- Oct 14 – Intro to Reproducible Research
- Oct 21 – RR Basic Skills (1): Data Manipulation
- Oct 28 – Intro to Latent Class and Latent Transition Models
- Nov 4 – RR Basic Skills (2): Graph Production
- Nov 11
- Nov 18 – RR Basic Skills (3): Statistical Modeling
- Nov 25 – RR Basic Skills (4): Dynamic Reporting
- Dec 2 – Migrating into R from other Statistical Software
October 31, 2014
Overview of the Series
Previously:
Tidy data
- Each variable forms a column
- Each observation forms a row
- Each type of observational unit forms a table
See Hadley Wickham's paper on tidy data
Previously:
"./Scripts/Data/dsL.R"
download the files to work along at GitHub
Previously:
NLSY97
- National Longitudinal Study of Youth 1997
- Household sample
- ~ 9,000 respondents
- 5 cohorts
- ages from 13 to 31
- started in 1997
- continues today
- outcome:
Church attendance
Previously:
"./Scripts/Data/dsL.R"
imported the raw data files
myExtract <- "./Data/Extract/NLSY97_Attend_20141021/NLSY97_Attend_20141021" pathSourceData <- paste0(myExtract,".csv") SourceData <- read.csv(pathSourceData,header=TRUE, skip=0,sep=",") ds0 <- SourceData
cleaned, transformed , and at the end, exported it.
pathdsLrds <- "./Data/Derived/dsL.rds" saveRDS(object=dsL, file=pathdsLrds, compress="xz")
we pick up right were we left off, by executing the script ./Scripts/Data/dsL.R
Load Data
source("./Scripts/Data/dsL.R")
str(dsL)
head(dsL)
Load Data
dplyr::filter(dsL, id==1)
id sex race bmonth byear year attend age sexF raceF bmonthF attendF 1 1 2 4 9 1981 2000 1 19 Female Non-B/Non-H Sep Never 2 1 2 4 9 1981 2001 6 20 Female Non-B/Non-H Sep About once/week 3 1 2 4 9 1981 2002 2 21 Female Non-B/Non-H Sep Once or Twice 4 1 2 4 9 1981 2003 1 22 Female Non-B/Non-H Sep Never 5 1 2 4 9 1981 2004 1 23 Female Non-B/Non-H Sep Never 6 1 2 4 9 1981 2005 1 24 Female Non-B/Non-H Sep Never 7 1 2 4 9 1981 2006 1 25 Female Non-B/Non-H Sep Never 8 1 2 4 9 1981 2007 1 26 Female Non-B/Non-H Sep Never 9 1 2 4 9 1981 2008 1 27 Female Non-B/Non-H Sep Never 10 1 2 4 9 1981 2009 1 28 Female Non-B/Non-H Sep Never 11 1 2 4 9 1981 2010 1 29 Female Non-B/Non-H Sep Never 12 1 2 4 9 1981 2011 1 30 Female Non-B/Non-H Sep Never
Load Data
dplyr::filter(dsL, id==1) %>% select(id, year, attend, attendF)
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
The anatomy of a ggplot
see ggplot quick reference by SAPE research group
Preview
Canvas
dsM <- dsL p <- ggplot2::ggplot(dsM,aes(x=year,y=attend)) p
Error: No layers in plot
Geom: point
dsM <- dplyr::filter(dsL, id==1) p <- ggplot2::ggplot(dsM,aes(x=year,y=attend)) p <- p + geom_point() p
dplyr::filter(dsL, id==1) %>% select(id,year, attend, attendF)
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Geom: line
dsM <- dplyr::filter(dsL, id==1) p <- ggplot2::ggplot(dsM,aes(x=year,y=attend)) p <- p + geom_line() p
dplyr::filter(dsL, id==1) %>% select(id,year, attend, attendF)
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Geom: line + point
dsM <- dplyr::filter(dsL, id==1) p <- ggplot2::ggplot(dsM,aes(x=year,y=attend)) p <- p + geom_line() p <- p + geom_point() p
dplyr::filter(dsL, id==1) %>% select(id,year, attend, attendF)
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Define theme
baseSize <- 12 plotTheme <- ggplot2::theme_bw() + ggplot2::theme_bw(base_size=baseSize)+ ggplot2::theme(title=ggplot2::element_text(colour="gray20",size = 12)) + ggplot2::theme(axis.text=ggplot2::element_text(colour="gray40"))+ ggplot2::theme(axis.title=ggplot2::element_text(colour="gray40"))+ ggplot2::theme(panel.border = ggplot2::element_rect(colour="gray80"))+ ggplot2::theme(axis.ticks.length = grid::unit(0, "cm"))
Add theme
dsM <- dplyr::filter(dsL, id==1) p <- ggplot2::ggplot(dsM,aes(x=year,y=attend)) p <- p + geom_line() p <- p + geom_point() p <- p + plotTheme p
dplyr::filter(dsL, id==1) %>% select(id,year, attend, attendF)
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Scales: X-Axis
dsM <- dplyr::filter(dsL, id==1)
p <- ggplot2::ggplot(dsM,aes(x=year,y=attend))
p <- p + geom_line()
p <- p + geom_point()
p <- p + scale_x_continuous("Year", limits=c(2000,2011), breaks=2000:2011)
p <- p + plotTheme
p
Scales: X-Axis
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Scales: y-Axis
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Add title
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Multiple Lines
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Multiple Lines with grouping
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Edit geoms
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
Facet
id year attend attendF 1 1 2000 1 Never 2 1 2001 6 About once/week 3 1 2002 2 Once or Twice 4 1 2003 1 Never 5 1 2004 1 Never 6 1 2005 1 Never 7 1 2006 1 Never 8 1 2007 1 Never 9 1 2008 1 Never 10 1 2009 1 Never 11 1 2010 1 Never 12 1 2011 1 Never
