R/NCRNbirds_Class_def.R

In NCRN/NCRNbirds: Data analysis and visualization for NPS I&M bird monitoring.

#' @title S4 Class Definition for NCRNbirds
#' 
#' @description
#' #' An S4 class that contains the data from bird monitoring at a set of monitoring points. This will typcially be a single park, but it could be any group of plots, including part of a park or a group of parks. 
#' @slot ParkCode A short code to designate the park (or group of plots), typically an NPS 4 letter code. Stored as a length 1 character vector. 
#' @slot ShortName A short name for the park. Stored as a length 1 character vector. 
#' @slot LongName  A long, formal name for the park. Stored as a length 1 character vector. 
#' @slot Network The code for the Inventory & Montoirng network (or other network) the park belongs to. Stored as a length 1 character vector. 
#' @slot VisitNumber A \code{numeric} vector of length 1. The number of visits that is typically made to each point. This serves as the default number of visits for other functions.
#' @slot Bands A \code{data.frame} with metadata for the distance bands used during monitoring. Includes a name, min distance and max distance for each band.
#' @slot Intervals A \code{data.frame} with mmeatdata for the time intervals used during monitroing. Includes a name start time in minutes and end time in minutes for each interval.
#' @slot Points A \code{data.frame} with metadata for the monitoring points, such as names and lat/long.
#' @slot Visits A \code{data.frame} with metadata for each sampling visit.
#' @slot Birds  A \code{data.frame} with the bird monitoring data. Each row is an observation of a number of individuals of a particular species at a particular point, visit, time interval and distance band.
#' @slot Species A \code{data.frame} with metadata about the bird species, including AOU (American Ornithological Union) Code, 
#' Latin and common names, as well as the "Taxonomic Order" which indicates the order the species should be in to make lists familiar to birders.
#' @slot Guilds A \code{data.frame} which indicates which birds species are in which guild to allow calculation of the BCI.
#' @exportClass NCRNbirds

setClass(Class="NCRNbirds",
         slots=c(
           ParkCode="character",
           ShortName="character",
           LongName="character",
           
           Network="character",
           
           VisitNumber="numeric",
           Bands="data.frame",
           Intervals="data.frame",
           
           Points="data.frame",
           Visits="data.frame",
           Birds="data.frame",
           Species='data.frame',
           Guilds='data.frame'
           ),
         
         prototype=list(ParkCode=character(),
                        ShortName=character(),
                        LongName=character(),
                        Network=character(),
                        
                        VisitNumber=numeric(),
                        Bands=data.frame(),
                        Intervals=data.frame(),
                        
                        Points=data.frame(),
                        Visits=data.frame(),
                        Birds=data.frame(),
                        Species=data.frame(),
                        Guilds=data.frame()
        )
)