r course 2014: lecture 3

8/11/2019 R Course 2014: Lecture 3

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Lecture 3: String Function

Ben FansonSimon Lisovski


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Quick Refresher1) R data types (major ones)

numeric

character

factor [think of as a hybrid of numeric and character]

2) R classes (major ones) vector: c(), factor(), length()

data frame: data.frame() or read.table()/read.csv()/read.xls(), dim

list: list(), str()


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Quick Refresher3) subsetting

vector_name[ position_number ]

data.frame_name[ row_number, column_number ] or

data.frame_name$column_name

list_name[ item_number ] orlist_name$item_name


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Quick Refresher4) useful functions that we have encountered

class( ) # to get object structure

names() # get column names

unique() # list of unique items in a vector(s)

rep() # repeat an something so many times

seq() # create a sequence of numbers

1:5 # ':' is shortcut for numeric vector


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Quick Refresher4) useful functions that we have encountered

as.numeric(), as.character(), as.factor() # convert a vector to another data type (if possib

mean(), sd(), median(), min(), max() # summary statistics

summary() # gives some statistics

log(), sqrt(), x^2


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Quick Refresher5) importing files

read.table(filename, header=T, sep='\t') # tab-delimited files

read.csv(filename,header=T) # comma-delimited files

read.xls(filename, sheet=1) # library(gdata)used for reading excel files


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Lecture Outline1) sorting (ben)

2) stringr package (ben)

3) regular expressions (ben)

4) dates (Simeon)

Helpful references- http://cran.r-project.org/web/packages/stringr/stringr.pdf

- http://journal.r-project.org/archive/2010-2/RJournal_2010-2_Wickham.pdf


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Sorting in R1) for vectors, use sort()

returns sorted items


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Sorting in R2) for data.frames, use order()

returns ordered row numbers


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dataframe_name[ row_order, ]


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dataframe_name[ row_order, ]


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String functionsString functions have two main purposes

1) cleaning and preparing data tables for analysis

name

Bactrocera tryoni

Bactrocera meloni

Ceratitis capitata

Anastrepha ludens

genus species

Bactrocera tryoni

Bactrocera meloni

Ceratitis capitataAnastrepha ludens

split


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model

output

Estimate

trtAwk1 0.23

trtAwk2 0.45

trtBwk1 0.12

trtBwk2 0.0001

trt Week Estimate

A 1 0.23

B 2 0.45

B 1 0.12

B 2 0.0001

split and strip offspecific text

split


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name

Bactrocera__tryoni

Bactrocera__meloni

Ceratitis__capitata

Anastrepha__ludensreplace'__' with ' '

name

Bactrocera tryoni

Bactrocera meloni

Ceratitis capitata

Anastrepha ludens


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1) cleaning and preparing data tables for analysis2) writing R scripts, especially generic script

automating file paths/names


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paste()1) one of the more important functions that you will use

2) concatenates two or more objects

genus species

Bactrocera tryoni

Bactrocera meloni

Ceratitis capitata

Anastrepha ludens

name

Bactrocera tryoni

Bactrocera meloni

Ceratitis capitata

Anastrepha ludens


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paste()


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paste()


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stringr packagefunctions start with 'str_'

Note - Like most R functions, there are many other functions that do similar things. stto add consistency and have all the main functions in one place (can just start typing s

t i B i t i


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str_c( object1, object2, ) # same as paste(...,sep='') or paste0()

stringr - Basic string opera

stringr Basic string opera


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str_split_fixed(object1, pattern, num_splits) # break apart a string by a




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str_split_fixed(object1, pattern, num_splits) # break apart a string by a




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str_length( object ) # gets the length of each element in a vector




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str_sub( object, start, end ) # substring - remove part of a string by po




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str_trim(object, side) # remove leading and/or trailing whitespace




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str_trim(object, side) # remove leading and/or trailing whitespace

stringr - Pattern matchi


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str_detect( object, pattern) # determine if the string contains the patte

# returns TRUE or FALSE




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str_replace(string, pattern, repalce_with) # replace pattern with anoth




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str_replace(string, pattern, repalce_with) # replace pattern with anoth

stringr Pattern matchi


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Regular expressioncomputer language built to find stuff in strings

'^' starts with


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'$' ends with


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'[0-9]' find strings with numbers


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'[0-9]' find strings with numbers


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'[a-z]' find strings with specific letters

Advanced (putting it al


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Advanced (putting it altogether):

Output for publication tabmod


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Advanced (putting it altogether):

Output for publication tabmod


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Output for publication ta

O t t f bli ti t


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Output for publication talibrary(rtf)

rtf


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Dates in R


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Dates in R

Three date/time classes are built-in in R

DatePOSIXct

POSIXlt

Dates in R


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Dates in R

Three date/time classes are built-in in R

DatePOSIXct - Portable Operating System Interface [for Unix] cale

POSIXlt - Portable Operating System Interface [for Unix] loca

Dates in R


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ClassDate

This is the class you could use if you have only dates, BUT no times,

Dates in R

Symbol Explanation

%a Abbreviated week

%A Full weekday (e.g.

%m Abbreviated mont

%M Full month (e.g. J

.%d Day of the month

.

%H Hours as decimal

.

%j Day of the year (0

.

Create a date:

Non-standard formats must be specified:


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Dates in R


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ClassPOSIXlt

This class enables easy extraction of specific components of a time.

Dates in R

Create some POSIXlt objects: NOTE:

Internal integer representation:

Extract components of a time object:

Dates in R


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Dates in Rfunctionformat()

Format R Objects (not specific to POSIXct and POSIXlt objects)

Symbol Explanation

%a Abbreviated weekd

%A Full weekday (e.g.

%m Abbreviated month

%M Full month (e.g. Ja

.

%d Day of the month (

.

%H Hours as decimal n

.

%j Day of the year (00

.

Dates in R


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atesR Package lubridate

?Dates and Times Made Easy?

- http://www.jstatsoft.org/v40/i03/paper

NAs OR Missing Data


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gIn R, missing values are represented by the symbol NA (not available). Imvalues (e.g., dividing by zero) are represented by the symbol NaN (not a n

Testing for missing values:

Excluding missing data from analysis

Next Week


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Data frame manipulation

grammar of data manipulation (dplyr package)

restructuring dataframes


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Lecture 3: Hands on Sectio


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Getting Started


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g

1) download zip file from http://github.com/bfanson/Rcourse_pr

2) move 'R programs/Lecture3.R' into your 'Rcourse_proj/R programs

3) move 'data/' folder and replace all your data files

r course 2014: lecture 3

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