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R basics workshop Part 3: Objects

R basics workshop Part 3: Objects. J. Sebasti án Tello Iván Jiménez. Center for Conservation and Sustainable Development. Object. In R, an object is a pointer to a piece of memory that contains some information One of the main uses for objects is to hold data

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R basics workshop Part 3: Objects

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  1. R basics workshop Part 3: Objects J. Sebastián Tello Iván Jiménez Center forConservation and SustainableDevelopment

  2. Object • In R, an object is a pointer to a piece of memory that contains some information • One of the main uses for objects is to hold data • There are many different classes of objects each with its own properties and uses

  3. Objects • If we counted the number of individuals of tree species in a plot, we can concatenate the values with the function c: c(1, 17, 34, 26, 82)

  4. Objects are frequently created with the operator “<-” • These values could be stored in an object with “any” name using the operator “<-”: abund<- c(1, 17, 34, 26, 82) abund

  5. Objects can be created other ways too • The same operation can also be like this: c(1, 17, 34, 26, 82) -> abund2 assign(x="abund3", value=c(1, 17, 34, 26, 82)) abund4 = c(1, 17, 34, 26, 82) abund abund2 abund3 abund4 identical(abund, abund2)

  6. Data in objects can be of various types • Numeric: E.g., number of individuals per species abund <- c(1, 17, 34, 26, 82) mode(x=abund) mode(abund)

  7. Data in objects can be of various types • Numeric: E.g., number of individuals per species • Character: E.g., names of species spp <- c("I.ynga", "I.edulis", "I.macrophylla", "I.punctata", "I.alba") spp mode(spp)

  8. Data in objects can be of various types • Numeric: E.g., number of individuals per species • Character: E.g., names of species • Logical(true/false): E.g., incrementin abundance? increm <- c(TRUE, FALSE, FALSE, TRUE, TRUE) increm mode(increm)

  9. Special values • NA: missing value; not available; not applicable • Inf and -Inf: infinite • NaN: not a number • NULL: object missing 100/0 -100/0 100 - Inf Inf - Inf

  10. An object in R is similar to an objeto in the real world • Objects have attributes which define their properties • Class is one of the main attributes and it helps determine others Height DBH Leaf shape Class Other attributes Tree (In the real world) matrix (In R) Number of rows Number of columns

  11. Basic classes of R objects

  12. Basic classes of R objects – The Vector • Vectors represent a linear sequence of values, e.g.: Value in first position Value in second position etc…

  13. Basic classes of R objects – Numericvectors abund <- c(1, 17, 34, 26, 82) class(abund) • Lengthisanimportantattribute of vectors: First position Fifth position length(x=abund)

  14. Basic classes of R objects – Numericvectors • Anotheroneisthenames of positions in the vector: Names of positions names(x=abund) names(abund) <- paste("sp", seq(1,length(abund)), sep="") names(abund) abund

  15. Basic classes of R objects – Character vectors spp <- c("I.ynga", "I.edulis", "I.macrophylla", "I.punctata", "I.alba") class(spp) length(spp)

  16. Basic classes of R objects – Character vectors • We can use one vector toassignnamestotheother: names(abund) names(abund)<- spp abund

  17. Basic classes of R objects – Logical vectors increm <- c(TRUE, FALSE, FALSE, TRUE, TRUE) names(increm) <- spp class(increm) length(increm) names(increm)

  18. Basic classes of R objects – The Matrix

  19. Basic classes of R objects – The Matrix • Matrices are data organized in two dimensions: rows and columns Columns Rows • Matrices can hold numeric, character orlogical data

  20. Basic classes of R objects – The Matrix • Onewaytocreate a matrixisthethefunction “matrix” seq(1,10) Abund<- matrix(seq(1,10), ncol=5) abund Abund class(abund) class(Abund)

  21. Basic classes of R objects – The Matrix • Matrices can be filled by columns (predetermined option) or by rows Abund.2 <- matrix(seq(1,10), ncol=5, byrow=TRUE) Abund Abund.2 identical(Abund, Abund.2) ?matrix

  22. Basic classes of R objects – The Matrix • A matrixwithabundance data: v1 <- c(10,2,15,20,34,34,2,1,68,57) Abund <- matrix(v1, ncol=5) Abund • Vectorshavelength, matrices alsohavedimensions dim(Abund) ncol(Abund) nrow(Abund) length(Abund)

  23. Basic classes of R objects – The Matrix • For matrices, we can putnamestocolums and rows spp colnames(Abund) colnames(Abund) <- spp rownames(Abund) <- c("plot_A", "plot_B") Abund • We can alsoputnamesto individual observations names(Abund) <- paste("obs", 1:length(Abund), sep="") Abund

  24. Basic classes of R objects – The Matrix • Matrices can alsoholdcharacterorlogicalvalues Spp<- matrix(esp, ncol=5, nrow=2, byrow=TRUE) Spp Increm <- matrix(increm, ncol=5, nrow=2, byrow=TRUE) Increm mode(Abund) mode(Spp) mode(Increm)

