cheat: Cheat Sheet
In JVAdams/jvamisc: A Collection of Utility Functions

A non-functioning function, which allows me to create a cheat sheet collection of examples.

cheat()

## Not run: 

# read in xls files
library(XLConnect)
wb <- loadWorkbook("c:/temp/junk.xlsx")
dat <- readWorksheet(wb, sheet=getSheets(wb)[1], startRow=1)






### update package ###
#update version number, R version, date
R.version.string
jvamisc::cleanup()
myPkg <- "jvamisc"
jvamisc::pkgup(myPkg)
jvamisc::pkgin(myPkg)

del C:\Users\jvadams\*.gz
"C:\Program Files\R\R-4.1.0\bin\x64\R.exe" CMD build C:\JVA\GitHub\jvamisc --resave-data
"C:\Program Files\R\R-4.1.0\bin\x64\R.exe" CMD check C:\Users\jvadams\jvamisc_1.0.2.9000.tar.gz

char <- paste0("package:", myPkg)
mvbutils::foodweb(where=char, charlim=50, boxcolor="transparent")














### package and function connections ###
# to see all of the functions and their interdependencies in WHERE
library(mvbutils)
library(jvamisc)
foodweb(where="package:jvamisc", charlim=50)
# to see what functions in WHERE, the function PRUNE depends on ...
library(sp)
library(maptools)
foodweb(where="package:sp", prune="latlong2")
foodweb(where="package:maptools", prune="latlong2")

### Greek and math symbols ###
# http://www.decodeunicode.org/
plot(1, 1, xlab="Length  (\U03BCm)", ylab="Temperature  (\U00b0 C)",
 main="Lambda squared=\\U03BB\\U00B2=\U03BB\U00B2")

### map scale and north arrow ###
library(GISTools)
map("state", region= "ohio")
maps::map.scale(x=-84, y=40, ratio=FALSE, relwidth=0.2)
north.arrow(xb=-83.4, yb=40.4, len=0.05, lab="N")

### error bars ###
x <- 1:10
y <- sample(10)
noise <- abs(rnorm(10))
plot(x, y, ylim=range(y-noise, y+noise))
arrows(x, lo, x, hi, length=0.1, angle=90, code=3)

### error shading ###
x <- 1:10
y <- sample(10)
noise <- abs(rnorm(10))
plot(x, y, ylim=range(y-noise, y+noise), type="n")
shadepoly(x, y, y-noise, y+noise)

### confidence limits ###
# of the mean
p <- predict(fit, interval="confidence")
# of a new observation
p <- predict(fit, interval="prediction")
# if you have a gam ...
p <- predict(fit, se.fit=TRUE)
pe <- p$fit
tt <- qt(1 - 0.05/2, fit$df.residual)
pl <- pe + tt*p$se.fit
pu <- pe - tt*p$se.fit

### multiple comparison Tukey test approach 1 ###
amod <- aov(breaks ~ tension, data=warpbreaks)
TukeyHSD(amod)

### multiple comparison Tukey test approach 2 ###
library(multcomp)
amod <- aov(breaks ~ tension, data=warpbreaks)
mc <- glht(amod, linfct=mcp(tension="Tukey"))
summary(amod)
summary(mc)
confint(mc)
dev.new()
plot(mc)

### set up two-way ANOVA with interactions ###
fit <- aov(y ~ f1 + f2 + f1:f2)
# set up linear hypotheses for all-pairs of both factors
wht <- glht(fit, linfct=mcp(f1="Tukey", f2="Tukey"))
# cf. Westfall et al. (1999, page 181)
summary(wht, test=adjusted("Shaffer"))

### label months on day of year or Julian day axis ###
plot(101:200, rnorm(100), axes=FALSE)
axis(1, at=doy(as.Date(paste(2000, 1:12, 1, sep="-")))-0.5,
 labels=FALSE)
axis(1, at=doy(as.Date(paste(2000, 1:12, 15, sep="-"))),
 labels=month.abb, tick=FALSE)
axis(2)
box()

### contour plot ###
library(akima)
y <- rnorm(50)
x <- runif(50)
z <- 2*x^2 - y^2 + 4
contour(interp(x, y, z, duplicate="mean"))

### get lat longs for locations ###
library(dismo)
geocode(c("1600 Pennsylvania Ave NW, Washington DC",
 "Luca, Italy", "Kampala", "Antigo, WI"))

### get a lat lon for a location ###
# from R-help post by Phil Spector, UC Berkeley, Mar 16, 2010
# https://stat.ethz.ch/pipermail/r-help/2010-March/232090.html
library(XML)
root <- xmlRoot(xmlTreeParse(
 paste0("http://maps.google.com/maps/api/geocode/xml?address=",
 "Antigo, WI", "&sensor=false")))
lat <- xmlValue(root[["result"]][["geometry"]][["location"]][["lat"]])
lon <- xmlValue(root[["result"]][["geometry"]][["location"]][["lng"]])

### plot points on a map ###
library(RgoogleMaps)
MyMap <- GetMap.bbox(c(-80, -79), c(45, 46), maptype="terrain",
 destfile="junk.png", zoom=8)
PlotOnStaticMap(MyMap, lat=seq(45, 46, 0.1), lon=seq(-80, -79, 0.1),
col="red", pch=16)

