+
+
+
+
+
+
+
+
{ReLTER} is an R package that: provides access to DEIMS-SDR), 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).
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);
elaborate the information of single site or merge info from national network sites or entire International LTER (ILTER) in order to provide maps, figures, graphs etc (see e.g. get_network_sites, produce_site_map or produce_site_parameters_pie functions);
interact with the ODSEurope managed by members of the Geo-harmonizer project starting with the dataset shared by DEIMS-SDR (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.
To cite {ReLTER} please use: Alessandro Oggioni, Micha Silver & Paolo Tagliolato. (2021). oggioniale/ReLTER: ReLTER v1.0.0 (1.0.0). Zenodo. https://doi.org/10.5281/zenodo.5576813
or:
+@software{alessandro_oggioni_2021_5576813,
+ author = {Alessandro Oggioni and Micha Silver and Paolo Tagliolato},
+ title = {oggioniale/ReLTER: ReLTER v1.0.0},
+ month = nov,
+ year = 2021,
+ publisher = {Zenodo},
+ version = {1.0.0},
+ doi = {10.5281/zenodo.5576813},
+ url = {https://doi.org/10.5281/zenodo.5576813}
+}Visit the {ReLTER} website at oggioniale.github.io/ReLTER/ for further documentation, examples, and installation of the package.
You can install the development version of {ReLTER} from GitHub with:
install.packages("devtools")
+devtools::install_github("oggioniale/ReLTER")Some examples of the possible capabilities of this library appear below. These examples demonstrate interaction with the DEIMS-SDR API.
+The get_site_info function, using category “Boundaries”, creates a Leaflet map overlayed with the boundaries of the site (e.g. Lake Maggiore) using the site geographical boundaries provided by DEIMS-SDR. This function returns an sf object.
library(dplyr)
+siteBoundaries <- ReLTER::get_site_info(
+ deimsid = 'https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe',
+ category = "Boundaries"
+)
+#> Found 1 records... Imported 1 records. Simplifying...
+#> Found 1 records... Imported 1 records. Simplifying...
+leaflet::leaflet(siteBoundaries) %>%
+ leaflet::addTiles() %>%
+ leaflet::addPolygons()
+
+#siteBoundariesThe get_network_parameters function retrieves a list of parameters collected by sites that are part of a given network (e.g. LTER-Italy). Information is gathered from those sites that are part of the specified network id, on DEIMS-SDR. The function returns a tibble.
library(dplyr)
+invisible(
+ utils::capture.output(
+ listParams <- ReLTER::get_network_parameters(
+ networkDEIMSID = 'https://deims.org/network/7fef6b73-e5cb-4cd2-b438-ed32eb1504b3'
+ )
+ )
+)
+knitr::kable(listParams[1:10, ] %>% dplyr::rows_insert(tibble(parameterLabel = "...", parameterUri = "...")))| parameterLabel | +parameterUri | +
|---|---|
| atmospheric parameter | +http://vocabs.lter-europe.net/EnvThes/20937 | +
| ecosystem parameter | +http://vocabs.lter-europe.net/EnvThes/20939 | +
| conductivity | +http://vocabs.lter-europe.net/EnvThes/22089 | +
| dissolved nutrient | +http://vocabs.lter-europe.net/EnvThes/22107 | +
| dissolved organic carbon in water | +http://vocabs.lter-europe.net/EnvThes/10307 | +
| ecosystem structure | +http://vocabs.lter-europe.net/EnvThes/21475 | +
| inorganic nutrient content | +http://vocabs.lter-europe.net/EnvThes/22137 | +
| percent carbon | +http://vocabs.lter-europe.net/EnvThes/22181 | +
| percent organic carbon | +http://vocabs.lter-europe.net/EnvThes/22183 | +
| total carbon | +http://vocabs.lter-europe.net/EnvThes/22296 | +
| … | +… | +
The get_dataset_info function retrieves a table with information about specific datasets shared through DEIMS-SDR.
+tDataset <- ReLTER::get_dataset_info(datasetid = "https://deims.org/dataset/38d604ef-decb-4d67-8ac3-cc843d10d3ef")
+#> Found 1 records... Imported 1 records. Simplifying...
