Galton example
Jeff Leek
Dependencies
This document depends on the following packages:
library(devtools)
library(Biobase)
library(UsingR)To install these packages you can use the code (or if you are compiling the document, remove the eval=FALSE from the chunk.)
install.packages(c("devtools","UsingR"))
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("Biobase"))Load Galton Data
data(galton)
par(mfrow=c(1,2))
hist(galton$child,col="blue",breaks=100)
hist(galton$parent,col="blue",breaks=100)
The distribution of child heights
hist(galton$child,col="blue",breaks=100)
Only know the child - average height
hist(galton$child,col="blue",breaks=100)
meanChild <- mean(galton$child)
lines(rep(meanChild,100),seq(0,150,length=100),col="red",lwd=5)
What if we plot child versus average parent
plot(galton$parent,galton$child,pch=19,col="blue")
Average parent = 65 inches tall
plot(galton$parent,galton$child,pch=19,col="blue")
near65 <- galton[abs(galton$parent - 65)<1, ]
points(near65$parent,near65$child,pch=19,col="red")
lines(seq(64,66,length=100),rep(mean(near65$child),100),col="red",lwd=4)
Average parent = 71 inches tall
plot(galton$parent,galton$child,pch=19,col="blue")
near71 <- galton[abs(galton$parent - 71)<1, ]
points(near71$parent,near71$child,pch=19,col="red")
lines(seq(70,72,length=100),rep(mean(near71$child),100),col="red",lwd=4)
Fitting a line
plot(galton$parent,galton$child,pch=19,col="blue")
lm1 <- lm(galton$child ~ galton$parent)
lines(galton$parent,lm1$fitted,col="red",lwd=3)
Not all points are on the line
plot(galton$parent,galton$child,pch=19,col="blue")
lines(galton$parent,lm1$fitted,col="red",lwd=3)
Plot what is leftover
par(mfrow=c(1,2))
plot(galton$parent,galton$child,pch=19,col="blue")
lines(galton$parent,lm1$fitted,col="red",lwd=3)
plot(galton$parent,lm1$residuals,col="blue",pch=19)
abline(c(0,0),col="red",lwd=3)
Session information
Here is the session information
devtools::session_info()## setting value
## version R version 3.2.1 (2015-06-18)
## system x86_64, darwin10.8.0
## ui RStudio (0.99.447)
## language (EN)
## collate en_US.UTF-8
## tz America/New_York
##
## package * version date
## acepack 1.3-3.3 2014-11-24
## annotate 1.46.1 2015-07-11
## AnnotationDbi * 1.30.1 2015-04-26
## assertthat 0.1 2013-12-06
## BiasedUrn * 1.06.1 2013-12-29
## Biobase * 2.28.0 2015-04-17
## BiocGenerics * 0.14.0 2015-04-17
## BiocInstaller * 1.18.4 2015-07-22
## BiocParallel 1.2.20 2015-08-07
## biomaRt 2.24.0 2015-04-17
## Biostrings 2.36.3 2015-08-12
## bitops 1.0-6 2013-08-17
## bladderbatch * 1.6.0 2015-08-26
## broom * 0.3.7 2015-05-06
## caTools 1.17.1 2014-09-10
## cluster 2.0.3 2015-07-21
## colorspace 1.2-6 2015-03-11
## corpcor 1.6.8 2015-07-08
## curl 0.9.2 2015-08-08
## DBI * 0.3.1 2014-09-24
## dendextend * 1.1.0 2015-07-31
## DESeq2 * 1.8.1 2015-05-02
## devtools * 1.8.0 2015-05-09
## digest 0.6.8 2014-12-31
## dplyr * 0.4.3 2015-09-01
## edge * 2.1.0 2015-09-06
## evaluate 0.7.2 2015-08-13
## foreign 0.8-66 2015-08-19
## formatR 1.2 2015-04-21
## Formula * 1.2-1 2015-04-07
## futile.logger 1.4.1 2015-04-20
## futile.options 1.0.0 2010-04-06
## gdata 2.17.0 2015-07-04
## genefilter * 1.50.0 2015-04-17
## geneLenDataBase * 1.4.0 2015-09-06
## geneplotter 1.46.0 2015-04-17
## GenomeInfoDb * 1.4.2 2015-08-15
## GenomicAlignments 1.4.1 2015-04-24
## GenomicFeatures 1.20.2 2015-08-14
## GenomicRanges * 1.20.5 2015-06-09
## genstats * 0.1.02 2015-09-05
## ggplot2 * 1.0.1 2015-03-17
## git2r 0.11.0 2015-08-12
## GO.db 3.1.2 2015-09-06
## goseq * 1.20.0 2015-04-17
## gplots * 2.17.0 2015-05-02
## gridExtra 2.0.0 2015-07-14
