abline {graphics} add straight lines to plot 2 4 5 8--10 12 13 abs {base} absolute value 3 12 acf {stats} autocorrelation function 12 add.grid {datasupport.R} add coastal regions to best.use 6 all {base} are all values true? 8 apply {base} apply functions over array margins 6 apropos {utils} find objects by name 2 ar {stats} fit autoregressive (AR) models 10 arima {stats} fit ARIMA models 10 arrows {graphics} add arrows to plot 5 6 as {methods} force object to belong to class 5 9 as.array {base} coerce to array 4 as.character {base} convert to character vector 5 as.data.frame {base} convert to data frame 6 as.Date {base} date conversion to/from character 4 5 10 as.integer {base} convert to integer 7 9 as.matrix {base} convert to matrix 5 10 12 as.numeric {base} convert to numeric 4 6 8 10--12 as.POSIXct {base} date/time conversion functions 5 as.ppp {spatstat} convert to spatial point pattern 11 as.psp {spatstat} convert to spatial lines 11 as.sociomatrix {network} coerce network to socio matrix 10 as.vector {base} convert to vector 5 6 10 as.windrose {oce} create wind rose object 13 attach {base} attach object to search path 2 10 attr {base} object attributes 5 11 axis {graphics} add axis to plot 4--8 10 12 barplot {graphics} create bar plot 2 4 7 12 bbox {sp} retrieve bounding box 9 12 beta.select {LearnBayes} find beta prior given quantiles 4 betweenness {sna} centrality scores of graph nodes 10 bic.glm {BMA} Bayesian model averaging for GLM 12 bic.poisson {prediction.R} Poisson prediction from BMA 12 blue2red {colorRamps} create gradient color ramp 9 12 blue2yellow {colorRamps} create gradient color ramp 9 boot {boot} bootstrap resampling 3 boot.ci {boot} bootstrap confidence interval 3 bootstrap {bootstrap} bootstrap resampling 12 box {graphics} draw box around plot 5 6 11 13 boxplot {graphics} create box and whisker plot 5 8 9 brewer.pal {RColorBrewer} create color palette 11 c {base} create vector or list 2--13 cat {base} concatenate and print 2 cbind {base} combine objects by columns 4--6 11 12 ceiling {base} smallest integer not less than x 5 cens {gamlss.cens} fit GAM using censored data 8 choose {base} n choose k 3 chooseCRANmirror {utils} choose CRAN mirror site 2 citation {utils} create citation for package 8 11 class {base} object class 2 5 6 coda.samples {rjags} samples in MCMC list format 4 12 coefficients {stats} extract model coefficients 11 13 colMeans {base} column means 11 colnames {base} column names 6 8--12 colorRampPalette {grDevices} color interpolation 5 9 12 colourmap {spatstat} color lookup tables 11 confint {stats} confidence ints model parameters 7 contour {graphics} plot contours 5 coordinates {sp} set/get spatial coordinates 5 9 11--13 coplot {graphics} create conditioning plot 5 cor {stats} correlation coefficient 3 7 cor.test {stats} correlation test 3 cos {base} cosine function 13 CRS {sp} class coordinate reference system 5 9 cumsum {base} cumulative sums 4 5 10 curve {graphics} draw function curve 3 4 8 12 13 cut {base} divide range into intervals 8 daisy {cluster} dissimilarity matrix 11 data.frame {base} create data frames 3 6--13 dbeta {stats} density beta distribution 4 dbinom {stats} density binomial distribution 3 dchisq {stats} density chi-squared distribution 11 degree {sna} degree centrality of node 10 density {stats} kernel density estimation 4 5 8 11 densityplot {lattice} kernel density estimation lattice 4 5 dev.off {grDevices} turn off current graphic device 2 dgamma {stats} density gamma distribution 12 13 diameter {igraph} diameter of graph 10 diff {base} lagged differences 3 10 difftime {base} time intervals 4--6 dim {base} dimensions of object 2 6 7 dimnames {base} dimension names 7 12 discint {LearnBayes} highest prob int discrete distr 4 dist {stats} distance matrix 11 dnbinom {stats} density negative binomial dist 12 dnorm {stats} density normal distribution 3 do.call {base} execute function call 8 10 dpois {stats} density Poisson distribution 3 7 drop1 {stats} drop model term 3 dweibull {stats} density Weibull distribution 3 ecdf {stats} empirical cumulative distribution 8 effectiveSize {coda} effective sample size for mean 12 ellipse {ellipse} outline confidence region 3 envelope {spatstat} simulation envelope of summary 11 equal.count {lattice} create plot shingles 5 example {utils} run example from online help 2 exp {base} exponential function 4 7--10 12 expression {base} unevaluated expressions 3--13 factor {base} encode vector as factor 2 10 factorial {base} factorial function 3 filter {stats} linear filter on time series 10 findColours {classInt} assign colors from classInt object 5 fit.variogram {gstat} fit model to sample variogram 9 fitdistr {MASS} fit univariate distributions 13 fitted {stats} extracts fitted values 3 10 fivenum {stats} five number summary 5 7 8 12 formatC {base} c-style formats 6 gamlss {gamlss} fit generalized additive models 10 gelman.plot {coda} shrink factor 12 geocode {ggmap} geocode google map location 5 get.max {get.max.R} get cyclone maxima 6 12 13 get.tracks {getTracks.R} get cyclone tracks 6 get.var.ncdf {ncdf} read from netCDF file 6 get.visibility {get.visibility.R}create visibility graph 10 getwd {base} retrieve working directory 2 ggmap {ggmap} create grammar of graphics map 5 ggmapplot {ggmap} plot ggmaps 5 ggplot {ggplot2} create grammar of graphics plot 6 13 glm {stats} fit generalized linear models 7 8 10 12 gpd.fit {ismev} fit generalized Pareto distr 8 graph.edgelist {igraph} methods for creating graphs 10 gray {grDevices} gray level specification 6 grid {graphics} add grid to plot 2 4 7 9--13 grid.circle {grid} draw circle 4 grid.curve {grid} draw curve 4 grid.newpage {grid} move to new page on grid device 5 grid.text {grid} add text 4 gridat {sp} N-S and E-W grid locations 5 gridlines {sp} add N-S and E-W grid lines 5 gsub {base} pattern matching and replacement 10 gwr {spgwr} geographically weighted regression 9 gwr.sel {spgwr} select bandwidth for gwr 9 head {utils} return first part of object 2 5--10 12 help {utils} open help page 2 HexPoints2SpatialPolygons {sp} make polygons from grid object 9 12 hist {graphics} compute/plot histogram 4--6 9 12 13 histogram {lattice} histogram using lattice 5 ifelse {base} conditional element selection 9 image {graphics} display color image 5 image.plot {fields} image plot with legend 12 imageplot.bma {BMA} image plot of models in BMA 12 imageplot.bma2 {imageplot.bma2.R}modification of imageplot.bma 12 imageplot.bma3 {imageplot.bma3.R}modification of imageplot.bma 12 import.grid {datasupport.R} import grid boundaries 6 install.packages {utils} install packages from repository 2 is.na {base} which elements are missing? 6 ISOdate {base} date/time conversion 4 6 ISOdatetime {base} date/time conversion 6 jags.model {rjags} create JAGS model object 4 12 Kest {spatstat} second moment spatial function 11 Kinhom {spatstat} inhomogeneous K function 11 kmeans {stats} perform k-means clustering 11 krige {gstats} perform kriging 9 lag.listw {spdep} compute spatial lag 9 12 lag.plot {stats} time series lag plots 5 lapply {base} apply function over list 6 10 12 layout {graphics} plot arrangement 4 7 13 leap_year {lubridate} is leap year? 5 legend {graphics} add legend to plot 3--6 8 10 12 length {base} length of object 2--13 library {base} load package to workspace 2 lines {graphics} add connected lines to plot 3--13 list {base} construct and check for lists 4 7 9 11 12 lm {stats} fit linear models 3 5 7 9 13 load {base} reload saved data sets 4 6 7--13 loess {stats} fit local polynomial regressions 13 loess.smooth {stats} scatter plot with loess smooth 9 log {base} logarithmic function 2 map {maps} draw maps 5 6 9 11--13 map2SpatialLines {maptools} convert map object to spatial line 5 9 11 12 marks {spatstat} get/set marks of point pattern 11 matrix {base} create a matrix 5 7 9 13 max {base} sample maximum 2 3 8 11 mean {base} sample mean 2 3 6--9 11 median {stats} sample median 3 9 10 12 melt {reshape} reshape object for easy casting 10 merge {base} merge data frames 8 13 min {base} sample minimum 3 8 minimum.spanning.tree {igraph} minimum