Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setupDarwin, include=FALSE, eval = Sys.info()[["sysname"]] == "Darwin"----
# The following line seems to be required by pkgdown::build_site() on my machine,
# but causes build to break with R-CMD-CHECK on GH
knitr::opts_chunk$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")
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")
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.