R package 'pascal'

Purpose

This R package contains a collection of functions I programmed mainly for my own use. I make them available here mainly for my own collaborators. Some functions are legacy code for which certainly there are (possibly better) implementations on CRAN.

These functions are reasonably well tested but use them at your own risk. Also, I do not provide any support. In case you find a bug, however, I am happy if you report it.

Content

I stopped documenting the functions by category, but here is a list of all objects and functions:

ls.str("package:pascal")

addColumns : function (trg, src, key, cols, after = NULL, before = NULL)
addpoly : function (mem, x, y1, y2)
aggr : function (d, factors = NULL, newcols = NULL, expand = FALSE, parallel = FALSE)
angles : Formal class 'standardGeneric' [package "methods"] with 8 slots aov.ftest : function (aovobj, test.formula, table = FALSE)
aov.ko : function (formula, data = NULL, projections = FALSE, qr = TRUE, contrasts = NULL, ...)
apply2D : function (m, x, y = NULL)
area : Formal class 'standardGeneric' [package "methods"] with 8 slots arrows2D : Formal class 'standardGeneric' [package "methods"] with 8 slots as.data.frame : Formal class 'standardGeneric' [package "methods"] with 8 slots asreml.nvc : function (...)
binvar : function (x, frac, width = 1)
bottom.axis : function (...)
catenary : function (x, a = NULL, dx = 1, y1 = 0, y2 = 0, smax = NULL)
catenary_normal : function (x, a = NULL, dx = 1, y1 = 0, y2 = 0, smax = NULL)
checkSink : function ()
circle2D : Formal class 'standardGeneric' [package "methods"] with 8 slots circumcircle : Formal class 'standardGeneric' [package "methods"] with 8 slots circumference : Formal class 'standardGeneric' [package "methods"] with 8 slots cloglog : function (x)
close_all : function ()
combn2 : function (x, m, replace = FALSE, FUN = NULL)
corner.label : function (label = NULL, pos = "topleft", units = "char", dist = 1, fun = NULL, frame = "plot", ...)
cot : function (z)
cotpi : function (z)
current_time : function (fmt = "%d-%b-%Y %H:%M:%S")
deleteColumns : function (d, cols, rx = FALSE)
demo2D : function ()
disableSink : function ()
E12 : num [1:12] 1 1.2 1.5 1.8 2.2 2.7 3.3 3.9 4.7 5.6 ... E24 : num [1:24] 1 1.1 1.2 1.3 1.5 1.6 1.8 2 2.2 2.4 ... E48 : num [1:48] 1 1.05 1.1 1.15 1.21 1.27 1.33 1.4 1.47 1.54 ... ellipse : function (data = NULL, cov = NULL, center = NULL, level = 0.95, npoints = 100)
emptyPlot : function (xlim = c(0, 1), ylim = c(0, 1), asp = NA, xpd = NA, xlab = "", ylab = "", bty = "n", xaxs = "i", yaxs = "i", xaxt = "n", yaxt = "n", ...)
enableSink : function (enabled = TRUE)
escape : function (x, to.escape = ":")
finite.only : function (x)
flushpoly : function (mem)
getDist : function (d, i, j)
getObjects : function (cls = "function")
getResolution : function ()
gfx2D : function (tx = c(0, 0), ty = tx[2], sx = c(1, 1), sy = sx[2], rot = 0)
glimpse : function (..., len = 5, pre = 1, post = 0, between = 1)
gline : function (x, y, frame = "plot", ...)
greatestCommonDenominator : function (a, b)
groupSpace : function (d, cols, equal = FALSE)
grow : Formal class 'standardGeneric' [package "methods"] with 8 slots guess_decompressor : function (file)
heading : function (txt = NULL, width = 80, right = FALSE, bottom = FALSE, char = "#", spc = " ", side.char = char, corner.char = rep(char, 4), post = 1, pre = 0, center = FALSE)
identity2D : function ()
incircle : Formal class 'standardGeneric' [package "methods"] with 8 slots indexof : function (d = NULL, col = NULL)
invcloglog : function (x)
isect : function (x1, y1, x2, y2, segment = T, eps = 1e-06)
killfactors : function (d, restore.numerics = FALSE, cols = seq_along(names(d)))
label : function (x, y, label = NULL, units = c("native", "lines"), just = "center", rot = 0, fun = NULL, frame = "plot", ...)
leastCommonMultiple : function (a, b = NULL)
left.axis : function (...)
lines2D : Formal class 'standardGeneric' [package "methods"] with 8 slots logstc : function (x, a = 1, b = 1, tau = 1)
logstc.der : function (x, a = 1, b = 1, tau = 1)
logstc.der2 : function (x, a = 1, b = 1, tau = 1)
max_NAsafe : function (x)
mean_NAsafe : function (x)
median_NAsafe : function (x)
memused : function (print = TRUE, total = TRUE, objs = TRUE, top = 10, base2 = FALSE, env = globalenv())
min_NAsafe : function (x)
modalpha : function (x, k = NULL, alpha = NULL)
months.len : int [1:12] 31 28 31 30 31 30 31 31 30 31 ... moveColumns : function (d, cols, after = NULL, before = NULL)
NAtozero : function (x)
newpoly : function (col = NULL, angle = NULL, density = NULL, lwd = NULL, lty = NULL)
place : Formal class 'standardGeneric' [package "methods"] with 8 slots plot : Formal class 'standardGeneric' [package "methods"] with 8 slots plotci.asreml : function (data, formula = NULL, subset = NULL, backfun = I, xfun = I, pts.col = NULL, pts.pch = 16, pts.cex = 1, fill.col = NULL, line.lty = 1, line.lwd = 1, line.col = NULL, ci.lty = 1, ci.lwd = 1, ci.col = NULL, ci.f = 1)
