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Minor edits & updates to vignettes #221
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* Minor text edits to taxonomic + temporal advanced vignettes
* Add `search_all(fields)` example in quick start vignette
* Update Rmd.orig files, rerender vignettes
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@daxkellie
daxkellie committed Dec 14, 2023
1 parent 41b1842 commit 8950f33
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236 changes: 132 additions & 104 deletions vignettes/choosing_an_atlas.Rmd
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125 changes: 63 additions & 62 deletions vignettes/download_data.Rmd
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
title: "Download data"
author: "Martin Westgate & Dax Kellie"
date: '2023-11-07'
date: '2023-12-14'
output:
rmarkdown::html_vignette
vignette: >
Expand Down Expand Up @@ -39,7 +39,7 @@ atlas_counts()
## # A tibble: 1 × 1
## count
## <int>
## 1 131963195
## 1 132342396
```

In addition to the filter arguments, it has an optional `group_by` argument,
Expand All @@ -56,16 +56,16 @@ galah_call() |>
## # A tibble: 11 × 2
## kingdom count
## <chr> <int>
## 1 Animalia 101176164
## 2 Plantae 26026027
## 3 Fungi 2285235
## 4 Chromista 1020325
## 5 Protista 352282
## 6 Bacteria 113165
## 7 Eukaryota 8821
## 8 Protozoa 4716
## 9 Archaea 4120
## 10 Virus 2306
## 1 Animalia 101442503
## 2 Plantae 26136825
## 3 Fungi 2293753
## 4 Chromista 1021828
## 5 Protista 352983
## 6 Bacteria 113118
## 7 Eukaryota 8826
## 8 Protozoa 4765
## 9 Archaea 4119
## 10 Virus 2307
## 11 Viroid 103
```

Expand All @@ -89,14 +89,14 @@ species |> head()

```
## # A tibble: 6 × 10
## kingdom phylum class order family genus species author species_guid vernacular_name
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 Animalia Chordata Mammalia Roden… Murid… Pseu… Pseudo… (Goul… https://bio… Delicate Mouse
## 2 Animalia Chordata Mammalia Roden… Murid… Mese… Mesemb… (J.E.… https://bio… Black-footed T…
## 3 Animalia Chordata Mammalia Roden… Murid… Zyzo… Zyzomy… (Thom… https://bio… Common Rock-rat
## 4 Animalia Chordata Mammalia Roden… Murid… Pseu… Pseudo… (Wait… https://bio… Sandy Inland M…
## 5 Animalia Chordata Mammalia Roden… Murid… Melo… Melomy… (Rams… https://bio… Grassland Melo…
## 6 Animalia Chordata Mammalia Roden… Murid… Noto… Notomy… Thoma… https://bio… Spinifex Hoppi…
## kingdom phylum class order family genus species author species_guid vernacular_name
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 Animalia Chordata Mammalia Rodentia Muridae Pseudomys Pseudomys delicatulus (Gould, 1842) https://biodiv… Delicate Mouse
## 2 Animalia Chordata Mammalia Rodentia Muridae Mesembriomys Mesembriomys gouldii (J.E. Gray, 1843) https://biodiv… Black-footed T…
## 3 Animalia Chordata Mammalia Rodentia Muridae Zyzomys Zyzomys argurus (Thomas, 1889) https://biodiv… Common Rock-rat
## 4 Animalia Chordata Mammalia Rodentia Muridae Pseudomys Pseudomys hermannsburgensis (Waite, 1896) https://biodiv… Sandy Inland M…
## 5 Animalia Chordata Mammalia Rodentia Muridae Melomys Melomys burtoni (Ramsay, 1887) https://biodiv… Grassland Melo…
## 6 Animalia Chordata Mammalia Rodentia Muridae Notomys Notomys alexis Thomas, 1922 https://biodiv… Spinifex Hoppi…
```


Expand Down Expand Up @@ -129,6 +129,7 @@ occ <- galah_call() |>
## Retrying in 1 seconds.
## Retrying in 2 seconds.
## Retrying in 4 seconds.
## Retrying in 8 seconds.
```

