Merge pull request #22 from oggioniale/dev

merge release 1.0.0

DESCRIPTION

@@ -1,19 +1,55 @@
 Package: ReLTER
 Type: Package
 Title: An interface to the eLTER for the R statistical programming environment
-Version: 0.2.0
-Date: 2021-10-19
+Version: 1.0.0
+Date: 2021-11-15
 Authors@R: c(
-        person("Alessandro", "Oggioni", email = "[email protected]", role = c("aut", "cre", "fnd"),
+        person("Alessandro", "Oggioni", email = "[email protected]", 
+          role = c("aut", "cre", "fnd"),
           comment = c(ORCID = "0000-0002-7997-219X")
         ),
-        person("Paolo", "Tagliolato", email = "[email protected]", role = "ctb",
-          comment = c(ORCID = "0000-0002-0261-313X")
+        person("Micha", "Silver", email = "[email protected]",
+          role = c("aut", "ctb"),
+          comment = c(ORCID = "0000-0002-1128-1325",
+          " Micha Silver is a coauthor of functions get_ilter_generalinfo and
+          get_site_info for category Boundaries, he develop get_site_ODS
+          function and he also is a reviewer of English wording for all
+          functions.")
+        ),
+        person("Paolo", "Tagliolato", email = "[email protected]",
+          role = c("aut", "ctb"),
+          comment = c(ORCID = "0000-0002-0261-313X",
+          " Paolo Tagliolato is a coauthor of package, he wrote the function
+          do_Q(), on which some ReLTER internal functions are based")
         )
       )
-Maintainer: The package maintainer Alessandro Oggioni, phD (2020) <[email protected]>
-Description: More about what it does (maybe more than one line)
-    Use four spaces when indenting paragraphs within the Description.
+Maintainer: The package maintainer Alessandro Oggioni, phD (2020)
+    <[email protected]>
+Description: ReLTER is an R package that: provides access to DEIMS-SDR
+    (https://deims.org/), allows interact with software implemented by eLTER
+    Research Infrastructure (RI) and improves the data/information shared by
+    them.
+    ReLTER is a R package devoted to access, interact and improve the
+    information and the data shared by Long Term Ecological Research (LTER)
+    network. This package is born within eLTER H2020 major project that will
+    help advance the development of European Long-Term Ecosystem Research
+    Infrastructures (eLTER RI - https://elter-ri.eu).
+    The ReLTER package functions in particular allow to:
+    - retrive the information about entities (e.g. sites, datasets, and
+    activities) shared by DEIMS-SDR (see e.g. get_site_info function);
+    - interact with the [ODSEurope](maps.opendatascience.eu) managed by members
+    of the [Geo-harmonizer](https://opendatascience.eu/geoharmonizer-project/)
+    project starting with the dataset shared by [DEIMS-SDR](https://deims.org/)
+    (see e.g. [get_site_ODS](https://oggioniale.github.io/ReLTER/reference/get_site_ODS.html)
+    function);
+    - use the site informations for download data from other platforms (see
+    e.g. get_site_ODS function);
+    - improve the quality of the dataset (see e.g. get_id_worms).
+    Functions currently implemented are derived from the discussion of the
+    needs declared by eLTER users community.
+    The ReLTER package shall definitely follow the progress of eLTER-RI
+    infrastructure and evolving with the improvements and develop of
+    new tools.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
@@ -29,6 +65,7 @@ Imports:
     rgeos (>= 0.5-3),
     rosm (>= 0.2.5),
     raster (>= 3.3-13),
+    terra (>= 1.4-11),
     tmap (>= 3.1),
     grid (>= 3.5.1),
     leaflet (>= 2.0.3),
@@ -46,7 +83,6 @@ Imports:
     xml2 (>= 1.3.2),
     magrittr (>= 2.0.1),
     stats (>= 4.0.3)
-RoxygenNote: 7.1.1
 Suggests: 
     testthat (>= 3.0.0),
     knitr,
@@ -55,3 +91,5 @@ VignetteBuilder: knitr
 URL: https://github.com/oggioniale/ReLTER
 BugReports: https://github.com/oggioniale/ReLTER/issues
 Config/testthat/edition: 3
+RoxygenNote: 7.1.2
+Language: en-GB

