Week 1 assignment for DATA 607 is to subset the data provided by the UCI for Mushroom dataset located at below address:
https://archive.ics.uci.edu/ml/datasets/Mushroom
The actual dataset can be found here:
https://archive.ics.uci.edu/ml/machine-learning-databases/mushroom/agaricus-lepiota.data
This data set includes descriptions of hypothetical samples corresponding to 23 species of gilled mushrooms in the Agaricus and Lepiota Family.Each species is identified as definitely edible, definitely poisonous, or of unknown edibility and not recommended. This latter class was combined with the poisonous one
Attribute Information:
Type : Edible e , Poisonous = p
cap-shape: bell=b,conical=c,convex=x,flat=f, knobbed=k,sunken=s
cap-surface: fibrous=f,grooves=g,scaly=y,smooth=s
cap-color: brown=n,buff=b,cinnamon=c,gray=g,green=r, pink=p,purple=u,red=e,white=w,yellow=y
bruises: bruises=t,no=f
odor: almond=a,anise=l,creosote=c,fishy=y,foul=f, musty=m,none=n,pungent=p,spicy=s
gill-attachment: attached=a,descending=d,free=f,notched=n
gill-spacing: close=c,crowded=w,distant=d
gill-size: broad=b,narrow=n
gill-color: black=k,brown=n,buff=b,chocolate=h,gray=g, green=r,orange=o,pink=p,purple=u,red=e, white=w,yellow=y
stalk-shape: enlarging=e,tapering=t
stalk-root: bulbous=b,club=c,cup=u,equal=e, rhizomorphs=z,rooted=r,missing=?
stalk-surface-above-ring: fibrous=f,scaly=y,silky=k,smooth=s
stalk-surface-below-ring: fibrous=f,scaly=y,silky=k,smooth=s
stalk-color-above-ring: brown=n,buff=b,cinnamon=c,gray=g,orange=o, pink=p,red=e,white=w,yellow=y
stalk-color-below-ring: brown=n,buff=b,cinnamon=c,gray=g,orange=o, pink=p,red=e,white=w,yellow=y
veil-type: partial=p,universal=u
veil-color: brown=n,orange=o,white=w,yellow=y
ring-number: none=n,one=o,two=t
ring-type: cobwebby=c,evanescent=e,flaring=f,large=l, none=n,pendant=p,sheathing=s,zone=z
spore-print-color: black=k,brown=n,buff=b,chocolate=h,green=r, orange=o,purple=u,white=w,yellow=y
population: abundant=a,clustered=c,numerous=n, scattered=s,several=v,solitary=y
habitat: grasses=g,leaves=l,meadows=m,paths=p, urban=u,waste=w,woods=d
Load data from given URL(https://archive.ics.uci.edu/ml/datasets/Mushroom) into R , subset and create a new Data frame selecting few columns from original including 1st column. Provide meangingfull name to columns Headers, and also update the values of each column based on the data dictionary values.
First step to load the necessary libraries required for this assignment.
library(stringr)
library(XML)## Warning: package 'XML' was built under R version 3.5.2library(maps)
library(httr)
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, unionmushroom_table <- read.table("https://archive.ics.uci.edu/ml/machine-learning-databases/mushroom/agaricus-lepiota.data",header=FALSE , sep="," )
mushrooms <- as.data.frame(mushroom_table)
# subsetting the data to create a a new data frame with 5 columns
mush_subset <- subset(mushrooms, select=c(1,2,3,4,6))
#providing columns meaningfull names
colnames(mush_subset) <- c("Type","Shape","Surface","Color","Odor")
#Changing the column values with meaningfull values based on conditional statements
mush_subset$Type <- ifelse(str_detect(mush_subset$Type, "e") == TRUE, "Edible", "Poisonous")
ELSE <- TRUE
##Pipe operator %>% allows you to pipe the output of one function to the input of another functione. It works from left to right
##mutate function will add new columns to dataframe
## with function hlps in constructing an environemnt from data, possible modifying(a copy of) the orignial data.e,g. with(data,expression,....)
#bell=b,conical=c,convex=x,flat=f, knobbed=k,sunken=s
mush_subset <- mush_subset %>% mutate(.,Shape1 = with(.,case_when(
(mush_subset$Shape == "x") ~ "convex",
(mush_subset$Shape == "b") ~ "bell",
(mush_subset$Shape == "c") ~ "conical",
(mush_subset$Shape == "k") ~ "knobbed",
(mush_subset$Shape == "f") ~ "flat",
ELSE ~ "sunken"
)))
#fibrous=f,grooves=g,scaly=y,smooth=s
mush_subset <- mush_subset %>% mutate(.,Surface = with(.,case_when(
(mush_subset$Surface == "f") ~ "fibrous",
(mush_subset$Surface == "g") ~ "grooves",
(mush_subset$Surface == "y") ~ "scaly",
ELSE ~ "smooth"
)))
#brown=n,buff=b,cinnamon=c,gray=g,green=r, pink=p,purple=u,red=e,white=w,yellow=y
mush_subset <- mush_subset %>% mutate(.,Color = with(.,case_when(
(mush_subset$Color == "n") ~ "brown",
(mush_subset$Color == "b") ~ "buff",
(mush_subset$Color == "c") ~ "cinnamon",
(mush_subset$Color == "g") ~ "gray",
(mush_subset$Color == "r") ~ "green",
(mush_subset$Color == "p") ~ "pink",
(mush_subset$Color == "u") ~ "purple",
(mush_subset$Color == "e") ~ "red",
(mush_subset$Color == "w") ~ "white",
ELSE ~ "yellow"
)))
#almond=a,anise=l,creosote=c,fishy=y,foul=f, musty=m,none=n,pungent=p,spicy=s
mush_subset <- mush_subset %>% mutate(.,Odor = with(.,case_when(
(mush_subset$Odor == "a") ~ "almond",
(mush_subset$Odor == "l") ~ "anise",
(mush_subset$Odor == "c") ~ "creosote",
(mush_subset$Odor == "y") ~ "fishy",
(mush_subset$Odor == "f") ~ "foul",
(mush_subset$Odor == "m") ~ "musty",
(mush_subset$Odor == "p") ~ "pungent",
(mush_subset$Odor == "n") ~ "none",
ELSE ~ "spicy"
)))The data frame after subsetting, has been given meaningfull name and updating column values is as below.
head(mush_subset,n=20)## Type Shape Surface Color Odor Shape1
## 1 Poisonous x smooth brown pungent convex
## 2 Edible x smooth yellow almond convex
## 3 Edible b smooth white anise bell
## 4 Poisonous x scaly white pungent convex
## 5 Edible x smooth gray none convex
## 6 Edible x scaly yellow almond convex
## 7 Edible b smooth white almond bell
## 8 Edible b scaly white anise bell
## 9 Poisonous x scaly white pungent convex
## 10 Edible b smooth yellow almond bell
## 11 Edible x scaly yellow anise convex
## 12 Edible x scaly yellow almond convex
## 13 Edible b smooth yellow almond bell
## 14 Poisonous x scaly white pungent convex
## 15 Edible x fibrous brown none convex
## 16 Edible s fibrous gray none sunken
## 17 Edible f fibrous white none flat
## 18 Poisonous x smooth brown pungent convex
## 19 Poisonous x scaly white pungent convex
## 20 Poisonous x smooth brown pungent convex