In mdelalay/FRAM-Cloud:

Global options and chunk options

rm(list=ls())

# Good websites ------------------------------

#shell.exec("http://r-pkgs.had.co.nz/r.html") Package
#shell.exec("http://style.tidyverse.org/") Style

# Good name of file ---------------------------

# This is a good name of file: 00_good_name.Rmd or 00_namified.Rmd

# General rules -------------------------------

# Install libraries and load them first
library("dplyr", "knitr") # to use pipe operator like %>%
# # In code, use comments to explain the "why" not the "what" or "how"

# Rmd Options ---------------------------------

#shell.exec("https://yihui.name/knitr/options/") Global options

knitr::opts_chunk$set(df_print = "kable", fig_caption = "yes", fig_height = 5, fig_width= 5, fig.keep = "all", # Global option
                      eval = TRUE, error = FALSE, # Evaluation. error: is knit interrupted if the chunks have error?
                      echo = FALSE, results = "asis", include = TRUE, warning = FALSE, message=FALSE) # Display. Displayed by default only (1) tables and (2) plots. echo: is the chunk printed?

Lists

A list has an empty line between the description and the beginning of the list

1. number 1
2. number 2 a. ident with two tabs b. ident 1. ident with four tabs
3. number 3

This is a unnumbered list:

• first item
• second item
  • second item A
  • second item B
• third item

Tables

Note:

• Captions for tables do not work: we tried in kable function and in chunk options without success.

# x must be a matrix or dataframe with set column names
fmtd_kable <- function(x, digits_args, align_args, rownames) {
  if (!missing(rownames)) { 
    x <- cbind(rownames, x)
    colnames(x)[1] <-  "Row content"
  }

  if (missing(digits_args)) (digits_args <- 2)
  if (missing(align_args)) (align_args <- "r")

  x <- as.data.frame(x)

  knitr::kable(x, row.names = FALSE, colnames = colnames(aa),
               digits = digits_args, align = align_args,
               format.args = list(nsmall = digits_args, big.mark  = ","))
}

# Example
aa <- data.frame(simple_x =c(1000.253,2,3), square_x = c(1,4,9), string_x = paste("equ_",1:3))
aa <- as.matrix(aa)
fmtd_kable(aa, digits_arg = 3, align_args =  "l", rownames = paste("example_",1:3))

Plots

Note:

• fig.cap allows to set the same caption for all plots in a chunk.

aa <- as.data.frame(aa)
plot(aa$simple_x, aa$square_x)
plot(aa$simple_x, aa$square_x, title ="second")

Insert a picture

What follows in the Rmd file is the ALt text

Syntax in R script

# Naming --------------------------------------

# Variable names
## They use lowercase letters, numbers, and  _ . 
## They should be nouns, adjectives, adverbs, but not prepositions or pronouns.E.g.: day_one, but not dayone or first_day

# Function names
# They use lowercase letters, numbers, and _ . 
## They should be verbs, adjectives, adverbs, but not prepositions or pronouns. E.g.: add_row() instead of row_adder()

# Argument names are either data or details.
## Repeating the name of the data is not necessary. Repeating the name of the details is necessary.
## mean (1:10, na.rm = TRUE)

# Spacing ------------------------------------
# average <- mean(feet / 12 + inches, na.rm = TRUE)
# x <- 1:10
# base::get
# if (debug) show(x)
# plot(x, y)
# diamonds[5, ]

# Curly braces -------------------------------
y <- 0
x <- 9

if (y == 0) {
  if (x > 0) {
    log(x)
  } else {
    message("x is negative or zero")
  }
} else {
  y ^ x
}

x <- if (y < 20) "Too low" else "Too high"

# Long lines ---------------------------------

#do_something_very_complicated(
#  "that",
#  requires = many,
#  arguments = "some of which may be long"
#)

#long_function_name <- function(a = "a long argument",
#                               b = "another argument",
#                               c = "another long argument") {
# 
#}

# return() -----------------------------------

# Only use  return()  for early returns. Otherwise rely on R to return the result of the last evaluated expression

# Design principles ------------------------

# A function is either a returning-value function or a side-effect function (like printing, plotting, or saving to disk), but not both at the same time.

# A function should be understandable in isolation

# Side-effect function ----------------------

# The function should return the first argument invisibly.

#print.url <- function(x, ...) {
#  cat("Url: ", build_url(x), "\n", sep = "")
#  invisible(x)
#}

# Avoid calling global options. If so, clean up after yourself with on.exit()

# Introduction to pipe %>%. Clearly, z is smarter than y.
x <- c(1,2,3,4,9,NA)

y <- quantile(x, na.rm=TRUE)
y <- max(y)
y <- sqrt(y)

z <- 
  x %>%
  quantile(na.rm=TRUE) %>%
  max() %>%
  sqrt()

z == y

Source

setwd(paste0("C:/Users/mdela/Dropbox/Prof/NUS/Projects/Modelling/Model", "/Analysis_and_documentation"))
ww <- source("test.R", local=TRUE)

ll(2)

function error

test_stop <- function (x){
  if (x > 0) {
    y <- sqrt(x)
  } else {
    stop("y smaller than 0")
  }
  y
}

test_stop(2)
test_stop(-2)

RMarkdown syntax

italics

bold

superscript^2^

~~striketrough~~

link, yes, click here!

inline equation: $xxx$

example inline equation: $A = \pi + \alpha * r^{(2+1)}$

An equation in text that calcluate that r 2 and r 2 make r 2 + 2.

mdelalay/FRAM-Cloud documentation built on May 30, 2019, 11:45 p.m.