Good Practices for Code

library(formatR)

# title: Time series analyses
# Author details: Author: John Smith, Contact details: John.Smith@unsw.edu.au
# Script and data info: This script performs a time series analyses on count data.  
# Data consists of counts of bird species.
# Data was collected in the hunter valley region between 1990 and 1991. 
# Copyright statement: This script is the product of UNSW etc.

setwd("C:/Users/JohnSmith/My_project_directory")
my.data <- read.csv("my_data.csv", sep = ",", header = T, check.names = FALSE)

library(car)
library(lme4)
library(Reshape2)
library(ggplot2)
source("R_scripts/myfunctions.R")

# title: Time series analyses
# Author details: Author: John Smith, Contact details: John.Smith@unsw.edu.au
# Script and data info: This script performs a time series analyses on count data.  
# Data consists of counts of bird species.
# Data was collected in the Hunter Valley region between 1990 and 1991. 
# Copyright statement: This script is the product of UNSW etc.
setwd("C:/Users/JohnSmith/myprojectdirectory")
my.data <- read.csv("mydata.csv", sep = ",", header = T, check.names = FALSE)

library(car)
library(lme4)
library(Reshape2)
library(ggplot2)
source("R_scripts/myfunctions.R")

# Checking data structure

summary(my.data)
str(my.data)
my.data[which(is.na(my.data)), ]
levels(my.data$variable1)

# Data cleaning
my.data$variable1 <- as.numeric(my.data$variable1)  # changed to numeric.
my.data[is.na(my.data)] <- 0  # replace NAs with zeros. 
my.data[6, 4] <- 46.01  # replace value 4601 with 46.01.

# begin data analyses.

# variables 
bird.mvment <- read.csv("bird_movement.csv")
bird.mvment.mdl <- lm(counts ~ location, data = bird.mvmnt)
bird.mvment$log.counts <- log(bird.mvmnt$counts)

# functions 
CalcStandardError <- function (x){
  sd(x)/sqrt(length(x))
}

# variables
data <- read.csv("bird_movement.csv") # uninformative, especially if you had to load two datasets. 
Bird.Mvment_Mdl <- lm(counts ~ location, data = bird.mvmnt) # inconsistent naming format. 
bird.mvment$log <- log(bird.mvmnt$counts) # uninformative and used function name to label variable. 

# functions
S <- function (x){ # S is uninformative. 
  sd(x)/sqrt(length(x))
}

bird.count <- 10

# Creates histogram of frequency of bird counts.
hist(bird_movement$counts,
     breaks = "scott",  # method for choosing number of buckets
     main   = "Histogram: bird counts")

x <- 10  # Bird counts - unneccesary, simply name the variable 'bird.count'

hist(bird_movement$counts,
     breaks = "scott",### method for choosing number of buckets - looks messy. 
     main   = "Histogram: bird counts")
# Creates histogram of frequency of bird counts. - place comment before code. 

CalculateStandardError <- function (x){
  # Computes the sample standard error
  #
  # Arguments:
  #  x: Vector whose standard error is to be calculated. x must have length greater than one,
  #     with no missingn values.
  #
  # Return:
  #  The standard error of x
  se<-sd(x)/sqrt(length(x))
  return(se)
}

bird.count <- bird.mvments$counts

bird.count = bird.mvments$counts

This is how long 80 characters is. Try not to type more than 80 on a single line.

bird.mvments[which(bird.mvments == max(bird.mvments)), ]

bird.var <- bird.mvments[, 4:10]

bird.mvments[which(bird.mvments==max(bird.mvments)),]  # spaces needed between operators and after comma.

bird.var <- bird.mvments[ ,4 : 10]  # space goes after comma not before, remove space around :.

bird.var<-bird.mvments[, 4:10]  # space needed around <-. 

for (i in 1:20) {
   bird.means[[i]] <- mean(bird.mvments$bird.count[[i]])
}

mean(bird.mvments$bird.count)

bird.mvments[2, ]

for(i in 1:20) {  # space needed betwen for and (i in 1:20).
   bird.means[[i]] <- mean (bird.mvments$bird.count[[i]])  # remove space after mean. 
}

mean( bird.mvments$bird.count )  # remove space around code.

bird.mvments[2,]  # needs a space after comma. 

for (i in 1:20) {
  bird.means[[i]] <- mean(bird.mvments$bird.count[[i]])
}

if (y == 0) {
    log(x)
  } else {
    y ^ x
}

for (i in 1:20) { bird.means[[i]] <- mean(bird.mvments$bird.count[[i]])  # opening curly followed by new line
} 

for (i in 1:20) { 
  bird.means[[i]] <- mean(bird.mvments$bird.count[[i]])}  # closing curly needs new line. 

if (y == 0) {
    log(x)
  } 
  else {  # inclose else within }{. 
    y ^ x
}

CalcStandardError <- function (x){
  se<-sd(x)/sqrt(length(x))
  return(se)
}

bird.mvments[which(bird.mvments$counts == max(bird.mvments$counts)), 
             10:ncols(bird.mvments)]

CalcStandardError <- function (x){
se<-sd(x)/sqrt(length(x))  # indent two spaces.
return(se)
}

bird.mvments[which(bird.mvments$counts == max(bird.mvments$counts)), 
  10:ncols(bird.mvments)]  # align with the square brackets.