+leaflet::leaflet(tDataset) %>%
+ leaflet::addTiles() %>%
+ leaflet::addPolygons()
+
+tDataset
+#> Simple feature collection with 1 feature and 33 fields
+#> Geometry type: POLYGON
+#> Dimension: XY
+#> Bounding box: xmin: 11.88721 ymin: 43.20518 xmax: 15.86426 ymax: 45.91294
+#> Geodetic CRS: WGS 84
+#> # A tibble: 1 × 34
+#> title abstract keywords uri type dateRange.from dateRange.to relatedSite contacts.corres… contacts.creator contacts.metada… observationPara… observationSpec… dataPolicy doi onlineLocation
+#> * <chr> <chr> <list> <chr> <chr> <chr> <lgl> <list> <list> <list> <lgl> <list> <list> <list> <chr> <list>
+#> 1 LTER N… The present … <df [5 ×… https… data… 1965-01-01 NA <df [1 × 4… <df [1 × 4]> <df [14 × 4]> NA <df [1 × 2]> <df [3 × 2]> <df [1 × … 10.3… <df [1 × 3]>
+#> # … with 18 more variables: legal.accessUse <list>, legal.rights <lgl>, legal.legalAct <lgl>, legal.citation <lgl>, method.instrumentation <lgl>, method.qualityAssurance <lgl>, method.methodUrl <list>,
+#> # method.methodDescription <list>, method.samplingTimeUnit.label <chr>, method.samplingTimeUnit.uri <lgl>, method.spatialDesign.label <chr>, method.spatialDesign.uri <lgl>,
+#> # method.spatialScale.label <chr>, method.spatialScale.uri <lgl>, method.temporalResolution.label <chr>, method.temporalResolution.uri <lgl>, boundaries <POLYGON [°]>, boundariesDescription <chr>The get_site_info function, using category = “RelateRes”, provides a list of related resources associated with a site within DEIMS-SDR.
+tSiteRelatedResources <- ReLTER::get_site_info(
+ deimsid = "https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe",
+ category = "RelateRes"
+)
+#> Found 1 records... Imported 1 records. Simplifying...
+#> Found 1 records... Imported 1 records. Simplifying...
+tSiteRelatedResources$relatedResources[[1]]
+#> relatedResourcesTitle relatedResourcesChanged uri
+#> 1 Biovolume of Phytoplankton in Lake Maggiore site code IT_SI001137_within the period 1981 - 2010 2021-08-25T16:38:25+0200 https://deims.org/dataset/d9e94776-e7a8-11e2-a655-005056ab003f
+#> 2 Atmospheric deposition in Pallanza, Lake Maggiore watershed, 1980-2018 2020-12-13T20:06:48+0100 https://deims.org/dataset/0ce46362-0aab-482a-b1f0-a444a5dada39
+#> 3 Phytoplankton_Biomass_Lake Maggiore_Ghiffa_station-1984-2018 2020-12-16T10:46:15+0100 https://deims.org/dataset/0ab8425a-d574-4575-8ba9-5275c607b0c5
+#> 4 Water chemistry of Lake Maggiore, Ghiffa station, 1988-2018 2021-11-03T06:10:14+0100 https://deims.org/dataset/69564188-89de-4879-ad88-4aa97c1d005d
+#> 5 Transparency (Secchi depth) of Lake Maggiore, Ghiffa station, 1988-2018 2020-12-13T20:10:34+0100 https://deims.org/dataset/e538c743-2149-49e3-9025-14a04ea7c90d
+#> 6 Chlorophyll a_Lake_Maggiore_Ghiffa_Station-1984-2018 2021-01-10T21:48:49+0100 https://deims.org/dataset/c857c8e2-48aa-4dcd-a7fb-e089bd4c5c4e
+#> 7 Water discharge of River Ticino, Lake Maggiore outlet, 1988-2018 2021-07-21T12:35:07+0200 https://deims.org/dataset/fb3a8fec-0c1f-4c3a-81d5-364c7e6078c4The produce_site_parameters_waffle function provides a grouping of parameters, as measured within a site, in a “waffle chart” representation.
+ReLTER::produce_site_parameters_waffle(
+ deimsid = "https://deims.org/f30007c4-8a6e-4f11-ab87-569db54638fe"
+)
+#> Found 1 records... Imported 1 records. Simplifying...
+#> Found 1 records... Imported 1 records. Simplifying...