```r
Expand All @@ -137,16 +138,15 @@ occ |> head()

```
## # A tibble: 6 × 9
## recordID scientificName taxonConceptID decimalLatitude decimalLongitude
## <chr> <chr> <chr> <dbl> <dbl>
## 1 0000a928-d756-42eb-8058-6f… Eolophus rose… https://biodi… -35.6 149.
## 2 0001bc78-d2e9-48aa-8b9d-d6… Eolophus rose… https://biodi… -35.2 149.
## 3 0002064f-08ea-425b-97c5-26… Eolophus rose… https://biodi… -35.3 149.
## 4 00022dd2-9f85-4802-b837-7f… Eolophus rose… https://biodi… -35.3 149.
## 5 0002cc35-8d5a-4d20-8012-12… Eolophus rose… https://biodi… -35.3 149.
## 6 00030a8c-082f-44f0-898a-ad… Eolophus rose… https://biodi… -35.3 149.
## # ℹ 4 more variables: eventDate <dttm>, occurrenceStatus <chr>, dataResourceName <chr>,
## # institutionID <lgl>
## recordID scientificName taxonConceptID decimalLatitude decimalLongitude eventDate occurrenceStatus dataResourceName
## <chr> <chr> <chr> <dbl> <dbl> <dttm> <chr> <chr>
## 1 0000a928-d756-42… Eolophus rose… https://biodi… -35.6 149. 2017-04-19 09:11:00 PRESENT eBird Australia
## 2 0001bc78-d2e9-48… Eolophus rose… https://biodi… -35.2 149. 2019-08-13 15:13:00 PRESENT eBird Australia
## 3 0002064f-08ea-42… Eolophus rose… https://biodi… -35.3 149. 2014-03-16 06:48:00 PRESENT eBird Australia
## 4 00022dd2-9f85-48… Eolophus rose… https://biodi… -35.3 149. 2022-05-08 08:20:00 PRESENT eBird Australia
## 5 0002cc35-8d5a-4d… Eolophus rose… https://biodi… -35.3 149. 2015-11-01 08:00:00 PRESENT eBird Australia
## 6 00030a8c-082f-44… Eolophus rose… https://biodi… -35.3 149. 2022-01-06 11:47:00 PRESENT eBird Australia
## # ℹ 1 more variable: institutionID <lgl>
```


Expand All @@ -168,6 +168,8 @@ media_data <- galah_call() |>

```
## Retrying in 1 seconds.
## Retrying in 2 seconds.
## Retrying in 4 seconds.
```

```r
Expand All @@ -176,17 +178,16 @@ media_data |> head()

```
## # A tibble: 6 × 19
## media_id recordID scientificName taxonConceptID decimalLatitude decimalLongitude
## <chr> <chr> <chr> <chr> <dbl> <dbl>
## 1 ff8322d0-f44c-47a… 003a192… Eolophus rose… https://biodi… -35.3 149.
## 2 c66fc819-7022-44f… 015ee7c… Eolophus rose… https://biodi… -35.4 149.
## 3 fe6d7b94-9e61-4ac… 05e86b7… Eolophus rose… https://biodi… -35.4 149.
## 4 2f4d32c0-a084-4bb… 063bb0f… Eolophus rose… https://biodi… -35.6 149.
## 5 73407414-0707-429… 063bb0f… Eolophus rose… https://biodi… -35.6 149.
## 6 89171c49-5a64-423… 063bb0f… Eolophus rose… https://biodi… -35.6 149.
## # ℹ 13 more variables: eventDate <dttm>, occurrenceStatus <chr>, dataResourceName <chr>,
## # multimedia <chr>, images <chr>, videos <lgl>, sounds <lgl>, creator <chr>,
## # license <chr>, mimetype <chr>, width <int>, height <int>, image_url <chr>
## media_id recordID scientificName taxonConceptID decimalLatitude decimalLongitude eventDate occurrenceStatus dataResourceName
## <chr> <chr> <chr> <chr> <dbl> <dbl> <dttm> <chr> <chr>
## 1 ff8322d… 003a192… Eolophus rose… https://biodi… -35.3 149. 2020-09-12 06:11:00 PRESENT iNaturalist Aus…
## 2 c66fc81… 015ee7c… Eolophus rose… https://biodi… -35.4 149. 2020-08-09 05:11:00 PRESENT iNaturalist Aus…
## 3 fe6d7b9… 05e86b7… Eolophus rose… https://biodi… -35.4 149. 2020-11-13 22:29:00 PRESENT NatureMapr
## 4 2f4d32c… 063bb0f… Eolophus rose… https://biodi… -35.6 149. 2020-08-04 01:50:00 PRESENT iNaturalist Aus…
## 5 7340741… 063bb0f… Eolophus rose… https://biodi… -35.6 149. 2020-08-04 01:50:00 PRESENT iNaturalist Aus…
## 6 89171c4… 063bb0f… Eolophus rose… https://biodi… -35.6 149. 2020-08-04 01:50:00 PRESENT iNaturalist Aus…
## # ℹ 10 more variables: multimedia <chr>, images <chr>, videos <lgl>, sounds <lgl>, creator <chr>, license <chr>, mimetype <chr>,
## # width <int>, height <int>, image_url <chr>
```

To actually download the media files to your computer, use [collect_media()].
Expand All @@ -207,27 +208,27 @@ galah_call() |>

