## ----setup, include=FALSE------------------------------------------------ knitr::opts_chunk$set(echo = TRUE) library(knitr) set.seed(12314159) imageDirectory <- "./img" dataDirectory <- "./data" path_concat <- function(path1, path2, sep="/") {paste(path1, path2, sep = sep)} ## ----libraries----------------------------------------------------------- library(eikosograms) library(gridExtra) ## ----UCBAdmissions 2 way, eval = FALSE, echo = TRUE, fig.width=8, fig.height=4, fig.align="center", out.width="80%"---- # e1 <- eikos(Admit ~ Gender, data = UCBAdmissions, # yaxs = FALSE, xaxs = FALSE, # draw = FALSE) # e2 <- eikos(Admit ~ Dept, data = UCBAdmissions, # yaxs = FALSE, xaxs = FALSE, # draw = FALSE) # # Using the gridExtra package, draw these in a single plot # grid.arrange(e1, e2, nrow = 1) ## ----png UCBAdmissions 2 way, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="80%"---- include_graphics("img/DataAnalysis/UCB2way.png") ## ----UCBAdmissions 3 way, echo = TRUE, eval = FALSE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- # eikos(Admit ~ Gender + Dept, data = UCBAdmissions, # yaxs = FALSE, xaxs = FALSE, # lock_aspect = FALSE, # xlab_rot = 90, xvals_size = 8, # ispace = list(bottom = 15)) ## ----png UCBAdmissions 3 way, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="80%"---- include_graphics("img/DataAnalysis/UCB3way.png") ## ----UCBAdmissions, eval = FALSE, echo = TRUE, fig.width=8, fig.height=4, fig.align="center", out.width="80%"---- # eikos(Gender ~ Dept, data = UCBAdmissions, yprobs = seq(0,1,0.25), xaxs = FALSE) ## ----png UCBAdmissions, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="50%"---- include_graphics("img/DataAnalysis/UCBAdmissions.png") ## ----read lizard data---------------------------------------------------- lizards <- read.table("data/AnolisLizards.txt", header=TRUE) lizards ## ----separate species---------------------------------------------------- sagrei <- lizards[lizards$species == "sagrei", -1] augusticeps <- lizards[lizards$species == "augusticeps", -1] ## ----sagreiTable, eval = TRUE, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- sagreiTable <- xtabs(count ~ perch_height_ft + perch_diameter_inches, data = sagrei) ## ----sagrei perch, eval = FALSE, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- # eikos(perch_height_ft ~ perch_diameter_inches, data = sagreiTable, # main = "Habitat of adult male anolis sagrei lizards") ## ----png sagrei perch, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="50%"---- include_graphics("img/DataAnalysis/sagreiPerch.png") ## ----sagrei independence------------------------------------------------- chisq.test(sagreiTable) ## ----augusticepsTable, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- augusticepsTable <- xtabs(count ~ perch_height_ft + perch_diameter_inches, data = augusticeps) ## ----augusticeps perch, eval = FALSE, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- # eikos(perch_height_ft ~ perch_diameter_inches, data = augusticepsTable, # main = "Habitat of adult male anolis augusticeps lizards") ## ----png augusticeps perch, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="50%"---- include_graphics("img/DataAnalysis/augusticepsPerch.png") ## ----lizards three way table, eval = TRUE, echo = TRUE, fig.width=7, fig.height=4, fig.align="center", out.width="80%"---- lizardsTable <- xtabs(count ~ species + perch_height_ft + perch_diameter_inches, data = lizards) ## ----lizards three way, eval = FALSE, echo = TRUE, fig.width=7, fig.height=4, fig.align="center", out.width="80%"---- # eikos(species ~ . , data = lizardsTable, lock_aspect = FALSE, yprobs = seq(0,1, 0.1)) ## ----png lizards three way, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="50%"---- include_graphics("img/DataAnalysis/lizards3way.png") ## ---- echo = FALSE------------------------------------------------------- knitr::kable(head(mtcars)) ## ----mtcars factor creation---------------------------------------------- mtcars$vs <- factor(mtcars$vs, labels = c("V-shaped", "straight")) mtcars$am <- factor(mtcars$am, labels = c("automatic", "manual")) ## ---- echo = FALSE------------------------------------------------------- knitr::kable(head(mtcars)) ## ----am vs, eval = FALSE, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- # eikos(am ~ vs, data = mtcars) ## ----png r am vs, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="50%"---- include_graphics("img/DataAnalysis/amvs.png") ## ----am and ordinal 1, eval = FALSE, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- # eikos(am ~ cyl, data = mtcars) ## ----png am and ordinal 1, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="40%"---- include_graphics("img/DataAnalysis/amordinal1.png") ## ----ordinal 2, eval = FALSE, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- # eikos(gear ~ cyl, data = mtcars) ## ----png ordinal 2, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="37%"---- include_graphics("img/DataAnalysis/ordinal2.png") ## ----poisson model, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- fittedModel <- glm(count ~ species + perch_height_ft, family="poisson", data = lizards) ## ----poisson model fitted data, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- # Can simply append the fitted values to the lizards to get a new data frame lizardsFit <- data.frame(lizards, fit = fittedModel$fitted.values) # and create the table fitTable <- xtabs(fit ~ species + perch_height_ft, data=lizardsFit) ## ----poisson model asserts, eval = FALSE, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- # eikos("species", "perch_height_ft", data = fitTable) ## ----png poisson model asserts, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="60%"---- include_graphics("img/DataAnalysis/poisson1.png") ## ----poisson model 3way, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- fittedModel3way <- glm(count ~ species + perch_height_ft + perch_diameter_inches + perch_height_ft * species + perch_diameter_inches * species, family="poisson", data = lizards) ## ----poisson model fitted data 3way, eval = FALSE, echo = TRUE, fig.width=12, fig.height=4, fig.align="center", out.width="80%"---- # # Can simply append the fitted values to the lizards to get a new data frame # lizardsFit3way <- data.frame(lizards, fit = fittedModel3way$fitted.values) # # and create the table # fitTable3way <- xtabs(fit ~ species + perch_height_ft + perch_diameter_inches, data=lizardsFit3way) # # and show the eikosograms # eikos(y = "perch_diameter_inches", x = c("perch_height_ft", "species"), data = fitTable3way, # xlab_rot = 30) ## ----png poisson model fitted data 3way, eval = TRUE, echo = FALSE, fig.width=8, fig.height=4, fig.align="center", out.width="60%"---- include_graphics("img/DataAnalysis/poisson2.png")