NAMESPACE

@@ -1,39 +1,45 @@
 # Generated by roxygen2: do not edit by hand
 
-export(createQRCode)
-export(getActivity)
-export(getDataset)
-export(getILTEREnvCharacts)
-export(getILTERGeneralInfo)
-export(getILTERParameters)
-export(getILTERResearchTopics)
-export(getNetworkEnvCharacts)
-export(getNetworkParameters)
-export(getNetworkRelatedResources)
-export(getNetworkResearchTopics)
-export(getNetworkSites)
-export(getSOSProcedureList)
-export(getSiteAffiliations)
-export(getSiteBoundaries)
-export(getSiteContact)
-export(getSiteEnvCharacts)
-export(getSiteGeneral)
-export(getSiteInfrastructure)
-export(getSiteParameters)
-export(getSiteRelatedResources)
-export(getSiteResearchTopics)
-export(mapNetworkPoint)
-export(parametersChartPie)
-export(parametersChartWaffle)
-export(produceMapOfSiteFromDEIMS)
-export(taxonIDPesi)
+export(get_activity_info)
+export(get_dataset_info)
+export(get_ilter_envcharacts)
+export(get_ilter_generalinfo)
+export(get_ilter_parameters)
+export(get_ilter_research_topics)
+export(get_network_envcharacts)
+export(get_network_parameters)
+export(get_network_related_resources)
+export(get_network_research_topics)
+export(get_network_sites)
+export(get_site_ODS)
+export(get_site_affiliations)
+export(get_site_boundaries)
+export(get_site_contact)
+export(get_site_envcharacts)
+export(get_site_general)
+export(get_site_info)
+export(get_site_infrastructure)
+export(get_site_parameters)
+export(get_site_related_resources)
+export(get_site_research_topics)
+export(get_sos_procedurelist)
+export(produce_network_points_map)
+export(produce_site_map)
+export(produce_site_parameters_pie)
+export(produce_site_parameters_waffle)
+export(produce_site_qrcode)
+export(taxon_id_pesi)
+export(taxon_id_worms)
+export(taxon_id_worms_refine)
 import(ISOcodes)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,case_when)
 importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(dplyr,tally)
@@ -61,6 +67,7 @@ importFrom(leaflet,addMarkers)
 importFrom(leaflet,addPolygons)
 importFrom(leaflet,addTiles)
 importFrom(leaflet,leaflet)
+importFrom(magrittr,"%>%")
 importFrom(mapview,mapshot)
 importFrom(qrcode,qrcode_gen)
 importFrom(raster,getData)
@@ -74,9 +81,17 @@ importFrom(sf,st_as_sf)
 importFrom(sf,st_as_sfc)
 importFrom(sf,st_bbox)
 importFrom(sf,st_crs)
+importFrom(sf,st_transform)
 importFrom(sf,st_write)
 importFrom(sf,write_sf)
+importFrom(stringr,str_detect)
 importFrom(taxize,eubon_search)
+importFrom(terra,crop)
+importFrom(terra,crs)
+importFrom(terra,mask)
+importFrom(terra,plot)
+importFrom(terra,rast)
+importFrom(terra,vect)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tribble)
 importFrom(tmap,tm_basemap)
@@ -93,6 +108,7 @@ importFrom(tmap,tm_shape)
 importFrom(utils,capture.output)
 importFrom(utils,data)
 importFrom(waffle,waffle)
+importFrom(worrms,wm_records_names)
 importFrom(xml2,read_xml)
 importFrom(xml2,xml_find_all)
 importFrom(xml2,xml_ns)

NEWS.md

@@ -1,3 +1,23 @@
+## ReLTER 1.0.0 Release Notes
+
+v1.0.0 was released on 15/11/2021
+
+### Major changes
+
+* all the getSite* functions could be merged into one, with an additional function parameter category;
+* all the functions are renamed according with CRAN suggestion;
+* first release of vignettes have been done;
+* new functions for interactive improvements of taxa names using PESI and WORMS repository have been done;
+* function acquires one of eight raster datasets from the European OpenDataScience maps website for a selected DEIMS site have been implemented by @micha-silver;
+* a fully review of functions and package description have been done.
+
+### Minor changes
+
+* CITATION file are been created;
+* this version has been submitted on rOpenSci.
+
+________________________________________________________________________________
+
 ## ReLTER 0.2.0 Release Notes
 
 v0.2.0 was released on 18/10/2021

R/do_Q.R

@@ -1,5 +1,5 @@
 #' @title eLTER do_Q function
-#' @description This function ...
+#' @description This function parses json content returned from an HTTP request
 #' @param q a character
 #' @param jj a character
 #' @return The output of the function is ...

