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ratatouille

Package to fetch data from the RATO database via the ESRI ArcGIS API

https://github.com/inbo/ratatouille

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Repository

Package to fetch data from the RATO database via the ESRI ArcGIS API

Basic Info
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Created about 1 year ago · Last pushed 9 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Codemeta

README.md

ratatouille

R-CMD-check Codecov test coverage <!-- badges: end -->

Rationale

This repository contains the functionality to access the unprocessed data of RATO vzw via an API call to an ESRI ArcGIS instance. Credentials are required to access this data. These credentials are stored as a github secrets under the RATO_USER and RATO_PWD environmental parameters, and can be set locally by editing the .Renviron file.

Set Up your RATO credentials locally

The easiest way to store the required username and password necessary to access the RATO database is by storing them in your .Renviron file. An easy way to edit this file is by using a function from the usethis package.

r install.packages("usethis") usethis::edit_r_environ()

The contents of the file may contain other secrets or settings used by other scripts or packages, but can be edited to have lines like:

RATO_USER = "RATO_INBO"
RATO_PWD = "a super fake password that should be replaced by your real one"

After restarting your R instance you should be able to fetch data from the RATO database without being prompted for your credentials.

Installation

You can install the development version of ratatouille from GitHub with:

``` r

install.packages("pak")

pak::pak("inbo/ratatouille") ```

Example

Once you have your credentials stored, getting raw data from RATO is as easy as:

r library(ratatouille) rato_data <- ratatouille()

The resulting object looks like this (but has many more columns):

r dplyr::slice_sample(rato_data, n = 5) |> dplyr::select(dplyr::all_of(c("Soort", "Materiaal_Vast", "Materiaal_Consumptie", "Laatst_Bewerkt_Datum"))) |> knitr::kable()

| Soort | MateriaalVast | MateriaalConsumptie | LaatstBewerktDatum | |:---|:---|:---|:---| | Bruine rat bak/buis | NA | Broma blok (aantal) = 1; | 2022-02-04 09:27:43 | | Roosters/kleppen | NA | NA | 2023-01-25 11:53:31 | | Bruine rat bak/buis | NA | Difa blok Groot (aantal) = 1; | 2025-01-03 10:27:46 | | Bruine rat bak/buis | NA | Broma blok (aantal) = 1; | 2023-08-17 12:47:00 | | Bruine rat bak/buis | NA | Geen gif bijgevuld (ok) = 1; | 2024-07-05 07:42:22 |

For this example only a few fields are shown because there is the possibility of personal data in other fields.

Species in the dataset

This is raw data, some cleaning will be required. Dutch names and GBIF taxon ids are provided, but these last are often unchecked and may contain errors.

``` r dplyr::count(rato_data, Soort, sort = TRUE)

> Soort n

>

> 1: Bruine rat bak/buis 113511

> 2: Bruine rat 28686

> 3: Muskusrat 19774

> 4: Aziatische hoornaar 7113

> 5: Zwerfkatten 4834

> 6: Roosters/kleppen 4434

> 7: Duiven 4374

> 8: Muizen 1320

> 9: Reuzenberenklauw 1030

> 10: Meetpunt 967

> 11: Lettersierschildpad 879

> 12: Bever 440

> 13: Voederplaats 390

> 14: Mollen 345

> 15: Steenmarter 302

> 16: Kippen 246

> 17: Vistrappen 227

> 18: Canadese Gans 153

> 19: Halsbandparkiet 126

> 20: Japanse Duizendknoop 115

> 21: Andere (soort vermelden): 77

> 22: Ganzenactie 76

> 23: Waterteunisbloem 75

> 24: Nijlgans 66

> 25: Neerhofdier(en) 64

> 26: Reuzenbalsemien 56

> 27: Obstructie waterloop 52

> 28: Parelvederkruid 51

> 29: Konijnen 47

> 30: gedomesticeerde gans 47

> 31: Grote Waternavel 32

> 32: Mantsjoerese wilde rijst 19

> 33: Aziatische hoornaar actie 17

> 34: Grauwe Gans 16

> 35: Sluikstorting 16

> 36: Amerikaanse Nerts 14

> 37: Rivierkreeft 12

> 38: Kippen: 8

> 39: structuurprobleem waterloop 8

> 40: Zwarte rat 7

> 41: Amerikaanse Stierkikker 6

> 42: Aziatische hoornaar: 6

> 43: Watercrassula 6

> 44: Exotische Eekhoorn 5

> 45: Neerhofdier(en): 5

> 46: Brandgans 4

> 47: slecht onderhoud 4

> 48: Leidse Plant 3

> 49: Watersla 3

> 50: Beverrat 2

> 51: Boerengans 2

> 52: Bruine rat: 2

> 53: Andere (soort vermelden) 1

> 54: Andere (soort vermelden): Eend 1

> 55: Andere (soort vermelden): Kraaien 1

> Soort n

```

Owner

  • Name: Research Institute for Nature and Forest (INBO)
  • Login: inbo
  • Kind: organization
  • Location: Belgium

Open source, data and science initiatives of the Research Institute for Nature and Forest (INBO)

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