GetTop5

R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

#read in files
myChild <- read.csv('ChildSpecies.csv',colClasses=c('character','numeric'))
myAdult <- read.csv('AdultSpecies.csv',colClasses=c('character','numeric'))

#Get top 5
myChild %>% top_n(5)

## Selecting by Count

##                           Species Count
## 1    Faecalibacterium prausnitzii  1153
## 2 Ruthenibacterium lactatiformans   380
## 3   Anaerocolumna cellulosilytica   294
## 4            Clostridium septicum   335
## 5                 Prevotella oris   504

myAdult %>% top_n(5)

## Selecting by Count

##                        Species Count
## 1           Bacteroides caccae  6268
## 2         Phocaeicola vulgatus  2959
## 3 Faecalibacterium prausnitzii  1324
## 4     Oscillibacter sp. NSJ-62   708
## 5      Akkermansia muciniphila  3060