R/getActivity.R → R/get_activity_info.R

@@ -1,30 +1,30 @@
-#' @title eLTER getActivity function
-#' @description This function allows to obtain the info of activity (actually
-#'  only title) provided in DEIMS-SDR.
-#' @param activityid A character. It is the DEIMS iD of activity make from
+#' @title eLTER get_activity_info function
+#' @description This function obtains the info of activity (actually
+#'  title) provided in DEIMS-SDR.
+#' @param activityid A character. The DEIMS activity ID from
 #' DEIMS-SDR website. More information about DEIMS iD in this
 #' \href{https://deims.org/docs/deimsid.html}{page}.
 #' @return The output of the function is a `tibble` with main features of
-#' the activity make in a site.
+#' the activities in a site, and a `leaflet` map plot.
 #' @author Alessandro Oggioni, phD (2020) \email{oggioni.a@@irea.cnr.it}
 #' @importFrom httr GET content
 #' @importFrom dplyr as_tibble
 #' @importFrom utils capture.output
 #' @importFrom sf st_as_sf
 #' @importFrom leaflet leaflet addTiles addPolygons
 #' @importFrom rgeos gIsValid
+#' @importFrom magrittr %>%
 #' @export
 #' @examples
-#' activities <- getActivity(activityid = "https://deims.org/activity/8786fc6d-5d70-495c-b901-42f480182845")
+#' activities <- get_activity_info(activityid = "https://deims.org/activity/8786fc6d-5d70-495c-b901-42f480182845")
 #' map <- leaflet::leaflet(activities) %>% 
 #'  leaflet::addTiles() %>% 
 #'  leaflet::addPolygons()
 #' print(map)
 #' activities
 #'
-### function getActivity
-getActivity <- function(activityid) {
-  require(dplyr)
+### function get_activity_info
+get_activity_info <- function(activityid) {
   q <- "{
         title: .title,
         boundaries: .attributes.geographic.boundaries
@@ -86,9 +86,7 @@ getActivity <- function(activityid) {
       map <- NULL
     }
   } else {
-    message("\n---- The requested page could not be found. Please check again the Activity.iD ----\n")
-    geoActivity <- NULL
-    map <- NULL
+    stop("\n---- Page Not Found. The requested page could not be found. Please check again the Activity.iD ----\n")
   }
   print(map)
   geoActivity

R/getDataset.R → R/get_dataset_info.R

@@ -1,4 +1,4 @@
-#' @title eLTER getDataset function
+#' @title eLTER get_dataset_info function
 #' @description This function allows to obtain the info of dataset provided in
 #' DEIMS-SDR.
 #' @param datasetid A character. It is the DEIMS iD of dataset make from
@@ -12,18 +12,18 @@
 #' @importFrom utils capture.output
 #' @importFrom sf st_as_sf
 #' @importFrom leaflet leaflet addTiles addPolygons
+#' @importFrom magrittr %>%
 #' @export
 #' @examples
-#' tDataset <- getDataset(datasetid = "https://deims.org/dataset/38d604ef-decb-4d67-8ac3-cc843d10d3ef")
+#' tDataset <- get_dataset_info(datasetid = "https://deims.org/dataset/38d604ef-decb-4d67-8ac3-cc843d10d3ef")
 #' map <- leaflet::leaflet(tDataset) %>% 
 #'  leaflet::addTiles() %>% 
 #'  leaflet::addPolygons()
 #' print(map)
 #' tDataset
 #'
-### function getDataset
-getDataset <- function(datasetid) {
-  require(dplyr)
+### function get_dataset_info
+get_dataset_info <- function(datasetid) {
   q <- '{
        title: .title,
        abstract: .attributes.general.abstract,
@@ -105,7 +105,7 @@ getDataset <- function(datasetid) {
         geoDataset_SP <- sf::as_Spatial(
           geoDataset$boundaries
         )
-        geoDataset_valid <- gIsValid(
+        geoDataset_valid <- rgeos::gIsValid(
           geoDataset_SP,
           byid = FALSE,
           reason = TRUE