refactor: turn data frames into tibbles for readability via attr()

DESCRIPTION

@@ -37,8 +37,7 @@ Imports:
 Suggests:
     testthat (>= 3.0.0),
     mapview,
-    dplyr,
-    tibble
+    dplyr
 Remotes: 
     eblondel/ows4R
 RoxygenNote: 7.2.0

R/eurobis_occurrences.R

@@ -259,5 +259,7 @@ eurobis_sf_df_handler <- function(sf_df){
 
   sf::st_crs(sf_df) <- 4326
 
+  try({ attr(sf_df, "class") <- c("sf", "tbl_df", "tbl", "data.frame") })
+
   return(sf_df)
 }

README.Rmd

@@ -1,5 +1,6 @@
 ---
 output: github_document
+df_print: "tibble"
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -54,8 +55,7 @@ A basic example is:
 library(eurobis)
 
 # Get one single dataset
-dataset <- eurobis_occurrences_basic(dasid = 8045)
-dplyr::glimpse(dataset)
+eurobis_occurrences_basic(dasid = 8045)
 ```
 
 For detailed information run:
@@ -67,16 +67,15 @@ help(eurobis_occurrences)
 ## Query by traits
 Use the `functional_group` argument:
 
-```{r func_groups}
+```{r func_groups, eval = FALSE}
 # Get one single dataset
-dataset <- eurobis_occurrences_basic(dasid = 8045, functional_groups = "angiosperms")
-dplyr::glimpse(dataset)
+eurobis_occurrences_basic(dasid = 8045, functional_groups = "angiosperms")
 ```
 
 See the full list of queriable traits in the exported dataset `species_traits`:
 
 ```{r traits}
-tibble::as_tibble(species_traits)
+species_traits
 ```
 
 

README.md

@@ -15,24 +15,24 @@ The `eurobis` R package allows you to download data from EurOBIS.
 
 You can query on:
 
--   **Dataset**: provide the Integrated Marine Information System
+  - **Dataset**: provide the Integrated Marine Information System
     ([IMIS](https://www.vliz.be/en/integrated-marine-information-system))
     unique identifier for datasets
     [DasID](https://www.vliz.be/imis?page=webservices).
--   **Taxon**: use a scientific name (e.g. the sea turtle *Caretta
+  - **Taxon**: use a scientific name (e.g. the sea turtle *Caretta
     caretta*) or a [WoRMS
     AphiaID](https://www.marinespecies.org/about.php#what_is_aphia)
     (e.g. [137205](https://www.marinespecies.org/aphia.php?p=taxdetails&id=137205))
--   **Traits**: get all occurrences that are benthos. Or zooplankton. Or
+  - **Traits**: get all occurrences that are benthos. Or zooplankton. Or
     both. Powered by [WoRMS](https://www.marinespecies.org/).
--   **Time**: just give start and end dates.
--   **Geographically**: it allows to query on more than 300 records from
+  - **Time**: just give start and end dates.
+  - **Geographically**: it allows to query on more than 300 records from
     the [Marine Regions
     Gazetteer](https://marineregions.org/gazetteer.php) by giving the
     [MRGID](https://marineregions.org/mrgid.php). Or just pass the area
     of your interest as a polygon written in as [Well Known
     Text](https://en.wikipedia.org/wiki/Well-known_text_representation_of_geometry)
--   Other important classifications as [IUCN Red
+  - Other important classifications as [IUCN Red
     List](https://www.iucnredlist.org/en), [MSDF
     Indicators](https://msfd.eu/knowseas/guidelines/3-INDICATORS-Guideline.pdf)
     or [Habitats
@@ -61,25 +61,35 @@ A basic example is:
 library(eurobis)
 
