https://github.com/ropensci/rfishbase
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README.Rmd
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output: github_document
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# rfishbase <img src="man/figures/logo.svg" align="right" alt="" width="120" />
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Welcome to `rfishbase 4`. This is the fourth rewrite of the original `rfishbase` package described in [Boettiger et al. (2012)](https://doi.org/10.1111/j.1095-8649.2012.03464.x).
- `rfishbase 1.0` relied on parsing of XML pages served directly from Fishbase.org.
- `rfishbase 2.0` relied on calls to a ruby-based API, `fishbaseapi`, that provided access to SQL snapshots of about 20 of the more popular tables in FishBase or SeaLifeBase.
- `rfishbase 3.0` side-stepped the API by making queries which directly downloaded compressed csv tables from a static web host. This substantially improved performance a reliability, particularly for large queries. The release largely remained backwards compatible with 2.0, and added more tables.
- `rfishbase 4.0` extends the static model and interface. Static tables are distributed in parquet and accessed through a provenance-based identifier. While old functions are retained, a new interface is introduced to provide easy access to all fishbase tables.
We welcome any feedback, issues or questions that users may encounter through our issues tracker on GitHub: <https://github.com/ropensci/rfishbase/issues>
```{r include=FALSE}
knitr::opts_chunk$set(warning=FALSE, comment=NA)
options("rfishbase_local_db" = FALSE)
```
## Installation
```{r message=FALSE, warning=FALSE, results="hide", eval=FALSE}
remotes::install_github("ropensci/rfishbase")
```
```{r message=FALSE, warning=FALSE, results="hide"}
library("rfishbase")
library("dplyr") # convenient but not required
```
## Getting started
## Generic table interface
All fishbase tables can be accessed by name using the `fb_tbl()` function:
```{r}
fb_tbl("ecosystem")
```
You can see all the tables using `fb_tables()` to see a list of all the table names (specify `sealifebase` if desired). Careful, there are a lot of them! The fishbase databases have grown a lot in the decades, and were not intended to be used directly by most end-users, so you may have considerable work to determine what's what. Keep in mind that many variables can be estimated in different ways (e.g. trophic level), and thus may report different values in different tables. Also note that species is name (or SpecCode) is not always the primary key for a table -- many tables are specific to stocks or even individual samples, and some tables are reference lists that are not species focused at all, but meant to be joined to other tables (`faoareas`, etc). Compare tables against what you see on fishbase.org, or ask on our issues forum for advice!
```{r}
fish <- c("Oreochromis niloticus", "Salmo trutta")
fb_tbl("species") %>%
mutate(sci_name = paste(Genus, Species)) %>%
filter(sci_name %in% fish) %>%
select(sci_name, FBname, Length)
```
## SeaLifeBase
SeaLifeBase.org is maintained by the same organization and largely parallels the database structure of Fishbase. As such, almost all `rfishbase` functions can instead be instructed to address the
```{r}
fb_tbl("species", "sealifebase")
```
## Versions and importing all tables
By default, tables are downloaded the first time they are used. `rfishbase` defaults to download the latest available snapshot; be aware that the most recent snapshot may be months behind the latest data on fishbase.org. Check available releases:
```{r}
available_releases()
```
## Low-memory environments
If you have very limited RAM (e.g. <= 1 GB available) it may be helpful to use `fishbase` tables in remote form by setting `collect = FALSE`. This allows the tables to remain on disk, while the user is still able to use almost all `dplyr` functions (see the `dbplyr` vignette). Once the table is appropriately subset, the user will need to call `dplyr::collect()` to use generic non-dplyr functions, such as plotting commands.
```{r}
fb_tbl("occurrence")
```
## Local copy
Set the option "rfishbase_local_db" = TRUE to create a local copy, otherwise will use a remote copy.
Local copy will get better performance after initial import, but may experience conflicts when
`duckdb` is upgraded or when multiple sessions attempt to access the directory. Remove the default
storage directory (given by `db_dir()`) after upgrading duckdb if using a local copy.
```{r}
options("rfishbase_local_db" = TRUE)
db_disconnect() # close previous remote connection
conn <- fb_conn()
conn
```
Users can trigger a one-time download of all fishbase tables (or a list of desired tables) using `fb_import()`. This will ensure later use of any function can operate smoothly even when no internet connection is available. Any table already downloaded will not be re-downloaded. (Note: `fb_import()` also returns a remote duckdb database connection to the tables, for users who prefer to work with the remote data objects.)
```{r}
fb_import()
```
```{r include=FALSE}
db_disconnect(conn)
```
## Interactive RStudio pane
RStudio users can also browse all fishbase tables interactively in the RStudio connection browser by using the function `fisbase_pane()`. Note that this function will first download a complete set of the fishbase tables.
## Backwards compatibility
`rfishbase` 4.0 tries to maintain as much backwards compatibility as possible with rfishbase 3.0. Because parquet preserves native data types, some encoded types may differ from earlier versions. As before, these are not always the native type -- e.g. fishbase encodes some boolean (logical TRUE/FALSE) values as integer (-1, 0) or character types. Use `as.logical()` to coerce into the appropriate type in that case.
Toggling between fishbase and sealifebase servers using an environmental variable, `FISHBASE_API`, is now deprecated.
Note that fishbase will store downloaded files by hash in the app directory, given by `db_dir()`. The default location can be set by configuring the desired path in the environmental variable, `FISHBASE_HOME`.
-----------
Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
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