```
## # A tibble: 19 × 4
## name rank parent_taxon_concept_id taxon_concept_id
## <chr> <chr> <chr> <chr>
## 1 Chordata phylum <NA> https://biodive…
## 2 Cephalochordata subphylum https://biodiversity.org.au/afd/taxa/065f1da4… https://biodive…
## 3 Tunicata subphylum https://biodiversity.org.au/afd/taxa/065f1da4… https://biodive…
## 4 Appendicularia class https://biodiversity.org.au/afd/taxa/1c20ed62… https://biodive…
## 5 Ascidiacea class https://biodiversity.org.au/afd/taxa/1c20ed62… https://biodive…
## 6 Thaliacea class https://biodiversity.org.au/afd/taxa/1c20ed62… https://biodive…
## 7 Vertebrata subphylum https://biodiversity.org.au/afd/taxa/065f1da4… https://biodive…
## 8 Agnatha informal https://biodiversity.org.au/afd/taxa/5d6076b1… https://biodive…
## 9 Myxini informal https://biodiversity.org.au/afd/taxa/66db22c8… https://biodive…
## 10 Petromyzontida informal https://biodiversity.org.au/afd/taxa/66db22c8… https://biodive…
## 11 Gnathostomata informal https://biodiversity.org.au/afd/taxa/5d6076b1… https://biodive…
## 12 Amphibia class https://biodiversity.org.au/afd/taxa/ef5515fd… https://biodive…
## 13 Aves class https://biodiversity.org.au/afd/taxa/ef5515fd… https://biodive…
## 14 Mammalia class https://biodiversity.org.au/afd/taxa/ef5515fd… https://biodive…
## 15 Pisces informal https://biodiversity.org.au/afd/taxa/ef5515fd… https://biodive…
## 16 Actinopterygii class https://biodiversity.org.au/afd/taxa/e22efeb4… https://biodive…
## 17 Chondrichthyes class https://biodiversity.org.au/afd/taxa/e22efeb4… https://biodive…
## 18 Sarcopterygii class https://biodiversity.org.au/afd/taxa/e22efeb4… https://biodive…
## 19 Reptilia class https://biodiversity.org.au/afd/taxa/ef5515fd… https://biodive…
## name rank parent_taxon_concept_id taxon_concept_id
## <chr> <chr> <chr> <chr>
## 1 Chordata phylum <NA> https://biodiversity.org.au/afd/…
## 2 Cephalochordata subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodiversity.org.au/afd/…
## 3 Tunicata subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodiversity.org.au/afd/…
## 4 Appendicularia class https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodiversity.org.au/afd/…
## 5 Ascidiacea class https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodiversity.org.au/afd/…
## 6 Thaliacea class https://biodiversity.org.au/afd/taxa/1c20ed62-d918-4e42-b625-8b86d533cc51 https://biodiversity.org.au/afd/…
## 7 Vertebrata subphylum https://biodiversity.org.au/afd/taxa/065f1da4-53cd-40b8-a396-80fa5c74dedd https://biodiversity.org.au/afd/…
## 8 Agnatha informal https://biodiversity.org.au/afd/taxa/5d6076b1-b7c7-487f-9d61-0fea0111cc7e https://biodiversity.org.au/afd/…
## 9 Myxini informal https://biodiversity.org.au/afd/taxa/66db22c8-891d-4b16-a1a2-b66feaeaa3e0 https://biodiversity.org.au/afd/…
## 10 Petromyzontida informal https://biodiversity.org.au/afd/taxa/66db22c8-891d-4b16-a1a2-b66feaeaa3e0 https://biodiversity.org.au/afd/…
## 11 Gnathostomata informal https://biodiversity.org.au/afd/taxa/5d6076b1-b7c7-487f-9d61-0fea0111cc7e https://biodiversity.org.au/afd/…
## 12 Amphibia class https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/…
## 13 Aves class https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/…
## 14 Mammalia class https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/…
## 15 Pisces informal https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/…
## 16 Actinopterygii class https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodiversity.org.au/afd/…
## 17 Chondrichthyes class https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodiversity.org.au/afd/…
## 18 Sarcopterygii class https://biodiversity.org.au/afd/taxa/e22efeb4-2cb5-4250-8d71-61c48bdaa051 https://biodiversity.org.au/afd/…
## 19 Reptilia class https://biodiversity.org.au/afd/taxa/ef5515fd-a0a2-4e16-b61a-0f19f8900f76 https://biodiversity.org.au/afd/…
```

# Configuring `galah`
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