 # Get one single dataset
-dataset <- eurobis_occurrences_basic(dasid = 8045)
+eurobis_occurrences_basic(dasid = 8045)
 #> Loading ISO 19139 XML schemas...
 #> Loading ISO 19115 codelists...
+#> Loading IANA mime types...
+#> No encoding supplied: defaulting to UTF-8.
 #> ✔ Downloading layer: EMODnet EurOBIS Basic Occurrence Data
 #> ℹ The Basic Occurrence Data download provides you data for the following 8 essential terms: datasetid, datecollected, decimallongitude, decimallatitude, coordinateuncertaintyinmeters, scientificname, aphiaid, scientificnameaccepted. For more information, please consult: https://www.emodnet-biology.eu/emodnet-data-format.
-dplyr::glimpse(dataset)
-#> Rows: 52
-#> Columns: 11
-#> $ gml_id                        <chr> "eurobis-obisenv_basic.fid-632d47d4_1860…
-#> $ id                            <int> 28840495, 28841810, 28837086, 28866685, …
-#> $ datasetid                     <chr> "http://www.emodnet-biology.eu/data-cata…
-#> $ datecollected                 <dttm> 2020-03-03 01:00:00, 2020-05-05 02:00:0…
-#> $ decimallongitude              <dbl> -8.73914, -8.73948, -8.73902, -8.73948, …
-#> $ decimallatitude               <dbl> 40.61804, 40.61899, 40.61773, 40.61899, …
-#> $ coordinateuncertaintyinmeters <dbl> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5…
-#> $ scientificname                <chr> "Zostera marina", "Zostera marina", "Zos…
-#> $ aphiaid                       <chr> "http://marinespecies.org/aphia.php?p=ta…
-#> $ scientificnameaccepted        <chr> "Zostera subg. Zostera marina", "Zostera…
-#> $ geometry                      <POINT [°]> POINT (-8.73914 40.61804), POINT (…
+#> Simple feature collection with 52 features and 10 fields
+#> Geometry type: POINT
+#> Dimension:     XY
+#> Bounding box:  xmin: -8.73964 ymin: 40.61773 xmax: -8.73902 ymax: 40.61899
+#> CRS:           EPSG:4326
+#> # A tibble: 52 × 11
+#>    gml_id         id datas…¹ datecollected       decim…² decim…³ coord…⁴ scien…⁵
+#>  * <fct>       <int> <chr>   <dttm>                <dbl>   <dbl>   <dbl> <chr>  
+#>  1 eurobis-o… 3.68e7 https:… 2020-05-05 00:00:00   -8.74    40.6       5 Zoster…
+#>  2 eurobis-o… 3.68e7 https:… 2019-12-13 00:00:00   -8.74    40.6       5 Zoster…
+#>  3 eurobis-o… 3.68e7 https:… 2020-03-03 00:00:00   -8.74    40.6       5 Zoster…
+#>  4 eurobis-o… 3.68e7 https:… 2019-12-13 00:00:00   -8.74    40.6       5 Zoster…
+#>  5 eurobis-o… 3.68e7 https:… 2020-08-10 00:00:00   -8.74    40.6       5 Zoster…
+#>  6 eurobis-o… 3.68e7 https:… 2020-08-10 00:00:00   -8.74    40.6       5 Zoster…
+#>  7 eurobis-o… 3.68e7 https:… 2020-05-05 00:00:00   -8.74    40.6       5 Zoster…
+#>  8 eurobis-o… 3.68e7 https:… 2020-05-05 00:00:00   -8.74    40.6       5 Zoster…
+#>  9 eurobis-o… 3.68e7 https:… 2020-03-03 00:00:00   -8.74    40.6       5 Zoster…
+#> 10 eurobis-o… 3.68e7 https:… 2020-05-05 00:00:00   -8.74    40.6       5 Zoster…
+#> # … with 42 more rows, 3 more variables: aphiaid <chr>,
+#> #   scientificnameaccepted <chr>, geometry <POINT [°]>, and abbreviated
+#> #   variable names ¹​datasetid, ²​decimallongitude, ³​decimallatitude,
+#> #   ⁴​coordinateuncertaintyinmeters, ⁵​scientificname
 ```
 
 For detailed information run:
@@ -94,46 +104,113 @@ Use the `functional_group` argument:
 