spanning tree of graph 10 moran {spdep} compute moran's I 9 12 moran.test {spdep} test spatial autocorrelation 9 mrl.plot {ismev} mean residual life plot 8 mrl.plot2 {mrl.plot2.R} revised mean residual life plot 8 mtext {graphics} add margin text 4--8 10--13 mvrnorm {MASS} samples from multivariate normal 3 mycontour {LearnBayes} contour bivariate density 4 names {base} get/set object names 2 5 6 9 11 12 nb2listw {spdep} spatial weights for neighbor list 9 12 nb2WB {spdep} output spatial weights for WinBUGS 12 ncol {base} number of columns in array 12 network {network} make/coerce to network object 10 now {lubridate} get current date 5 nrow {base} number of rows in array 9 11 numeric {base} create numeric vector 3 4 7 8 10 12 13 object.size {utils} space allocation for object 6 objects {base} list objects in working directory 2 open.ncdf {ncdf} open netCDF file 6 optim {stats} general purpose optimizer 12 options {base} set/get options 2 order {base} return permutation in ascending 10 11 outer {base} outer product of arrays 7 12 over {sp} overlay points grids and polygons 9 12 13 pairs {graphics} matrix of scatter plots 3 par {graphics} set graph parameters 2--13 parse {base} parse expressions 5 paste {base} concatenate character strings 3--13 pbeta {stats} beta distribution function 4 pbetap {LearnBayes} predict dist binom w/ beta prior 4 pchisq {stats} chi-squared distribution function 7 pgamma {stats} gamma distribution function 12 pixellate {spatstat} convert object to pixel image 11 plot {graphics} generic x-y plotting 3--13 plot.im {spatstat} plot pixel image 11 plot.rq.process {quantreg} plot quantile regression process 8 plot.windrose2 {plot.windrose2.R}modified plot wind rose diagram 13 plotfits {correlationfuns.R} annual count vs cluster rate 11 plotmo {plotmo} plot model response 7 pnbinom {stats} negative binomial distribution 12 pnorm {stats} normal distribution function 3 points {graphics} add points to plot 4--8 10--13 poly2nb {spdep} neighborhood from polygon list 9 12 polygon {graphics} draw polygons with given vertices 4 5 7 8 10 11 13 Polygon {sp} create spatial polygons object 9 13 Polygons {sp} polygons object 9 ppois {stats} Poisson distribution function 3 7 predict {stats]} generic function for predictions 3 5 7 12 13 print {base} print objects 3 5--7 9 10 12 prod {base } product of values in object 3 proj4string {sp} projection attributes for sp data 9 11 12 projInfo {rgdal} list proj.4 tag information 5 prop.test {stats} test of equal or given proportions 4 pt {stats} student-t distribution function 3 pushViewport {grid} navigate grid viewport tree 5 q {base} terminate session 2 qbeta {stats} quantile beta distribution 4 qnorm {stats} quantile normal distribution 3 8 qplot {ggplot2} quick plot wrapper for ggplot 5 10 qqline {stats} plot line on qqplot/qqnorm 5 qqnorm {stats} quantile quantile plot 5 qr {base} qr decomposition of a matrix 12 qr.Q {base} recover Q matrix from qr object 12 qr.R {base} recover R matrix from qr object 12 quadratcount {spatstat} quadrat counts for point pattern 11 quantile {stats} sample quantiles 2--4 8 10 12 13 randomForest {randomForest} random forest algorithm 7 range {base} range of values 5 rank {base} sample ranks 3 8 rbeta {stats} random numbers beta distribution 4 rbind {base} combine objects by rows 11 rbinom {stats} random numbers binomial 4 7 read.bugs {R2WinBUGS} read output files in coda format 4 read.csv {utils} read comma separated values file 4 6 7 11 read.table {utils} read space separated values file 2--12 readCov {datasupport.R} read environmental covariates 6 readShapeSpatial {maptools} read shape files 5 regionTable {correlationfuns.R} table counts by region 11 rep {base} replicate elements 2 6 8 require {base} load package to workspace 2--13 resid {stats} extract model residuals 3 rev {base} reverse elements 2 4 6--9 11--13 rgamma {stats} random numbers gamma distribution 4 rle {base} run length encoding 3 rlWeibPois {CountyWinds.R} return level Weibull Poisson model 8 rm {utils} remove objects from workspace 