### make a quick map ###
library(ggmap)
qmap("Antigo, Wisconsin", zoom=14)

### convert between lat/lon and projections ###
library(proj4)
project(xy, proj, inverse=FALSE, degrees=TRUE,
 silent=FALSE, ellps.default="sphere")

### other map stuff of interest ###
# http://cartodb.com/
# https://github.com/Vizzuality/cartodb-r

### see the details of a function
methods(function)
package:::function.default

### dendrogram reorder ###
x <- sample(100, 10)
names(x) <- x
hc <- hclust(dist(x))
dd <- as.dendrogram(hc)
dd.reorder <- reorder(dd, x, mean)
par(mfcol=1:2)
plot(dd, main="default dendrogram")
plot(dd.reorder, main="reordered")

### background jpeg image in plot ###
library(jpeg)
x <- rnorm(20)
y <- rnorm(20)
img <- readJPEG("C:/Users/Public/Pictures/Sample Pictures/Chrysanthemum.jpg")
plot(x, y, type="n")
pusr <- par("usr")
rasterImage(img, pusr[1], pusr[3], pusr[2], pusr[4])
points(x, y, pch=16, cex=3)

### fit all subsets models ###
# select all possible combinations of 8 independent variables
var.names <- names(train)[1:8]
comb <- as.data.frame(all.combs(8))
dimnames(comb)[[2]] <- var.names
fits <- vector("list", dim(comb)[1])
fits[[1]] <- lm(lpsa ~ 1, dat=train)
for(i in 2:length(fits)) {
  fits[[i]] <- lm(formula=paste("lpsa ~",
   paste(var.names[comb[i, ]==1], collapse=" + ")), dat=train)
  }
comb2 <- comb
comb2$nx <- apply(comb, 1, sum)
# AIC
aic <- AICc(fits)
aic <- aic[order(as.numeric(row.names(aic))), -1]
comb2 <- data.frame(comb2, aic)
comb2 <- comb2[order(comb2$aicc), ]
comb2[comb2$daicc <= 2, ]
fits[[as.numeric(row.names(comb2)[1])]]

### regular expression examples ###
# get rid of spaces before commas or periods
t2 <- gsub("[[:space:]]\\.", "\\.", charvec)
gsub("[[:space:]]\\,", "\\,", t2)
# insert a space between all punctuation and letters
gsub("([[:punct:]])([[:alpha:]])", "\\1 \\2", charvec)
# add a period to any single alpha character
t2 <- gsub("([[:space:]][[:alpha:]])([[:space:]])", "\\1\\.\\2", charvec)
gsub("([[:space:]].)$", "\\1\\.", t2)
# insert a space before and after an equal sign
t2 <- gsub("([[:alpha:]]|[[:punct:]])=", "\\1 =", charvec)
gsub("=([[:alpha:]]|[[:punct:]])", "= \\1", t2)
# make sure Jr has a period after it
gsub("Jr$", "Jr.", t2)
# remove all apostrophes (and any surrounding spaces)
t2 <- gsub('[[:space:]]\\"[[:space:]]', "", charvec)
t2 <- gsub('[[:space:]]\\"', "", t2)
gsub('\\"[[:space:]]', "", t2)
# cut off equal sign and everything after
gsub("=.*", "", charvec)
# replace all punctuation marks with spaces
gsub("[[:punct:]]", " ", charvec)
# get rid of leading and trailing white space
gsub("^[ \t]+|[ \t]+$", "", charvec)
# change double spaces to single spaces
gsub("[ \t]+", " ", charvec)

### convert a data frame to json ###
library(RJSONIO)
data <- toJSON(y)
cat(data, file="data.json")

### read in internet table ###
library(XML)
allTables <- readHTMLTable(
 "http://en.wikipedia.org/wiki/United_States_presidential_election,_2012")
# Look at the allTables object to find the specific table we want
str(allTables)
# if you have problems reading the URL, you could try this ...
mylines <- readLines(url(
 "http://en.wikipedia.org/wiki/United_States_presidential_election,_2012"))
closeAllConnections()
mylist <- readHTMLTable(mylines, asText=TRUE)
mytable <- mylist1$xTable

### allow users to browse to a file ###
library(tcltk)
myfile <- tk_choose.files(default="C:/JVA/*.csv")

### one slider ###
library(rpanel)
density.draw <- function(panel) {
  plot(density(panel$x, bw=panel$h))
  panel
  }
panel <- rp.control(x=rnorm(50))
rp.slider(panel, h, 0.5, 5, log=TRUE, action=density.draw)

### two sliders ###
library(rpanel)
loess.draw <- function(panel) {
  plot(panel$x, panel$y)
  lines(loess.smooth(panel$x, panel$y, span=panel$s, degree=panel$d))
  panel
  }
panel <- rp.control(x=rnorm(50), y=rnorm(50), s=rep(3, 50), d=1)
rp.slider(panel, s, 0.1, 10, showvalue=TRUE, action=loess.draw)
rp.slider(panel, d, 1, 2, showvalue=TRUE, action=loess.draw)

### animation ###
for(i in 1:10) {
  dev.new()
  plot(1:10, 1:10, type="l")
  points(i, i, pch=16, cex=2)
  savePlot(filename=paste("Rplot", i), type="bmp")
}
cat(paste("Plots saved to", getwd()), "\n")
# GIF Construction Set
# Animation wizard
# add the bitmaps and save as gif animation file
# GIMP file open as layers ... save as animated gif

## End(Not run)