 ``` r
 # Get one single dataset
-dataset <- eurobis_occurrences_basic(dasid = 8045, functional_groups = "angiosperms")
-#> ✔ Downloading layer: EMODnet EurOBIS Basic Occurrence Data
-#> ℹ The Basic Occurrence Data download provides you data for the following 8 essential terms: datasetid, datecollected, decimallongitude, decimallatitude, coordinateuncertaintyinmeters, scientificname, aphiaid, scientificnameaccepted. For more information, please consult: https://www.emodnet-biology.eu/emodnet-data-format.
-#> Warning in eurobis_occurrences(type = "basic", ...): There are 0 occurrences in
-#> EurOBIS for this query at the moment
-dplyr::glimpse(dataset)
-#> Rows: 0
-#> Columns: 11
-#> $ gml_id                        <chr> 
-#> $ id                            <int> 
-#> $ datasetid                     <chr> 
-#> $ datecollected                 <dttm> 
-#> $ decimallongitude              <dbl> 
-#> $ decimallatitude               <dbl> 
-#> $ coordinateuncertaintyinmeters <dbl> 
-#> $ scientificname                <chr> 
-#> $ aphiaid                       <chr> 
-#> $ scientificnameaccepted        <chr> 
-#> $ geometry                      <GEOMETRY [°]>
+eurobis_occurrences_basic(dasid = 8045, functional_groups = "angiosperms")
 ```
 
 See the full list of queriable traits in the exported dataset
 `species_traits`:
 