2 6 8 rMatClust {spatstat} simulate Matern cluster process 11 rMaternI {spatstat} simulate Matern inhibition process 11 rnorm {stats} random numbers normal distribution 3 roc {roc.R} plot roc curve 7 round {base} round the number 3--10 12 rowMeans {base} row averages 11 rownames {base} get/set row names in data frame 6 7 12 rpois {stats} random count Poisson distribution 3 7 11 rq {quantreg} fits quantile regression models 8 13 rug {graphics} add rug to plot 4--6 8 10 runif {stats} random number uniform distribution 4 11 rweibull {stats} random number Weibull distribution 3 sample {base} random samples and permutations 3 7 8 12 sampleParameters {CountWinds.R} sample return levels 8 sapply {base} wrapper for lapply 8 10--12 save {base} save objects 6 savgol.best {savgol.R} filter best track data 6 scale {base} scale and center object 11 scatterhist {scatterplothist.R} scatter plot with histogram 5 sd {stats} sample standard deviation 2 3 seq {base} sequence generator 2--5 7--9 12 13 set.seed {base} set seed value for random numbers 3 7 signif {base} round the number 3 simcontour {LearnBayes} random draws bivariate density 4 sin {base} sine function 2 13 slot {methods} list slots in object 9 12 sort {base} sort elements of a vector 5 8 10 source {base} input code from file 4--8 10 11 13 SpatialPointsDataFrame {sp} create spatial points data frame 5 SpatialPolygons {sp} create spatial polygons 9 SpatialPolygonsDataFrame {sp} create spatial polygons data frame 9 12 split {base} divide into groups 11 12 13 spplot {sp} plot method for spatial data 5 9 12 spsample {sp} sample locations in spatial object 9 spTransform {rgdal} map projections and transforms 5 9 11 sqrt {base} square root function 2 3 7 8 12 step {stats} choose model stepwise 3 stl {stats} seasonal decomposition of series 10 str {utils} display object structure 5 6 9 10 strptime {base} date/time conversion 5 strsplit {base} split elements of character vector 6 12 subset {base} subset data objects 3 6 10 11 13 substring {base} substring of character vector 12 sum {base} sum of vector elements 2--4 6 7 9--12 summary {base} summarize objects 2--5 7--9 11--13 switch {base} select one from list of choices 12 Sys.time {base} get current date and time 6 Szero {spdep} give constant for spatial weights 9 12 t {base} matrix transpose 11 12 t.test {stats} perform student's-t test 3 table {base} cross tabulations 2--4 7 10 13 tail {utils} return last part of object 3 5 terrain.colors {grDevices} color palette 11 testfits {correlationsfuns.R} test for time clustering 11 text {graphics} add text to plot 4 5 9 11 time {stats} create vector of times 5 title {graphics} add title to plot 12 toBibtex {util} convert to bibtex/latex 8 topo.colors {grDevices} color palette 9 traceplot {code} successive iterations of mcmc 12 transitivity {igraph} prob adjacent vertices connected 10 tree {tree} regression/classification tree 7 trellis.par.get {lattice} get parameters of trellis display 12 trellis.par.set {lattice} set parameters of trellis display 12 try {base} try expression 2 ts {stats} create time series object 5 10 unique {base} remove duplicate elements 12 unlist {base} flatten lists 6 11 unmark {spatstat} remove marks from spatial points 11 update {stats} refit model 4 5 9 12 var {stats} sample variance 2 3 7 var.test {stats} test comparing two variances 3 variogram {gstat} sample variogram 9 viewport {grid} create grid viewport 5 wday {lubridate} get day of the week 5 week {lubridate} get week of the year 5 which {base} which indices are true? 2 10 12 which.max {base} where is the maximum? 3 wilcox.test {stat} rank/sign test difference in mean 3 with {base} evaluate expression in data enviro 5 6 with_tz {lubridate} get date-time in diff time zone 5 write.table {utils} output data frame 6 writeDataFileR {writedatafileR.R}output WinBUGS data 12 xtable {xtable} create export table 3 7 8 10--12 year {lubridate} get/set year of date-time object 5 ymd {lubridate} parse dates to specified formats 6 zeroinfl {gamlss} fit zero-inflated Poisson model 7