Getting Started with PAMvieweR • PAMvieweR

library(PAMvieweR)

New Occurrence R6 Class

First things first. You’ll need to set up a connection to nefscdb1, which is the database (db) where the PAGROUP schema lives (colloquially known as Makara).

# db connection
db_conn <- ROracle::dbConnect(ROracle::Oracle(), 
                              dbname = 'NEFSC_USERS',
                              username = '[uid]', 
                              password = '[pwd]')

Once you’ve established a db connection, you can get started by generating an object with an Occurrence R6 class. For those familiar with python, the syntax of R6 classes should feel familiar. For those more acquainted with R, R6 classes will take some getting used to. A good resource on R6 classes can be found here.

In order to initialize an object with an Occurrence R6 class, we must provide 2 arguments: 1) a db connection and 2) the name of data table / view we’re interested in pulling data from. For example,

# new Occurrence object
huwh_occ <- Occurrence$new(connection = db_conn, table = 'V_PRJCT_DPLYMNT_DTCTN_O')

A method is provided to filter the db query by species using an SQL where clause. To do this, implement the following:

# only interested in HUWHs
huwh_occ$where_species(76)

Or you could chain the whole thing together for succinctness,

# illustration of chaining
huwh_occ <- Occurrence$new(connection = db_conn, table = 'V_PRJCT_DPLYMNT_DTCTN_O')$where_species(76)

Now we can execute the query to pull the data from the db,

# get data
huwh_occ$get_data()
huwh_occ

Wrappers around dplyr functions are also provided, so that the resulting data can be further modified. As an example,

# only interested in HUWHs present at the Nantucket Sound site
huwh_occ$filter(SITE_NAME == 'NANTUCKETSOUND')$group(ACOUSTIC_PRESENCE)$aggregate(n = dplyr::n())