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Copy file name to clipboardExpand all lines: vignettes/Using_rerddap.Rmd
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servers()
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```
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The list of <spanstyle="color:red">ERDDAP</span> servers is based on the list maintained at the [Awesome ERDDAP site](https://irishmarineinstitute.github.io/awesome-erddap).
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The list of <spanstyle="color:red">ERDDAP</span> servers is based on the list maintained at the *Awesome ERDDAP* site compiled by the Irish Marine Institute.
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The second way to find and obtain the desired data is to use functions in `rerddap`. The basic steps are:
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Note that in `tabledap()` character strings usually must be passed as "double-quoted", as seen in the example with the scientific name. A full `tabledap()` request to retrieve 'latitude', 'longitude', 'time', 'scientific_name', and 'subsample_count' with these constraints would be:
The functions in `rerddap` work with any <spanstyle="color:red">ERDDAP</span> server as long as the base URL is provided. A list of advertised <spanstyle="color:red">ERDDAP</span> servers is provided at https://irishmarineinstitute.github.io/awesome-erddap and the `rerddap` function `servers()` will download this list.
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The functions in `rerddap` work with any <spanstyle="color:red">ERDDAP</span> server as long as the base URL is provided. A list of advertised <spanstyle="color:red">ERDDAP</span> servers is provided by the Irish Marine Institute's *Awesome ERDDAP* web page, and the `rerddap` function `servers()` will download this list.
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Given a base <spanstyle="color:red">ERDDAP</span> URL, the function `ed_search()` will search the server for the given search terms. The default <spanstyle="color:red">ERDDAP</span> server is https://upwell.pfeg.noaa.gov/erddap/. Alternately, the function `global_search()` will search a list of <spanstyle="color:red">ERDDAP</span> servers for the given search terms. The function `ed_datasets()` lists the datasets available from the given <spanstyle="color:red">ERDDAP</span> server.
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### Temperature at 70m in the north Pacific from the SODA model output
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This is an example of an extract from a 4-D dataset (results from the "Simple Ocean Data Assimilation (SODA)" model - see https://www.atmos.umd.edu/~ocean/), and illustrate the case where the z-coordinate does not have the default name "altitude". Water temperature at 70m depth is extracted for the North Pacific Ocean.
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This is an example of an extract from a 4-D dataset (results from the "Simple Ocean Data Assimilation (SODA)" model - see https://www2.atmos.umd.edu/~ocean/), and illustrate the case where the z-coordinate does not have the default name "altitude". Water temperature at 70m depth is extracted for the North Pacific Ocean.
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```{r eval = FALSE, echo = TRUE}
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### Irish Marine Institute {#hourly}
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The Irish Marine Institute has an <spanstyle="color:red">ERDDAP</span> server at https://erddap.marine.ie/erddap. Among other datasets, they have hourly output from a model of the North Altantic ocean, with a variety of ocean related parameters, see https://erddap.marine.ie/erddap/griddap/IMI_NEATL.html. To obtain the latest sea surface salinity for the domain of the model:
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The Irish Marine Institute has an <spanstyle="color:red">ERDDAP</span> server at https://erddap.marine.ie/erddap. Among other datasets, they have hourly output from a model of the North Altantic ocean, with a variety of ocean related parameters, see the dataset *IMI_NEATL*. To obtain the latest sea surface salinity for the domain of the model:
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```{r NAtlSSS, eval = FALSE, echo = TRUE}
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require("rerddap")
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## California Current System Integrated Ecosystem Assessment (CCSIEA)
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The primary goals of the CCIEA are to better understand the web of interactions that drive patterns and trends of components within the California Current ecosystem, and forecast how changing environmental conditions and management actions affect the status of these components. The conceptual model of the social-ecological system of the California Current illustrates how humans and their social systems are inextricably linked to these marine, coastal, and upland environments (see https://www.integratedecosystemassessment.noaa.gov/regions/california-current-region/index.html).
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The primary goals of the CCIEA are to better understand the web of interactions that drive patterns and trends of components within the California Current ecosystem, and forecast how changing environmental conditions and management actions affect the status of these components. The conceptual model of the social-ecological system of the California Current illustrates how humans and their social systems are inextricably linked to these marine, coastal, and upland environments (see https://www.integratedecosystemassessment.noaa.gov/regions/california-current/projects).
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The over 300 indices developed for the CCSIEA are available through `rerddap`. Here an index of coho abundance in California is compared with the February value of an index of the strength and location of the North Pacific High, developed in "The North Pacific High and wintertime pre-conditioning of California current productivity" by Schroeder et al. (Geophys. Res. Lett., 40, 541–546).
Copy file name to clipboardExpand all lines: vignettes/rerddap.Rmd
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---
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title: rerddap introduction
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author: Scott Chamberlain
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date: "2022-02-05"
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date: "2022-09-30"
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{rerddap introduction}
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## ERDDAP servers
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You can get a data.frame of ERDDAP servers using the function `servers()`. The list of ERDDAP servers is drawn from the [Awesome ERDDAP site](https://irishmarineinstitute.github.io/awesome-erddap). If you know of more ERDDAP servers, follow the instructions on that page to add the server.
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You can get a data.frame of ERDDAP servers using the function `servers()`. The list of ERDDAP servers is drawn from the *Awesome ERDDAP* page maintained by the Irish Marine Institute . If you know of more ERDDAP servers, follow the instructions on that page to add the server.
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## Install
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Stable version from CRAN
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```r{cran_install, eval = FALSE, echo = TRUE}
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```r
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install.packages("rerddap")
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```
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Or, the development version from GitHub
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```r{remote_install, eval = FALSE, echo = TRUE}
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```r
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remotes::install_github("ropensci/rerddap")
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```
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```r{load, eval = FALSE, echo = TRUE}
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```r
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library("rerddap")
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```
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First, you likely want to search for data, specify either `griddadp` or `tabledap`
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```r{ed_search_table, eval = FALSE, echo = TRUE}
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```r
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ed_search(query='size', which="table")
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#> # A tibble: 42 × 2
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#> title dataset_id
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#> <chr> <chr>
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#> 1 CCE Prey Size and Hard Part Size Regressions mmtdPreyS…
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#> 2 CCE Teleost Prey Size and Hard Part Size Measurements mmtdTeleo…
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#> 3 CalCOFI Larvae Sizes erdCalCOF…
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#> 4 Seabird Prey Size cciea_B_L…
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#> 5 CCE Non-Teleost Prey Size and Hard Part Size Measurements mmtdNonTe…
Since both `griddap()` and `tabledap()` give back data.frame's, it's easy to do downstream manipulation. For example, we can use `dplyr` to filter, summarize, group, and sort:
Copy file name to clipboardExpand all lines: vignettes/rerddap.Rmd.og
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## ERDDAP servers
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You can get a data.frame of ERDDAP servers using the function `servers()`. The list of ERDDAP servers is drawn from the [Awesome ERDDAP site](https://irishmarineinstitute.github.io/awesome-erddap). If you know of more ERDDAP servers, follow the instructions on that page to add the server.
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You can get a data.frame of ERDDAP servers using the function `servers()`. The list of ERDDAP servers is drawn from the *Awesome ERDDAP* page maintained by the Irish Marine Institute . If you know of more ERDDAP servers, follow the instructions on that page to add the server.
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