inst/doc/Week0_BasicR.R

In hhwagner1/LandGenCourse: Interface for course "Landscape Genetic Data Analysis with R"

## ----------------------------------------------------------------------------------------------------
if(!requireNamespace("popgraph", quietly = TRUE))
{
  install.packages(c("RgoogleMaps", "geosphere", "proto", "sampling", 
                      "seqinr", "spacetime", "spdep"), dependencies=TRUE)
  remotes::install_github("dyerlab/popgraph")
}
  
if(!requireNamespace("gstudio", quietly = TRUE)) remotes::install_github("dyerlab/gstudio")


## ----eval=FALSE--------------------------------------------------------------------------------------
## variable <- value


## ----eval=FALSE--------------------------------------------------------------------------------------
## class( variable )


## ----eval=FALSE--------------------------------------------------------------------------------------
## ?help


## ----eval=FALSE--------------------------------------------------------------------------------------
## vignette()


## ----------------------------------------------------------------------------------------------------
x <- 3
x


## ----------------------------------------------------------------------------------------------------
y <- 22/7
y


## ----------------------------------------------------------------------------------------------------
c(x,y)


## ----------------------------------------------------------------------------------------------------
x <- .3 / 3
x


## ----------------------------------------------------------------------------------------------------
print(x, digits=20)


## ----------------------------------------------------------------------------------------------------
rnorm(10)


## ----------------------------------------------------------------------------------------------------
rnorm(10,mean=42,sd=12)


## ----------------------------------------------------------------------------------------------------
rpois(10,lambda = 2)


## ----------------------------------------------------------------------------------------------------
rchisq(10, df=1)


## ----------------------------------------------------------------------------------------------------
x <- c("42","99")
x


## ----------------------------------------------------------------------------------------------------
y <- as.numeric( x )
y


## ----------------------------------------------------------------------------------------------------
x <- "The night is dark and full of terrors..."
as.numeric( x )


## ----------------------------------------------------------------------------------------------------
prof <- "Rodney J. Dyer"
prof



## ----------------------------------------------------------------------------------------------------
length(prof)


## ----------------------------------------------------------------------------------------------------
nchar(prof)


## ----------------------------------------------------------------------------------------------------
nchar(" \t ")


## ----------------------------------------------------------------------------------------------------
x <- "I am"
y <- "not"
z <- 'a looser'
terms <- c(x,y,z)
terms


## ----------------------------------------------------------------------------------------------------
length(terms)
nchar(terms)


## ----------------------------------------------------------------------------------------------------
paste(terms, collapse=" ")


## ----------------------------------------------------------------------------------------------------
paste(x,z)


## ----------------------------------------------------------------------------------------------------
paste(x,z,sep=" not ")


## ----------------------------------------------------------------------------------------------------
x <- 42
x


## ----------------------------------------------------------------------------------------------------
y <- as.character(x)
y


## ----------------------------------------------------------------------------------------------------
region <- c("North","North","South","East","East","South","West","West","West")
region <- factor( region )
region


## ----------------------------------------------------------------------------------------------------
region <- factor( region, levels=c("North","South","East","West","Central"))
region


## ----------------------------------------------------------------------------------------------------
region[1] <- "Bob"


## ----------------------------------------------------------------------------------------------------
region[1] <- "North"


## ----------------------------------------------------------------------------------------------------
region <- factor( region, ordered=TRUE, levels = c("West", "North", "South", "East") )
region


## ----------------------------------------------------------------------------------------------------
subregion <- region[ 3:9 ]
subregion


## ----------------------------------------------------------------------------------------------------
table( subregion )


## ----------------------------------------------------------------------------------------------------
canThrow <- c(FALSE, TRUE, FALSE, FALSE, FALSE)
canThrow


## ----------------------------------------------------------------------------------------------------
stable <- c( "RGIII" == 0, nchar("Marshawn") == 8)
stable


## ----------------------------------------------------------------------------------------------------
data <- rnorm(20)
data


## ----------------------------------------------------------------------------------------------------
data[ data > 0 ]


## ----------------------------------------------------------------------------------------------------
data > 0


## ----------------------------------------------------------------------------------------------------
1:20 %% 2


## ----------------------------------------------------------------------------------------------------
data[ (1:20 %% 2) > 0 ]