+
+#> # A tibble: 11 × 4
+#> parameterGroups n freq label
+#> <chr> <int> <dbl> <chr>
+#> 1 agricultural parameter 1 0.0105 1.1%
+#> 2 atmospheric parameter 14 0.147 14.7%
+#> 3 biological parameter 8 0.0842 8.4%
+#> 4 chemical parameter 24 0.253 25.3%
+#> 5 ecosystem parameter 23 0.242 24.2%
+#> 6 genetic parameter 2 0.0211 2.1%
+#> 7 landscape parameter 4 0.0421 4.2%
+#> 8 physical parameter 1 0.0105 1.1%
+#> 9 remote sensing parameter 1 0.0105 1.1%
+#> 10 soil parameter 1 0.0105 1.1%
+#> 11 water parameter 16 0.168 16.8%The get_site_ODS function retrieves datasets from OpenDataScience, and crops to the boundary of the specified eLTER site.
+siteNDVI <- ReLTER::get_site_ODS(
+ deimsid = "https://deims.org/d0a8da18-0881-4ebe-bccf-bc4cb4e25701",
+ dataset = "ndvi_summer"
+)
+#> Found 1 records... Imported 1 records. Simplifying...
+#> Found 1 records... Imported 1 records. Simplifying...
+siteBoundary <- ReLTER::get_site_info(
+ deimsid = "https://deims.org/d0a8da18-0881-4ebe-bccf-bc4cb4e25701",
+ category = "Boundaries"
+)
+#> Found 1 records... Imported 1 records. Simplifying...
+#> Found 1 records... Imported 1 records. Simplifying...
+
+tmap::tmap_mode("view")
+pal <- RColorBrewer::brewer.pal("RdYlGn", n = 5)
+tmap::tm_basemap(leaflet::providers$OpenStreetMap.Mapnik) +
+ tmap::tm_shape(siteNDVI, raster.downsample = TRUE) +
+ tmap::tm_raster(palette = pal, alpha = 0.7) +
+ tmap::tm_shape(siteBoundary) +
+ tmap::tm_borders("black")
+
+Alessandro Oggioni https://orcid.org/0000-0002-7997-219X (CNR, Institute for Electromagnetic Sensing of the Environment - IREA)
+ + +Micha Silver https://orcid.org/0000-0002-1128-1325 (Ben Gurion University - BGU)
+Paolo Tagliolato https:://orcid.org/0000-0002-0261-313X (CNR, Institute for Electromagnetic Sensing of the Environment - IREA)
+For a exhaustive list of contributors please visit authors page.
+
+
+
+
+
+
+
+
diff --git a/README.md b/README.md
index 22241bbf..4d7f1634 100644
--- a/README.md
+++ b/README.md
@@ -1,48 +1,94 @@
----
-title: ReLTER
-output: github_document
-always_allow_html: true
----
+ReLTER
+================
-
-
-
+
[](https://doi.org/10.5281/zenodo.5576813)
-[](https://github.com/oggioniale/ReLTER)
+[](https://github.com/oggioniale/ReLTER)
[](https://github.com/oggioniale/ReLTER)
[](https://github.com/oggioniale/ReLTER/commits/main)
-[](https://www.repostatus.org/#active)
+[](https://www.repostatus.org/#active)
+
+
+
+
-The `{ReLTER}` package allows interacting with online datasets such as [DEIMS-SDR](https://deims.org/), implemented by eLTER Research Infrastructure (RI), and the [ODSEurope](maps.opendatascience.eu) managed by members of the [Geo-harmonizer](https://opendatascience.eu/geoharmonizer-project/) project. The package contains functions to acquire, crop and visualize datasets and information shared by those archives.
+`{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](https://deims.org/) (see
+ e.g. [get_site_info
+ function](https://oggioniale.github.io/ReLTER/reference/get_site_info.html));
+
+- elaborate the information of single site or merge info from national
+ network sites or entire International LTER (ILTER) in order to
+ provide maps, figures, graphs etc (see
+ e.g. [get_network_sites](https://oggioniale.github.io/ReLTER/reference/get_network_sites.html),
+ [produce_site_map](https://oggioniale.github.io/ReLTER/reference/produce_site_map.html)
+ or
+ [produce_site_parameters_pie](https://oggioniale.github.io/ReLTER/reference/produce_site_parameters_pie.html)
+ functions);
+
+- 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);
+
+- improve the quality of the dataset (see
+ e.g. [get_id_worms](https://oggioniale.github.io/ReLTER/reference/get_id_worms.html)).
+
+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.
