introduction

This is my first Rmarkdown document!

load packages

library(readr)
library(dplyr)
library(ggplot2)
library(knitr)

let’s embed some R code!

Let’s load the Gapminder data from bioconnector.org.

# this is a comment
gm <- read_csv("data/gapminder.csv")
head(gm)
## Source: local data frame [6 x 6]
## 
##       country continent  year lifeExp      pop gdpPercap
##         (chr)     (chr) (int)   (dbl)    (int)     (dbl)
## 1 Afghanistan      Asia  1952  28.801  8425333  779.4453
## 2 Afghanistan      Asia  1957  30.332  9240934  820.8530
## 3 Afghanistan      Asia  1962  31.997 10267083  853.1007
## 4 Afghanistan      Asia  1967  34.020 11537966  836.1971
## 5 Afghanistan      Asia  1972  36.088 13079460  739.9811
## 6 Afghanistan      Asia  1977  38.438 14880372  786.1134

The mean life expectancy is 59.4744394 years.

The years surveyed in this data include: 1952, 1957, 1962, 1967, 1972, 1977, 1982, 1987, 1992, 1997, 2002, 2007.

Add figures

ggplot(gm, aes(gdpPercap, lifeExp)) + geom_point()

Creating nice tables

“kabled” output:

kable(head(gm))
country continent year lifeExp pop gdpPercap
Afghanistan Asia 1952 28.801 8425333 779.4453
Afghanistan Asia 1957 30.332 9240934 820.8530
Afghanistan Asia 1962 31.997 10267083 853.1007
Afghanistan Asia 1967 34.020 11537966 836.1971
Afghanistan Asia 1972 36.088 13079460 739.9811
Afghanistan Asia 1977 38.438 14880372 786.1134

some analysis

gm %>% 
  filter(continent=="Oceania") %>% 
  group_by(country) %>% 
  summarize(meanlife=mean(lifeExp)) %>% 
  kable()
country meanlife
Australia 74.66292
New Zealand 73.98950

Session Information

This is for reproducibility! Yay reproducibility!

sessionInfo()
## R version 3.2.3 (2015-12-10)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.10.5 (Yosemite)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] knitr_1.12.3  ggplot2_2.1.0 dplyr_0.4.3   readr_0.2.2  
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.3      digest_0.6.9     assertthat_0.1   plyr_1.8.3      
##  [5] grid_3.2.3       R6_2.1.2         gtable_0.1.2     DBI_0.3.1       
##  [9] formatR_1.2.1    magrittr_1.5     scales_0.3.0     evaluate_0.8    
## [13] highr_0.5.1      stringi_1.0-1    lazyeval_0.1.10  rmarkdown_0.9.2 
## [17] labeling_0.3     tools_3.2.3      stringr_1.0.0    munsell_0.4.3   
## [21] yaml_2.1.13      parallel_3.2.3   colorspace_1.2-6 htmltools_0.3