## ----------------------------------------------------------------------------------------------------
x <- c(1,2,3)
x
y <- c(TRUE,TRUE,FALSE)
y
z <- c("I","am","not","a","looser")
z


## ----------------------------------------------------------------------------------------------------
w <- c(TRUE, "1", pi, ls())
w
class(w)


## ----------------------------------------------------------------------------------------------------
x
x[1] <- 2
x[3] <- 1
x
x[2]


## ----------------------------------------------------------------------------------------------------
x <- 1:6
x


## ----------------------------------------------------------------------------------------------------
x <- 5:2
x


## ----------------------------------------------------------------------------------------------------
x <- 3.2:8.4
x


## ----------------------------------------------------------------------------------------------------
y <- seq(1,6)
y


## ----------------------------------------------------------------------------------------------------
z <- seq(1,20,by=2)
z


## ----------------------------------------------------------------------------------------------------
rep("Beetlejuice",3)


## ----------------------------------------------------------------------------------------------------
x <- c("No","Free","Lunch")
rep(x,time=3)


## ----------------------------------------------------------------------------------------------------
rep(x,each=3)


## ----------------------------------------------------------------------------------------------------
matrix(nrow=2, ncol=2)


## ----------------------------------------------------------------------------------------------------
matrix(1:4, nrow=2 )


## ----------------------------------------------------------------------------------------------------
matrix(1:4, nrow=2, byrow=TRUE)


## ----------------------------------------------------------------------------------------------------
Y <- matrix(c(1,2,3,4,5,6),ncol=2,byrow=TRUE)
Y


## ----------------------------------------------------------------------------------------------------
X <- matrix(c(1,2,3,4,5,6),nrow=2)
X


## ----------------------------------------------------------------------------------------------------
X == t(Y)


## ----------------------------------------------------------------------------------------------------
X <- matrix(c(1,2,3,4,5,6),ncol=4, byrow=TRUE)


## ----------------------------------------------------------------------------------------------------
X


## ----------------------------------------------------------------------------------------------------
dim(X)


## ----------------------------------------------------------------------------------------------------
X[1,3]


## ----------------------------------------------------------------------------------------------------
X[1,]


## ----------------------------------------------------------------------------------------------------
X[,3]


## ----------------------------------------------------------------------------------------------------
length(X[,3])


## ----------------------------------------------------------------------------------------------------
X[,2:3]


## ----eval=FALSE--------------------------------------------------------------------------------------
## X[1,8]


## ----------------------------------------------------------------------------------------------------
indices <- cbind( rep(1:2, each=3), rep(1:3,times=2), rep(5,length.out=6)  )
indices


## ----------------------------------------------------------------------------------------------------
theList <- list( x=seq(2,40, by=2), dog=LETTERS[1:5], hasStyle=logical(5) )
summary(theList)


## ----------------------------------------------------------------------------------------------------
theList


## ----------------------------------------------------------------------------------------------------
theList$my_favoriate_number <- 2.9 + 3i


## ----------------------------------------------------------------------------------------------------
theList[["lotto numbers"]] <- rpois(7,lambda=42)


## ----------------------------------------------------------------------------------------------------
names(theList)


## ----------------------------------------------------------------------------------------------------
theList$x
theList$x[2] <- 42
theList$x


## ----------------------------------------------------------------------------------------------------
theList[["x"]]


## ----------------------------------------------------------------------------------------------------
theList[[2]]


## ----------------------------------------------------------------------------------------------------
theList[[1]][3]


## ----eval=FALSE--------------------------------------------------------------------------------------
## theList[1,3]


## ----------------------------------------------------------------------------------------------------
df <- data.frame( ID=1:5, Names=c("Bob","Alice","Vicki","John","Sarah"), Score=100 - rpois(5,lambda=10))
df


## ----------------------------------------------------------------------------------------------------
df$Passed_Class <- c(TRUE,TRUE,TRUE,FALSE,TRUE)


## ----------------------------------------------------------------------------------------------------
summary(df)


## ----------------------------------------------------------------------------------------------------
df[1,3]


## ----------------------------------------------------------------------------------------------------
df[1,]


## ----------------------------------------------------------------------------------------------------
df[,3]


## ----------------------------------------------------------------------------------------------------
df$Names[3]


## ----------------------------------------------------------------------------------------------------
df[1:3,]


## ----------------------------------------------------------------------------------------------------
df$Names[df$Score > 90 & df$Passed_Class==TRUE]