+
## :notebook_with_decorative_cover: Citation
-To cite `{ReLTER}` please use:
-Alessandro Oggioni. (2021). oggioniale/ReLTER: v0.2.0 (0.2.0). Zenodo. https://doi.org/10.5281/zenodo.5576813
+To cite `{ReLTER}` please use: Alessandro Oggioni, Micha Silver & Paolo
+Tagliolato. (2021). oggioniale/ReLTER: ReLTER v1.0.0 (1.0.0). Zenodo.
+
+
+``` r
#siteBoundaries
```
---------------------------------
+------------------------------------------------------------------------
#### *get_network_parameters()*
-The *get_network_parameters* function retrieves a list of parameters collected by sites that are part of a given network (e.g. LTER-Italy). Information is gathered from those sites that are part of the specified network id, on [DEIMS-SDR](https://deims.org/). The function returns a `tibble`.
-
+The *get_network_parameters* function retrieves a list of parameters
+collected by sites that are part of a given network (e.g. LTER-Italy).
+Information is gathered from those sites that are part of the specified
+network id, on [DEIMS-SDR](https://deims.org/). The function returns a
+`tibble`.
-```r
+``` r
library(dplyr)
invisible(
utils::capture.output(
@@ -107,41 +164,38 @@ invisible(
knitr::kable(listParams[1:10, ] %>% dplyr::rows_insert(tibble(parameterLabel = "...", parameterUri = "...")))
```
-
-
-|parameterLabel |parameterUri |
-|:---------------------------------|:-------------------------------------------|
-|atmospheric parameter |http://vocabs.lter-europe.net/EnvThes/20937 |
-|ecosystem parameter |http://vocabs.lter-europe.net/EnvThes/20939 |
-|conductivity |http://vocabs.lter-europe.net/EnvThes/22089 |
-|dissolved nutrient |http://vocabs.lter-europe.net/EnvThes/22107 |
-|dissolved organic carbon in water |http://vocabs.lter-europe.net/EnvThes/10307 |
-|ecosystem structure |http://vocabs.lter-europe.net/EnvThes/21475 |
-|inorganic nutrient content |http://vocabs.lter-europe.net/EnvThes/22137 |
-|percent carbon |http://vocabs.lter-europe.net/EnvThes/22181 |
-|percent organic carbon |http://vocabs.lter-europe.net/EnvThes/22183 |
-|total carbon |http://vocabs.lter-europe.net/EnvThes/22296 |
-|... |... |
-
---------------------------------
+| parameterLabel | parameterUri |
+|:----------------------------------|:----------------------------------------------|
+| atmospheric parameter | 
+
+``` r
tDataset
#> Simple feature collection with 1 feature and 33 fields
#> Geometry type: POLYGON
@@ -149,113 +203,94 @@ tDataset
#> Bounding box: xmin: 11.88721 ymin: 43.20518 xmax: 15.86426 ymax: 45.91294
#> Geodetic CRS: WGS 84
#> # A tibble: 1 × 34
-#> title abstract keywords uri type dateRange.from dateRange.to relatedSite
-#> * 
-
-```
-#> # A tibble: 11 × 4
-#> parameterGroups n freq label
-#>
+
+ #> # A tibble: 11 × 4
+ #> parameterGroups n freq label
+ #> 
+
## :woman_technologist: Persons involved :man_technologist:
-Alessandro Oggioni 
-{height="80"}
+
diff --git a/codemeta.json b/codemeta.json
index 3d61cfbd..72376668 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -5,12 +5,12 @@
],
"@type": "SoftwareSourceCode",
"identifier": "ReLTER",
- "description": "ReLTER is an R package that: provides access to DEIMS-SDR\n (https://deims.org/), allows interact with software implemented by eLTER\n Research Infrastructure (RI) and improves the data/information shared by\n them.\n ReLTER is a R package devoted to access, interact and improve the\n information and the data shared by Long Term Ecological Research (LTER)\n network. This package is born within eLTER H2020 major project that will\n help advance the development of European Long-Term Ecosystem Research\n Infrastructures (eLTER RI - https://elter-ri.eu).\n The ReLTER package functions in particular allow to:\n - retrive the information about entities (e.g. sites, datasets, and\n activities) shared by DEIMS-SDR (see e.g. get_site_info function);\n - elaborate the information of single site or merge info from national\n network sites or entire International LTER (ILTER) in order to provide\n maps, figures, graphs etc (see e.g. get_network_sites, produce_site_map\n or produce_site_parameters_pie functions);\n - use the site informations for download data from other platforms (see\n e.g. get_site_ODS function);\n - improve the quality of the dataset (see e.g. get_id_worms).\n Functions currently implemented are derived from the discussion of the\n needs declared by eLTER users community.\n The ReLTER package shall definitely follow the progress of eLTER-RI\n infrastructure and evolving with the improvements and develop of\n new tools.",
