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

## -----------------------------------------------------------------------------
mat <- matrix(c(1, 0.5, 0.5, 1),nrow=2,ncol=2,dimnames=list(c("a", "b"), c("a", "b")))

## -----------------------------------------------------------------------------
library(lotri)
library(microbenchmark)
library(ggplot2)

mat <- lotri(a+b ~ c(1,
                     0.5, 1))

## -----------------------------------------------------------------------------
mat <- lotri({
    a+b ~ c(1,
            0.5, 1)
    c ~ 1
    d +e ~ c(1,
             0.5, 1)
})

## -----------------------------------------------------------------------------
mat <- matrix(c(1, 0.5, 0, 0, 0,
                0.5, 1, 0, 0, 0,
                0, 0, 1, 0, 0,
                0, 0, 0, 1, 0.5,
                0, 0, 0, 0.5, 1),
              nrow=5, ncol=5,
              dimnames= list(c("a", "b", "c", "d", "e"), c("a", "b", "c", "d", "e")))

## -----------------------------------------------------------------------------
library(Matrix)
mat <- matrix(c(1, 0.5, 0.5, 1),nrow=2,ncol=2,dimnames=list(c("a", "b"), c("a", "b")))
mat <- bdiag(list(mat, matrix(1), mat))
## Convert back to standard matrix
mat <- as.matrix(mat)
##
dimnames(mat) <- list(c("a", "b", "c", "d", "e"), c("a", "b", "c", "d", "e"))

## -----------------------------------------------------------------------------
mat <- lotri({
    a+b ~ c(1,
            0.5, 1) | id
    c ~ 1 | occ
    d +e ~ c(1,
             0.5, 1) | id(lower=3, upper=2, omegaIsChol=FALSE)
})

print(mat)

print(mat$lower)
print(mat$upper)
print(mat$omegaIsChol)

## -----------------------------------------------------------------------------
testList <- list(lotri({et2 + et3 + et4 ~ c(40,
                            0.1, 20,
                            0.1, 0.1, 30)}),
                     lotri(et5 ~ 6),
                     lotri(et1+et6 ~c(0.1, 0.01, 1)),
                     matrix(c(1L, 0L, 0L, 1L), 2, 2,
                            dimnames=list(c("et7", "et8"),
                                          c("et7", "et8"))))

matf <- function(.mats){
  .omega <- as.matrix(Matrix::bdiag(.mats))
  .d <- unlist(lapply(seq_along(.mats),
                      function(x) {
                        dimnames(.mats[[x]])[2]
                      }))
  dimnames(.omega) <- list(.d, .d)
  return(.omega)
}

print(matf(testList))

print(lotriMat(testList))


mb <- microbenchmark(matf(testList),lotriMat(testList))

print(mb)
autoplot(mb)