## ----eval=FALSE--------------------------------------------------------------------------------------
## function_name <- function( arguments ) { Stuff you want the function to do }


## ----message=FALSE, warning=FALSE--------------------------------------------------------------------
library(gstudio)
loc1 <- locus( c(128,130) )
loc2 <- locus( c(128,128) )
cat( loc1, loc2 )


## ----------------------------------------------------------------------------------------------------
off.alleles <- alleles( loc1 )
off.alleles
mom.alleles <- alleles( loc2 )
mom.alleles


## ----------------------------------------------------------------------------------------------------
shared <- intersect( off.alleles, mom.alleles )
shared


## ----------------------------------------------------------------------------------------------------
loc3 <- locus( c(132,132))
dad.alleles <- alleles( loc3 )
intersect( mom.alleles, dad.alleles )


## ----------------------------------------------------------------------------------------------------
potential_offspring <- function( parent, offspring ) {
  off <- alleles( offspring )
  par <- alleles( loc2 )
  shared <- intersect( off, par )
  return( length( shared ) > 0 )
}


## ----------------------------------------------------------------------------------------------------
potential_offspring(loc1, loc2)


## ----------------------------------------------------------------------------------------------------
potential_offspring(loc2, loc3)


## ----------------------------------------------------------------------------------------------------
x <- 10


## ----------------------------------------------------------------------------------------------------
do_it <- function( x ) {
  x <- x + 10
  return( x )
}


## ----eval=FALSE--------------------------------------------------------------------------------------
## if( CRITERIA ) {
## 	DO_SOMETHING
## }


## ----------------------------------------------------------------------------------------------------
is_heterozygote( c(loc1, loc2) )


## ----------------------------------------------------------------------------------------------------
if( is_heterozygote(loc1) ){
  print("It's a het!")
}


## ----------------------------------------------------------------------------------------------------
if( is_heterozygote(loc2) ){
  print("It's a het!")
}


## ----------------------------------------------------------------------------------------------------
if( is_heterozygote(loc1) ) {
  cat(loc1, "is a heterozygote")
} else {
  cat(loc1, "is a homozygote")
}


## ----------------------------------------------------------------------------------------------------
if( is_heterozygote(loc2) ) {
  cat(loc2, "is a heterozygote")
} else {
  cat(loc2, "is a homozygote")
}


## ----------------------------------------------------------------------------------------------------
ans <- ifelse( is_heterozygote( c(loc1, loc2)) , "heterozygote", "Not")
ans


## ----------------------------------------------------------------------------------------------------
which_is_het <- function( A, B) {
  if( is_heterozygote(A) & !is_heterozygote(B) ) {
    print("First is heterozygote")
  } else if( !is_heterozygote(A) & is_heterozygote(B) ){
    print("Second is heterozygote")
  } else if( is_heterozygote(A) & is_heterozygote(B) ){
    print("Both are heterozygotes")
  } else {
    print( "Neither are heterozygotes")
  }
}


## ----------------------------------------------------------------------------------------------------
x <- c(3,8,5,4,6)
x


## ----eval=FALSE--------------------------------------------------------------------------------------
## for( SOME_SEQUENCE ){
##   DO_SOMETHING
## }


## ----------------------------------------------------------------------------------------------------
for( val in x ){
  print(val)
}


## ----------------------------------------------------------------------------------------------------
for( i in 1:length(x)){
  print( x[i] )
}


## ----------------------------------------------------------------------------------------------------
y <- 1:5
for( i in 1:length(x)){
  if( x[i] %% 2)
    print( x[i] + y[i])
  else
    print( x[i] - y[i] )
}


## ----------------------------------------------------------------------------------------------------
for( i in 1:20 ){
  if( i %% 3 )
    next
  cat("The value of i =",i,"\n")
}


## ----------------------------------------------------------------------------------------------------
for( i in 1:10){
  if( i > 2 )
    break
  cat("The value of i=",i,"\n")
}


## ----message=FALSE, warning=TRUE, include=FALSE------------------------------------------------------
LandGenCourse::detachAllPackages()