  25. Basic classes of R objects – The Matrix • What happens when we try to merge a character and numeric vectors into the same matrix? Abund mode(abund) spp mode(spp) Mixed.matrix <- cbind(spp, abund) Mixed.matrix mode(Mixed.matrix)

  26. Basic classes of R objects – Array • Arrays are verysimilaryto matrices… buttheyhave3 or more dimensions! 2003 2012

  27. Basic classes of R objects – Array • Arrays are verysimilaryto matrices… buttheyhave 3 or more dimensions! Columns Rows 2012 2003 3rd. dimension

  28. Basic classes of R objects – Array • Arrays are verysimilaryto matrices… buttheyhave 3 or more dimensions! Abund Abund.array<-array(data=Abund, dim=c(2,5,2)) Abund.array class(Abund.array) Ej.Array<-array(seq(1, 10*3), dim=c(2,5,3)) Ej.Array

  29. Basic classes of R objects – Factors • Factorscontainvalues of a categoricalvariable and informationotitslevelsortreatments • Forexample, 8 trees of I. yngawithin a plot can havevariousfenologicstates feno.I.ynga<- c("ster.", "ster.", "flower.", "fruit.", "ster.", "flower.", "flower.", "ster.") class(feno.I.ynga) Feno.I.ynga <- factor(x=feno.I.ynga) Feno.I.ynga class(Feno.I.ynga)

  30. Basic classes of R objects – Factors levels(Feno.I.ynga) length(Feno.I.ynga) length(levels(Feno.I.ynga)) plot(feno.I.ynga) plot(Feno.I.ynga) • Theclass of anobjecthelps determine how a functionwillhandleit

  31. Basic classes of R objects – Data Frame • Data frames organize data in two dimensions, each column is a variable; variables can be of different types Variables Observations

  32. Basic classes of R objects – Data Frame • Data frames organize data in two dimensions, each column is a variable; variables can be of different types spp Abund t(Abund) increm spp.code<-1:length(spp) Data<-data.frame(spp.code, spp, t(Abund), increm) Data

  33. Basic classes of R objects – Data Frame class(Data) Data.M <- as.matrix(Data) class(Data.M) Data.M mode(Data.M) dim(Data) dim(Data.M) length(Data) length(Data.M)

  34. Basic classes of R objects – Data Frame x <- c("a", "b") y <- 1:5 z <- 1:6 x.Y <- data.frame(x,y) • Elements (columns) in a data framemusthavethesamelength length(x) length(y) length(z) x.z <- data.frame(x,z) x.z

  35. Basic classes of R objects – R’s List

  36. Basic classes of R objects – List • Lists can contain data of differnt types, dimensions and even classes List 1 2012 2003 2 3

  37. Basic classes of R objects – List Soils.plot <- matrix(c(0.072, 0.16, 5.29, 0.038, 0.071, 4.2), byrow=TRUE, nrow=2) Climate.year <- matrix(c(24, 26, 15, 19), byrow=TRUE, nrow=2) ListData <- list(Abund, Soils.plot, Climate.year) ListData

  38. Basic classes of R objects – List class(ListData) dim(ListData) length(ListData) names(ListData) names(ListData)<-c("Abund.", "Soils", "Climate") ListData str(ListData)

  39. Other classes of R objects • There is a large number of other R objects, • Most rely on the same structure as vectors, matrices, data frames and lists. E.g.: v1 <- rnorm(100, 10, 5) v2 <- v1 + rnorm(100, 0, 2) plot(v2~v1) LM.v2v1 <- lm(v2~v1) summary(LM.v2v1) class(LM.v2v1) str(LM.v2v1)

  40. Basic classes of R objects

  41. Saveand Open Data • Toknowwhattheworkingdirectoryis: getwd() • Tomodifytheworkingdirectory: setwd("C:/MyFiles/Are/InThisFolder") • Alsoyou can gotoFileand use theChangedir…option

  42. Saveand Open Data • Tosave data tables: write.table • Toread data tables: read.table

  43. Save Data • Tosave data tables : ?write.table • Mainarguments: • x:isthe R objectthatyouwanttosave – usually a vector, matrixor data frame • file: isthename and location of the file youwanttocreate • sep: defines the character that separates columns; frequently “,” o “\t”

  44. Save Data M <- matrix(rnorm(100), ncol=5) colnames(M) <- 1:ncol(M) M save.as <- "matriz_M.txt" save.as <- "folder_test/matriz_M.txt" write.table(x=M, file=save.as, sep="\t")

  45. Open Data • To read data tables : read.table • Main arguments: • file: where the file is located and what its name is • header: TRUE or FALSE, whether the first row are the names of the variables • sep: defines the character that separates columns; frequently “,” o “\t”

  46. Open Data Data <-read.table(file = file.choose(), header=TRUE, sep="\t") Data <- read.table(file = "matrix_M.txt", header=TRUE, sep="\t") class(Data) names(Data)

  47. Exercise 3: Objects and opening/saving files • Objective: create and use different types of objects, and practice how to open or save tables with data

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