## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setupDarwin, include=FALSE, eval = Sys.info()[["sysname"]] == "Darwin"----
# Prefer cairo-png for pkgdown on macOS when available, but fall back quietly
# when XQuartz/Cairo is not installed.
png_probe <- tempfile(fileext = ".png")
can_use_cairo_png <- isTRUE(tryCatch(
  {
    grDevices::png(filename = png_probe, type = "cairo-png")
    grDevices::dev.off()
    TRUE
  },
  error = function(...) FALSE,
  warning = function(...) FALSE
))
unlink(png_probe)

if (can_use_cairo_png) {
  knitr::opts_chunk$set(dev = "png", dev.args = list(type = "cairo-png"))
}

## ----eval = TRUE,echo=FALSE---------------------------------------------------
library(Rcompadre)

## ----fake load the data, eval=FALSE-------------------------------------------
# load("COMPADRE_v.4.0.1.RData")
# compadre <- as_cdb(compadre)

## ----fake fetch data with cdb_fetch, eval=FALSE-------------------------------
# Compadre <- cdb_fetch("compadre")

## ----load example COMPADRE data, eval=TRUE------------------------------------
data(Compadre)

## ----Summarise the database---------------------------------------------------
summary(Compadre)
Compadre

## ----Version of database------------------------------------------------------
VersionData(Compadre)

## ----Names--------------------------------------------------------------------
names(Compadre)

## ----Tables_and_Histograms----------------------------------------------------
table(Compadre$DicotMonoc)
hist(Compadre$StudyDuration, main = "StudyDuration")

## ----Tables_and_Histograms2---------------------------------------------------
plot(Compadre$Lon, Compadre$Lat, main = "Location")

## ----Check species------------------------------------------------------------
cdb_check_species(Compadre, "Succisa pratensis")

## ----Check species 2----------------------------------------------------------
spList <- c("Succisa pratensis", "Onodrim ent", "Aster amellus")
cdb_check_species(Compadre, spList)

## ----Check species3-----------------------------------------------------------
compadre_succisa <- cdb_check_species(Compadre, "Succisa pratensis",
  return_db = TRUE
)
compadre_succisa

## ----get matrices 1-----------------------------------------------------------
matA(compadre_succisa)

## ----get matrices 2-----------------------------------------------------------
x <- matA(compadre_succisa)
x[[1]]

## ----get matrices 3-----------------------------------------------------------
classInfo <- matrixClass(compadre_succisa)
classInfo[[1]]
classInfo[[1]]$MatrixClassAuthor

## ----subset 1-----------------------------------------------------------------
x <- subset(Compadre, DicotMonoc == "Eudicot")
x

## ----subset 2-----------------------------------------------------------------
x <- subset(Compadre, DicotMonoc == "Eudicot" &
  Country %in% c("USA", "CAN") &
  MatrixDimension > 2)

## ----compare------------------------------------------------------------------
cdb_compare(Compadre, x)

## ----cdb_flag-----------------------------------------------------------------
Compadre_flagged <- cdb_flag(Compadre)

## ----subset flagged-----------------------------------------------------------
x <- subset(Compadre_flagged, check_NA_A == FALSE & check_ergodic == TRUE)

## ----matrix_calculations------------------------------------------------------
lambdaVals <- sapply(matA(x), popdemo::eigs, what = "lambda")
summary(lambdaVals)
hist(lambdaVals, main = "Lambda values")