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Update package names of INBO package #171

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Jul 1, 2020
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Update package names of INBO package #171

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49b1b28
add forrescalc to inbo software
ElsLommelen Jun 29, 2020
5c1ee4e
replace 'inborutils' with 'inbodb' in tutorials on databases
ElsLommelen Jun 29, 2020
43aad41
add description inbodb to inbo software
ElsLommelen Jun 29, 2020
93af023
Update content/articles/inbo_software/index.md
ElsLommelen Jun 30, 2020
e5ce034
Update content/articles/inbo_software/index.Rmd
ElsLommelen Jun 30, 2020
736c1ad
Update content/articles/inbo_software/index.Rmd
ElsLommelen Jun 30, 2020
fa3404f
delete Rmd file of inbo_software
ElsLommelen Jun 30, 2020
ff98912
re-insert accidentally moved package
ElsLommelen Jun 30, 2020
c56149e
move inbodb to new topic 'retrieve data: general' and generalise on d…
ElsLommelen Jun 30, 2020
310d673
Update content/articles/inbo_software/index.md
ElsLommelen Jul 1, 2020
3bc0999
remove spaces in table
ElsLommelen Jul 1, 2020
0cfe04d
remove superfluous line
ElsLommelen Jul 1, 2020
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154 changes: 0 additions & 154 deletions content/articles/inbo_software/index.Rmd
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41 changes: 26 additions & 15 deletions content/articles/inbo_software/index.md
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Expand Up @@ -28,21 +28,21 @@ website**, if available. When there is no documentation website, often
one or more **vignettes** are available within the package, describing
the package’s purpose and demonstrating its use.

The following table gives a **quick
overview**:

| Research stage | Related INBO packages |
| :---------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Study design | [grts](https://github.com/ThierryO/grts) |
| Retrieve data: environmental | [wateRinfo](https://ropensci.github.io/wateRinfo/), [pydov](https://pydov.readthedocs.io/), [watina](https://inbo.github.io/watina) |
| Retrieve data: biological | [pyinaturalist](https://github.com/inbo/pyinaturalist), [uvabits](https://inbo.github.io/uvabits/), [etn](https://inbo.github.io/etn/), [n2khab](https://inbo.github.io/n2khab) |
| Store data | [git2rdata](https://inbo.github.io/git2rdata/) |
| Validate data | [pywhip](https://inbo.github.io/pywhip/) |
| Analyze data: graphs | [inboggvegan](https://github.com/inbo/inboggvegan) |
| Analyze data: models | [inlatools](https://inlatools.netlify.com/), [multimput](https://github.com/inbo/multimput), [effectclass](https://effectclass.netlify.com), [niche\_vlaanderen](https://inbo.github.io/niche_vlaanderen/), [gwloggeR](https://dov-vlaanderen.github.io/groundwater-logger-validation/gwloggeR/docs/articles/gwloggeR.html) |
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@ElsLommelen can you re-insert this part? It was added in #160 but only in the md file.

| Analyze data: indices | [LSVI](https://inbo.github.io/LSVI) |
| Publish | [INBOmd](https://inbomd.netlify.com/articles/introduction.html), [INBOtheme](https://inbo.github.io/INBOtheme/) |
| Miscellaneous (mixed content) | [inborutils](https://inbo.github.io/inborutils/) |
The following table gives a **quick overview**:
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I suggest to delete in the md file the many generated extra spaces (cf. my earlier comment: use the one from the Rmd file)


