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