+ "description": "ReLTER is an R package that: provides access to DEIMS-SDR\n (https://deims.org/), allows interact with software implemented by eLTER\n Research Infrastructure (RI) and improves the data/information shared by\n them.\n ReLTER is a R package devoted to access, interact and improve the\n information and the data shared by Long Term Ecological Research (LTER)\n network. This package is born within eLTER H2020 major project that will\n help advance the development of European Long-Term Ecosystem Research\n Infrastructures (eLTER RI - https://elter-ri.eu).\n The ReLTER package functions in particular allow to:\n - retrive the information about entities (e.g. sites, datasets, and\n activities) shared by DEIMS-SDR (see e.g. get_site_info function);\n - interact with the [ODSEurope](maps.opendatascience.eu) managed by members\n of the [Geo-harmonizer](https://opendatascience.eu/geoharmonizer-project/)\n project starting with the dataset shared by [DEIMS-SDR](https://deims.org/)\n (see e.g. [get_site_ODS](https://oggioniale.github.io/ReLTER/reference/get_site_ODS.html)\n function);\n - use the site informations for download data from other platforms (see\n e.g. get_site_ODS function);\n - improve the quality of the dataset (see e.g. get_id_worms).\n Functions currently implemented are derived from the discussion of the\n needs declared by eLTER users community.\n The ReLTER package shall definitely follow the progress of eLTER-RI\n infrastructure and evolving with the improvements and develop of\n new tools.",
"name": "ReLTER: An interface to the eLTER for the R statistical programming environment",
"codeRepository": "https://github.com/oggioniale/ReLTER",
"issueTracker": "https://github.com/oggioniale/ReLTER/issues",
"license": "https://spdx.org/licenses/GPL-3.0",
- "version": "0.2.0",
+ "version": "1.0.0",
"programmingLanguage": {
"@type": "ComputerLanguage",
"name": "R",
@@ -472,7 +472,8 @@
}
],
"releaseNotes": "https://github.com/oggioniale/ReLTER/blob/master/NEWS.md",
- "fileSize": "6135.385KB",
+ "fileSize": "6685.62KB",
"readme": "https://github.com/oggioniale/ReLTER/blob/main/README.md",
- "developmentStatus": "https://www.repostatus.org/#active"
+ "developmentStatus": "https://www.repostatus.org/#active",
+ "citation": []
}
diff --git a/docs/articles/ReLTER.html b/docs/articles/ReLTER.html
index c2b229a7..26a73db9 100644
--- a/docs/articles/ReLTER.html
+++ b/docs/articles/ReLTER.html
@@ -125,11 +125,18 @@ To cite ReLTER please use: …
+To cite ReLTER please use: Alessandro Oggioni, Micha Silver & Paolo Tagliolato. (2021). oggioniale/ReLTER: ReLTER v1.0.0 (1.0.0). Zenodo. https://doi.org/10.5281/zenodo.5576813
or:
-@software{
-...
-}@software{alessandro_oggioni_2021_5576813,
+ author = {Alessandro Oggioni and Micha Silver and Paolo Tagliolato},
+ title = {oggioniale/ReLTER: ReLTER v1.0.0},
+ month = nov,
+ year = 2021,
+ publisher = {Zenodo},
+ version = {1.0.0},
+ doi = {10.5281/zenodo.5576813},
+ url = {https://doi.org/10.5281/zenodo.5576813}
+}To cite ReLTER please use: …
+To cite ReLTER please use: Alessandro Oggioni, Micha Silver & Paolo Tagliolato. (2021). oggioniale/ReLTER: ReLTER v1.0.0 (1.0.0). Zenodo. https://doi.org/10.5281/zenodo.5576813
or:
-...@software{alessandro_oggioni_2021_5576813,
+ author = {Alessandro Oggioni and Micha Silver and Paolo Tagliolato},
+ title = {oggioniale/ReLTER: ReLTER v1.0.0},
+ month = nov,
+ year = 2021,
+ publisher = {Zenodo},
+ version = {1.0.0},
+ doi = {10.5281/zenodo.5576813},
+ url = {https://doi.org/10.5281/zenodo.5576813}
+}