 ``` r
-tibble::as_tibble(species_traits)
-#> # A tibble: 32 × 4
-#>    category                      group            selection     selectid     
-#>    <chr>                         <chr>            <chr>         <chr>        
-#>  1 Species group                 Functional group algae         Algae        
-#>  2 Species group                 Functional group angiosperms   Angiosperms  
-#>  3 Species group                 Functional group benthos       Benthos      
-#>  4 Species group                 Functional group birds         Birds        
-#>  5 Species group                 Functional group mammals       Mammals      
-#>  6 Species group                 Functional group phytoplankton phytoplankton
-#>  7 Species group                 Functional group pisces        pisces       
-#>  8 Species group                 Functional group reptiles      Reptiles     
-#>  9 Species group                 Functional group zooplankton   zooplankton  
-#> 10 Species importance to society CITES Annex      I             28_280_0     
-#> # … with 22 more rows
+species_traits
+#>                         category                    group
+#> 1                  Species group         Functional group
+#> 2                  Species group         Functional group
+#> 3                  Species group         Functional group
+#> 4                  Species group         Functional group
+#> 5                  Species group         Functional group
+#> 6                  Species group         Functional group
+#> 7                  Species group         Functional group
+#> 8                  Species group         Functional group
+#> 9                  Species group         Functional group
+#> 10 Species importance to society              CITES Annex
+#> 11 Species importance to society              CITES Annex
+#> 12 Species importance to society              CITES Annex
+#> 13 Species importance to society Habitats Directive Annex
+#> 14 Species importance to society Habitats Directive Annex
+#> 15 Species importance to society   IUCN Red List Category
+#> 16 Species importance to society   IUCN Red List Category
+#> 17 Species importance to society   IUCN Red List Category
+#> 18 Species importance to society          MSFD indicators
+#> 19 Species importance to society          MSFD indicators
+#> 20 Species importance to society          MSFD indicators
+#> 21 Species importance to society          MSFD indicators
+#> 22 Species importance to society          MSFD indicators
+#> 23 Species importance to society          MSFD indicators
+#> 24 Species importance to society          MSFD indicators
+#> 25 Species importance to society          MSFD indicators
+#> 26 Species importance to society          MSFD indicators
+#> 27 Species importance to society          MSFD indicators
+#> 28 Species importance to society          MSFD indicators
+#> 29 Species importance to society          MSFD indicators
+#> 30 Species importance to society          MSFD indicators
+#> 31 Species importance to society          MSFD indicators
+#> 32 Species importance to society          MSFD indicators
+#>                                                             selection
+#> 1                                                               algae
+#> 2                                                         angiosperms
+#> 3                                                             benthos
+#> 4                                                               birds
+#> 5                                                             mammals
+#> 6                                                       phytoplankton
+#> 7                                                              pisces
+#> 8                                                            reptiles
+#> 9                                                         zooplankton
+#> 10                                                                  I
+#> 11                                                                 II
+#> 12                                                                III
+#> 13                                                                 II
+#> 14                                                                 IV
+#> 15                                                     data deficient
+#> 16                                                      least concern
+#> 17                                                    near threatened
+#> 18                                      Black Sea proposed indicators
+#> 19                                HELCOM core biodiversity indicators
+#> 20                   Mediterranean proposed indicators - Adriatic Sea
+#> 21           Mediterranean proposed indicators - Aegean-Levantine Sea
+#> 22                     Mediterranean proposed indicators - Ionian Sea
+#> 23              Mediterranean proposed indicators - Mediterranean Sea
+#> 24          Mediterranean proposed indicators - Western Mediterranean
+#> 25    OSPAR candidate indicators: Bay of Biscay and the Iberian Coast
+#> 26                            OSPAR candidate indicators: Celtic Seas
+#> 27 OSPAR candidate indicators: Greater North Sea including outside EU
+#> 28                              OSPAR candidate indicators: North Sea
+#> 29           OSPAR common indicators: Bay of Biscay and Iberian Coast
+#> 30                               OSPAR common indicators: Celtic Seas
+#> 31                         OSPAR common indicators: Greater North Sea
+#> 32    OSPAR common indicators: Greater North Sea including outside EU
+#>         selectid
+#> 1          Algae
+#> 2    Angiosperms
+#> 3        Benthos
+#> 4          Birds
+#> 5        Mammals
+#> 6  phytoplankton
+#> 7         pisces
+#> 8       Reptiles
+#> 9    zooplankton
+#> 10      28_280_0
+#> 11      28_281_0
+#> 12      28_282_0
+#> 13      26_269_0
+#> 14      26_271_0
+#> 15         1_8_3
+#> 16         1_7_3
+#> 17         1_6_3
+#> 18     23_285_41
+#> 19     23_285_29
+#> 20     23_285_31
+#> 21     23_285_32
+#> 22     23_285_33
+#> 23     23_285_34
+#> 24     23_285_30
+#> 25     23_285_35
+#> 26     23_285_36
+#> 27     23_285_37
+#> 28     23_285_38
+#> 29     23_285_44
+#> 30     23_285_45
+#> 31     23_285_46
+#> 32     23_285_40
 ```
 
 ## Query by location
@@ -206,21 +283,21 @@ www.emodnet-biology.eu/toolbox, consulted on yyyy-mm-dd.
 Regarding the citation of the individual datasets, the following
 guidelines should be taken into account:
 
--   If any individual data source of EurOBIS constitutes a significant
+  - If any individual data source of EurOBIS constitutes a significant
     proportion of the downloaded and used records (e.g. more than 10% of
     the data is derived from a single source), the individual data
     source should also be cited.
--   If any individual data source of EurOBIS constitutes a substantial
+  - If any individual data source of EurOBIS constitutes a substantial
     proportion of the downloaded and used records (e.g. more than 25% of
     the data is derived from a single source or the data is essential to
     arrive at the conclusion of the analysis), the manager or custodian
     of this data set should be contacted.
--   In any case, it may be useful to contact the data custodian
+  - In any case, it may be useful to contact the data custodian
     directly. The data custodian might have additional data available
     that may strengthen the analysis or he/she might be able to provide
     additional helpful information that may not be apparent from the
     provided metadata.
--   The data may not be redistributed without the permission of the
+  - The data may not be redistributed without the permission of the
     appropriate data owners. If data are extracted from the EMODnet Data
     Portal for redistribution, please contact us at <[email protected]>.