| Research stage | Related INBO packages |
| :------------- | :-------------------- |
| Study design | [grts](https://github.com/ThierryO/grts) |
| Retrieve data: general | [inbodb](https://inbo.github.io/inbodb) |
| Retrieve data: environmental | [wateRinfo](https://ropensci.github.io/wateRinfo/), [pydov](https://pydov.readthedocs.io/), [watina](https://inbo.github.io/watina) |
| Retrieve data: biological | [pyinaturalist](https://github.com/inbo/pyinaturalist), [uvabits](https://inbo.github.io/uvabits/), [etn](https://inbo.github.io/etn/), [n2khab](https://inbo.github.io/n2khab), [forrescalc](https://github.com/inbo/forrescalc) |
| Store data | [git2rdata](https://inbo.github.io/git2rdata/) |
| Validate data | [pywhip](https://inbo.github.io/pywhip/) |
| Analyze data: graphs | [inboggvegan](https://github.com/inbo/inboggvegan) |
| Analyze data: models | [inlatools](https://inlatools.netlify.com/), [multimput](https://github.com/inbo/multimput), [effectclass](https://effectclass.netlify.com), [niche\_vlaanderen](https://inbo.github.io/niche_vlaanderen/), [gwloggeR](https://dov-vlaanderen.github.io/groundwater-logger-validation/gwloggeR/docs/articles/gwloggeR.html) |
| Analyze data: indices | [LSVI](https://inbo.github.io/LSVI) |
| Publish | [INBOmd](https://inbomd.netlify.com/articles/introduction.html), [INBOtheme](https://inbo.github.io/INBOtheme/) |
| Miscellaneous (mixed content) | [inborutils](https://inbo.github.io/inborutils/) |

## Study design

Expand All @@ -52,6 +52,12 @@ overview**:

## Retrieve data

### General

- **R package \[inbodb\]((<https://inbo.github.io/inbodb>)**: connect
to and retrieve data from databases on the INBO server, with
dedicated functions to query some of these databases.

### Environmental data

- **R package [wateRinfo](https://ropensci.github.io/wateRinfo/)**:
Expand Down Expand Up @@ -100,6 +106,11 @@ overview**:
GRTSmaster\_habitats)* and preprocessing functions, supporting
reproducible and transparent analyses on Flemish Natura 2000 (*n2k*)
habitats (*hab*) and regionally important biotopes (RIBs).
- **R package [forrescalc](https://github.com/inbo/forrescalc)**:
provides aggregated values on dendrometry, regeneration and
vegetation of the Flemish forest reserve monitoring network, and
functions to derive these data starting from individual tree
measurements in Fieldmap.

## Store data

Expand Down
12 changes: 6 additions & 6 deletions content/tutorials/r_database_access/index.Rmd
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Expand Up @@ -28,20 +28,20 @@ library(tidyverse)

To create a database connection, different approaches are available as explained in the next section:

1. Use the dedicated `connect_inbo_dbase` function in the inborutils package
1. Use the dedicated `connect_inbo_dbase` function in the inbodb package
2. Setup the required parameters yourself
3. Reuse existing registered connections on your computer

### Inborutils function
### Inbodb function

To support the connection to INBO databases, a dedicated function is available in the [inborutils package](https://inbo.github.io/inborutils/index.html), called `connect_inbo_dbase`. The function provides support to connect to INBO databases and uses the _Connections pane_ in the Rstudio interface:
To support the connection to INBO databases, a dedicated function is available in the [inbodb package](https://inbo.github.io/inbodb), called `connect_inbo_dbase`. The function provides support to connect to INBO databases and uses the _Connections pane_ in the Rstudio interface:

![odbc-connecties](./database-R/connections_pane.png)

To use the `connect_inbo_dbase` function, make sure to install the `inborutils` package, following the [installation instructions](https://inbo.github.io/inborutils/#installation). After a successfull installation, load the library and create a database connection:
To use the `connect_inbo_dbase` function, make sure to install the `inbodb` package, following the [installation instructions](https://inbo.github.io/inbodb/#installation). After a successfull installation, load the library and create a database connection:

```{r connect-fn-default}
library(inborutils)
library(inbodb)
my_connection <- connect_inbo_dbase("D0021_00_userFlora")
```

Expand All @@ -51,7 +51,7 @@ __Remark for Linux users__: When working in Linux, this setup (using `Trusted co

### Setting up the connection yourself

In case you want to setup the connection yourself (e.g. errors using inborutils),
In case you want to setup the connection yourself (e.g. errors using inbodb),
you can do so by providing the necessary parameters:


Expand Down
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