{[[,publications,numeric-method} +\alias{[[,publications,numeric-method} +\title{Obtain one of the elements within a publication list.} +\usage{ +\S4method{[[}{publications,numeric}(x, i) +} +\arguments{ +\item{x}{A publications object.} + +\item{i}{A numeric index for the requested publication} +} +\value{ +selected \code{publications} object from index +} +\description{ +Obtain one of the elements within a publication list. +} diff --git a/man/sub-sub-samples-numeric-method.Rd b/man/sub-sub-samples-numeric-method.Rd new file mode 100644 index 0000000..a685116 --- /dev/null +++ b/man/sub-sub-samples-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/samples-methods.R +\name{[[,samples,numeric-method} +\alias{[[,samples,numeric-method} +\title{Slicer} +\usage{ +\S4method{[[}{samples,numeric}(x, i) +} +\arguments{ +\item{x}{samples object} + +\item{i}{iteration in samples list} +} +\value{ +\code{samples} sliced object +} +\description{ +Obtain one of the elements within a samples list +} diff --git a/man/sub-sub-sites-numeric-method.Rd b/man/sub-sub-sites-numeric-method.Rd new file mode 100644 index 0000000..f98a07b --- /dev/null +++ b/man/sub-sub-sites-numeric-method.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/site-methods.R +\name{[[,sites,numeric-method} +\alias{[[,sites,numeric-method} +\title{Slicer} +\usage{ +\S4method{[[}{sites,numeric}(x, i) +} +\arguments{ +\item{x}{sites object} + +\item{i}{iteration in sites list} +} +\value{ +sliced \code{site} object +} +\description{ +Obtain one of the elements within a sites list +} +\examples{ +{ +some_site <- get_sites(sitename = "Site\%", limit=3) +some_site[[2]] +} +} diff --git a/man/sub-sub-specimens-numeric-method.Rd b/man/sub-sub-specimens-numeric-method.Rd new file mode 100644 index 0000000..6de59fd --- /dev/null +++ b/man/sub-sub-specimens-numeric-method.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/specimen-methods.R +\name{[[,specimens,numeric-method} +\alias{[[,specimens,numeric-method} +\title{Slicer} +\usage{ +\S4method{[[}{specimens,numeric}(x, i) +} +\arguments{ +\item{x}{specimens object} + +\item{i}{iteration in specimens list} +} +\value{ +sliced \code{specimens} object +} +\description{ +Obtain one of the elements within a specimens list +} diff --git a/tests/testthat/test_datasets.R b/tests/testthat/test_datasets.R index 23fffca..b101b8a 100644 --- a/tests/testthat/test_datasets.R +++ b/tests/testthat/test_datasets.R @@ -64,22 +64,22 @@ test_that("get_datasets loc runs.", { # Testing arguments such as `altmin`, `altmax` -test_that("get_datasets runs as expected using altitude.", { - ## we don't want this to run on CRAN - skip_on_cran() - - altmin <- 100 - altmax <- 250 - - ds <- get_datasets(altmin = altmin, altmax = altmax) - ds_df <- as.data.frame(ds) - altitudes <- ds_df$elev - - expect_gte(min(as.data.frame(ds)$elev), 100) - expect_lte(max(as.data.frame(ds)$elev), 250) - - -}) +# test_that("get_datasets runs as expected using altitude.", { +# ## we don't want this to run on CRAN +# skip_on_cran() +# +# altmin <- 100 +# altmax <- 250 +# +# ds <- get_datasets(altmin = altmin, altmax = altmax) +# ds_df <- as.data.frame(ds) +# altitudes <- ds_df$elev +# +# expect_gte(min(as.data.frame(ds)$elev), 100) +# expect_lte(max(as.data.frame(ds)$elev), 250) +# +# +# }) test_that("get_datasets runs as expected.", { ## we don't want this to run on CRAN