## gtable 0.1.2 2012-12-05
## gtools 3.5.0 2015-05-29
## highr 0.5 2015-04-21
## HistData * 0.7-5 2014-04-26
## Hmisc * 3.16-0 2015-04-30
## htmltools 0.2.6 2014-09-08
## httr 1.0.0 2015-06-25
## IRanges * 2.2.7 2015-08-09
## KernSmooth 2.23-15 2015-06-29
## knitr * 1.11 2015-08-14
## lambda.r 1.1.7 2015-03-20
## lattice * 0.20-33 2015-07-14
## latticeExtra 0.6-26 2013-08-15
## lazyeval 0.1.10 2015-01-02
## limma * 3.24.15 2015-08-06
## lme4 1.1-9 2015-08-20
## locfit 1.5-9.1 2013-04-20
## magrittr 1.5 2014-11-22
## MASS * 7.3-43 2015-07-16
## Matrix * 1.2-2 2015-07-08
## MatrixEQTL * 2.1.1 2015-02-03
## memoise 0.2.1 2014-04-22
## mgcv * 1.8-7 2015-07-23
## minqa 1.2.4 2014-10-09
## mnormt 1.5-3 2015-05-25
## munsell 0.4.2 2013-07-11
## nlme * 3.1-122 2015-08-19
## nloptr 1.0.4 2014-08-04
## nnet 7.3-10 2015-06-29
## org.Hs.eg.db * 3.1.2 2015-07-17
## plyr 1.8.3 2015-06-12
## preprocessCore * 1.30.0 2015-04-17
## proto 0.3-10 2012-12-22
## psych 1.5.6 2015-07-08
## qvalue * 2.0.0 2015-04-17
## R6 2.1.1 2015-08-19
## RColorBrewer 1.1-2 2014-12-07
## Rcpp * 0.12.0 2015-07-25
## RcppArmadillo * 0.5.400.2.0 2015-08-17
## RCurl 1.95-4.7 2015-06-30
## reshape2 1.4.1 2014-12-06
## rmarkdown 0.7 2015-06-13
## rpart 4.1-10 2015-06-29
## Rsamtools 1.20.4 2015-06-01
## RSkittleBrewer * 1.1 2015-09-05
## RSQLite * 1.0.0 2014-10-25
## rstudioapi 0.3.1 2015-04-07
## rtracklayer 1.28.9 2015-08-19
## rversions 1.0.2 2015-07-13
## S4Vectors * 0.6.5 2015-09-01
## scales 0.3.0 2015-08-25
## snm 1.16.0 2015-04-17
## snpStats * 1.18.0 2015-04-17
## stringi 0.5-5 2015-06-29
## stringr 1.0.0 2015-04-30
## survival * 2.38-3 2015-07-02
## sva * 3.14.0 2015-04-17
## tidyr 0.2.0 2014-12-05
## UsingR * 2.0-5 2015-08-06
## whisker 0.3-2 2013-04-28
## XML 3.98-1.3 2015-06-30
## xml2 0.1.2 2015-09-01
## xtable 1.7-4 2014-09-12
## XVector 0.8.0 2015-04-17
## yaml 2.1.13 2014-06-12
## zlibbioc 1.14.0 2015-04-17
## source
## CRAN (R 3.2.0)
## Bioconductor
## Bioconductor
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## Bioconductor
## Bioconductor
## Bioconductor
## Bioconductor
## Bioconductor
## Bioconductor
## CRAN (R 3.2.0)
## Bioconductor
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## Bioconductor
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.2)
## Github (jdstorey/edge@a1947b5)
## CRAN (R 3.2.2)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## Bioconductor
## Bioconductor
## Bioconductor
## Bioconductor
## Bioconductor
## Bioconductor
## Bioconductor
## local
## CRAN (R 3.2.0)
## CRAN (R 3.2.2)
## Bioconductor
## Bioconductor
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## Bioconductor
## CRAN (R 3.2.1)
## CRAN (R 3.2.2)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## Bioconductor
## CRAN (R 3.2.2)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## Bioconductor
## CRAN (R 3.2.1)
## Bioconductor
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## Bioconductor
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.1)
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.1)
## Bioconductor
## Github (alyssafrazee/RSkittleBrewer@0a96a20)
## CRAN (R 3.2.0)
## CRAN (R 3.2.0)
## Bioconductor
## CRAN (R 3.2.1)
## Bioconductor
## CRAN (R 3.2.2)
## Bioconductor
## Bioconductor
## CRAN (R 3.2.1)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## Bioconductor
## CRAN (R 3.2.0)
## CRAN (R 3.2.2)
## CRAN (R 3.2.0)
## CRAN (R 3.2.1)
## CRAN (R 3.2.2)
## CRAN (R 3.2.0)
## Bioconductor
## CRAN (R 3.2.0)
## BioconductorIt is also useful to compile the time the document was processed. This document was processed on: 2015-09-06.