plotellipse : function (data, columns = c(1, 2), subset = NULL, level = 0.67, which = c(1, 2), fill.ellipse = NA, col.ellipse = "black", col.ma = "black", lwd.ellipse = 1, lwd.ma = 1, lty.ellipse = 1, lty.ma = 1, caps = 0)
points2D : Formal class 'standardGeneric' [package "methods"] with 8 slots polyarea : function (x)
polycircle : function (x, y = NULL, r = NULL, rx = r, ry = rx, pos = "center", phi = 0, n = 16)
polygon2D : Formal class 'standardGeneric' [package "methods"] with 8 slots polyrect : function (x, y, w, h, pos = "center", phi = 0)
polystar : function (x, y = NULL, r = NULL, r1 = r, r2 = r/2, phi = 0, n = 5)
power.posneg : function (x, posexp = 0.5, negexp = 0.5, slope = 1)
power.posneg.backtransform : function (x, posexp = 0.5, negexp = 0.5, slope = 1)
progressBar : function (step = 0)
progressInit : function (steps = 10, pre = "[", post = "]", done = "*", spc = "-", maxwidth = 60)
progressPct : function (step = 0)
progressStep : function ()
progressStep0 : function ()
pwr10label : function (x, ndec = 1, exp = floor(log10(abs(x))), expOnly = FALSE)
read_filtered : function (file, condition, decompressor = NULL, sep = ",", debug = FALSE, ...)
read_partial : function (file, lines = c(1, NA), decompressor = NULL, debug = FALSE, ...)
rect2D : Formal class 'standardGeneric' [package "methods"] with 8 slots reflectx2D : function ()
reflectxy2D : function ()
reflecty2D : function ()
reload.pascal : function ()
resDivider : function (ratio, rmin = 1000, rmax = 1e+06, series = pascal::E24, exponents = 0:6, n = 2, tol = 0.05, ntop = 10)
restorefactors : function (d, cols = seq_along(names(d)))
right.axis : function (...)
rotate2D : function (theta)
rxmatches : function (x, m)
safen : function (x)
safeSample : function (x, size, replace = FALSE, prob = NULL)
scale2D : function (kx, ky = kx)
sd_NAsafe : function (x)
se : function (x, na.rm = FALSE)
se_NAsafe : function (x)
sgnsqrt : function (x)
shearx2D : function (phi)
sheary2D : function (phi)
show : Formal class 'standardGeneric' [package "methods"] with 8 slots showSymbols : function ()
sides : Formal class 'standardGeneric' [package "methods"] with 8 slots sigStars : function (x)
simple.heading : function (txt = NULL, width = 80, char = "#", side.char = char, corner.char = rep(char, 4), spc = " ", pre = 0, post = 1, center = TRUE)
simple.trailer : function (txt = NULL, width = 80, char = "#", side.char = char, corner.char = rep(char, 4), spc = " ", pre = 0, post = 1, center = TRUE)
Sink : function (..., width = NA)
snapToGrid : function (d, theta = 0, sz = 1, which = "points")
sorted.code : function (..., split = NULL, collapse = NULL, unique = FALSE)
splitScreen : function (nx = 2, ny = 1, gapx = 0, gapy = 0, topy = 0, bottomy = 0.2, leftx = 0.2, rightx = 0, byrow = TRUE, debug = FALSE, addLeft = FALSE, addRight = FALSE, addBottom = FALSE, addTop = FALSE)
splittxt : function (x, n = 80)
splt : function (d, by, to.split, factors = NULL, new.names = NULL, expand = FALSE, sep = ":")
stck : function (d, factors = NULL, covars = NULL, to.stack, cat.names = NULL, expand = FALSE)
suc : function (x)
test.asreml : function (d.asr, returnWald = FALSE, silent = FALSE)
text2D : Formal class 'standardGeneric' [package "methods"] with 8 slots top.axis : function (...)
trailer : function (txt = NULL, width = 80, right = FALSE, char = "#", spc = " ", side.char = char, corner.char = rep(char, 4), post = 1, pre = 0, center = FALSE)
transform2D : Formal class 'standardGeneric' [package "methods"] with 8 slots transformation : Formal class 'standardGeneric' [package "methods"] with 8 slots transformation<- : Formal class 'standardGeneric' [package "methods"] with 8 slots translate2D : function (x, y)
triangle : function (sides = rep(NA, 3), angles = rep(NA, 3), x = NULL, y = NULL, degrees = TRUE, simplify = TRUE)
trim.ws : function (x)
unescape : function (x)
var_NAsafe : function (x)
vector.crossprod : function (a, b)
vector.norm : function (x, p = 2)
xpand : function (formula, data, verbose = FALSE, cols = NULL, unit = NULL, unname = FALSE, expand = FALSE)
xtreme : function (x, f = 3.5)
xy.errbar : function (x, y, yplus = NULL, yminus = NULL, xplus = NULL, xminus = NULL, yerr = NULL, xerr = NULL, cap = 0.015, lty = 1, lwd = 1, add = FALSE, ...)
Zr : function (F, dendf, df = 1)

Deprecated

I'll remove these functions eventually, since they are remainings from old code.

• niceDiag: Draw path diagram from sem object, using graphviz
• indexof

Installation

• download the ready-built package from the pkgs directory
• use install_github:
  library(devtools)
install_github("pascal-niklaus/pascal/pascal")