Scrape_Surveys

#Loading in "rvest" and "dplyr" libraries
library(rvest)
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

Using chosen Biosample ID

#Collecting data from American Gut Project via URL and just my NCBI Biosample ID (31280774)
namePage <- paste0("https://www.ncbi.nlm.nih.gov/biosample/?term=",31280774)

#testPage variable will store all data from the webpage
#similar to what you see with "Inspect Element"
myPage <- read_html(namePage)

#Transforming the testpage into a table for just my biosample ID
tableText <- myPage %>%
    html_node("table") %>%
    html_table()

names(tableText)<-c('Question','Response')

head(tableText)

## # A tibble: 6 × 2
##   Question              Response         
##   <chr>                 <chr>            
## 1 dominant hand         I am right handed
## 2 environmental medium  feces            
## 3 environmental package human-gut        
## 4 host body habitat     UBERON:feces     
## 5 host body mass index  20.4             
## 6 host body product     UBERON:feces

Using class biosample IDs

#Creating list for multiple entries
class_data <- list()

#Collecting data from American Gut Project via URL and NCBI Biosample IDs (31280770-31280777)
for (i in 1:8){
  m = i + 31280769
  namePage <- paste0("https://www.ncbi.nlm.nih.gov/biosample/?term=", m)
  
#Storing html webpage data into a new format for class biosample IDs
classPage <- read_html(namePage)

#Creating a table from the collected data
tableText <- classPage %>%
    html_node("table") %>%
    html_table()

names(tableText)<-c('Question','Response')

head(tableText)

class_data[[as.character(m)]] <- tableText

}

#Using "sapply" to receive data from class_survey_data list
survey_responses <- sapply(class_data, function(x){x[,2]})
height <- sapply(survey_responses, function (x) {x[8]})

#Using numerical format of "height" to create a pie chart
pie(table(height), main = "Pie Chart of Height")