vignettes/going-further.R

In n8thangreen/treeSimR: treeSimR

## ----save in vignette folder---------------------------------------------
# devtools::document(roclets = "vignette")

## ----set-options, echo=FALSE, cache=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
options(width = 1000)

## ----setup, echo=FALSE, results="hide"------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# define YAML and R code chunk header and footer

lang_output <- function(x, lang) {
  cat(c(sprintf("```%s", lang), x, "```"), sep="\n")
}

r_output <- function(x) lang_output(x, "r")
yaml_output <- function(x) lang_output(x, "yaml")

knitr::opts_chunk$set(
  fig.width=7,
  fig.height=5)

## ----load packages, echo=FALSE, warning=FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(yaml)
library(data.tree)
library(magrittr)
library(rprojroot)

devtools::load_all(".", quiet = TRUE)

## ----load_yaml------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
path_dtree <- system.file("raw data/LTBI_dtree-cost_SIMPLE.yaml", package = "treeSimR")
osList <- yaml.load_file(path_dtree)