##### R Code for 'Obtaining References' #####

# https://compadre-db.org/Education/article/obtaining-references

# Compiled on 28 May 2021


##### Preliminaries #####

# Use the command following commands if you haven't already
# downloaded the packages:

# install.packages("Rcompadre")
# Alternatively, see https://jonesor.github.io/Rcompadre/index.html for instructions to download the Rcompadre package
# install.packages("rcrossref")


# load packages
library(Rcompadre)
library(rcrossref)



##### Load COMPADRE and COMADRE databases #####

# Download and load either the COMPADRE or COMADRE database from the website
# In this example, we use the COMADRE database

# COMPADRE: https://compadre-db.org/Data/Compadre
# COMADRE: https://compadre-db.org/Data/Comadre

# load dataset
comadre <- load("COMPADRE_v.6.21.1.0.RData")

## Then convert to an S4 CompadreDB object to work with Rcompadre package
comadre <- as_cdb(comadre) 


# OR, you may also download the COMPADRE or COMADRE objects using the Rcompadre package if you have Rcompadre installed:
# COMPADRE 
compadre <- cdb_fetch("compadre")

# COMADRE
comadre <- cdb_fetch("comadre")



##### Obtaining references #####

## Examine the number of matrices for species in the Canidae family (wolves, foxes, and similar animals) in the COMADRE database.
## Then create a subset of the database containing only data for animals in Canidae
comadre$MatrixID[which(comadre$Family == "Canidae")] 
comadre_subset <- comadre[which(comadre$Family == "Canidae")]

## Examine some of the fields in COMPADRE and COMADRE metadata for finding references associated with matrix population models 
comadre_subset$Authors 
comadre_subset$YearPublication
comadre_subset$DOI_ISBN

## number of unique references
length(unique(comadre_subset$DOI_ISBN))

## Use the rcrossref package to create a references list based on our data subset
rcrossref::cr_cn(unique(comadre_subset$DOI_ISBN), format = "text", style = "apa" )