[PDF] Package ‘mosaic’ - R

Using R: Frequency Distributions, Histograms, Scatterplots

Histograms in R: In the text, we created a histogram from the raw data Scores on Test #2 - Males 42 Scores: Average = 73 5 84 88 76 44 80 83 51 93 69 78 49 55 78 93 64 84 54 92 96 72 97 37 97 67 83 93 95 67 72 67 86 76 80 58 62 69 64 82 48 54 80 69 Raw Databecomes Histogram Here, we’ll let R create the histogram using the hist command

Package ‘histogram’ - The Comprehensive R Archive Network

histogram thus defined is the maximum likelihood estimate among all densities that are piecewise constant w r t this partition The arguments of histogram given above determine the way the partition is chosen In a regular histogram, the partition consists of Dbins of the same widths, and

Checking normality in R - University of Sheffield

/file/stcp-karadimitriou-normalR.pdf

57 Appendix: Using R for Sampling Distributions

In Section 5 3 we displayed a histogram of 2000 values of ¯x from another discrete dis-tribution This was done using the same procedure we used here Of course the particular discrete distribution must be entered into R as the necessary first step It is sometimes difficult to know how many values to generate is a simulation study In

Colors in R - Columbia University

Colors in R 1 color name color name white aliceblue antiquewhite antiquewhite1 antiquewhite2 antiquewhite3 antiquewhite4 aquamarine aquamarine1 aquamarine2 aquamarine3

Discrete distributions with R - University of Michigan

This would be harder to do from a regular histogram (Figure 1): Figure 3: Histogram of the number of heads in repeated experiments of 100 coin tosses 2 4 Simulating switches and runs in coin tossing experiments (don’t try this at home kids, just sit back, relax, and watch)

ul R ands - Calvin University

R Commands for MATH 143 Examples of usage Examples of usage help() help(mean) example() require(lattice) example(histogram) c(), rep() seq() > x = c(8, 6, 7, 5, 3, 0, 9)

Package ‘mosaic’ - R

width The histogram bin width adjust A numeric adjustment to width Primarily useful when width is not specified Increasing adjust makes the plot smoother panel A panel function prepanel A prepanel function darg a list of arguments for the function computing the ASH

Data Visualization - RStudio

x =) ) ** ++-- ## ↵ ↵ ↵ ↵ ↵

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Package 'mosaic"

October 13, 2022

TypePackage

TitleProject MOSAIC Statistics and Mathematics Teaching Utilities

Version1.8.4.2

DescriptionData sets and utilities from Project MOSAIC () used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.

DependsR (>= 3.0.0),

Importsdplyr, lattice (>= 0.20-21), ggformula, mosaicData, Matrix, mosaicCore (>= 0.7.0), ggplot2, rlang (>= 0.4.7), purrr, MASS, grid, tidyr, methods, utils Suggestsggstance, ggridges, vdiffr, lubridate, magrittr, NHANES, RCurl, sp, maptools, vcd, testthat, knitr, tools, parallel, mapproj, rgl, rmarkdown, covr, formatR, palmerpenguins, ggrepel, readr, ggdendro, gridExtra, splines, latticeExtra, glue, broom, leaflet

Enhancesmanipulate

VignetteBuilderknitr

LicenseGPL (>= 2)

LazyLoadyes

LazyDatayes

https://www.mosaic-web.org/mosaic/

RoxygenNote7.2.1

EncodingUTF-8

NeedsCompilationno

1

2Rtopics documented:

AuthorRandall Pruim [aut, cre],

Daniel T. Kaplan [aut],

Nicholas J. Horton [aut]

MaintainerRandall Pruim

RepositoryCRAN

Date/Publication2022-09-20 18:10:02 UTC

Rtopics documented:

mosaic-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 adapt_seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 aggregatingFunction1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 aggregatingFunction1or2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 aggregatingFunction2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 as.xtabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 ashplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 bargraph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 binom.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Broyden . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 cdist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 chisq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 CIAdata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 CIsim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 cnorm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
compareMean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
confint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
confint.htest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
cor_test.formula . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
cross . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
cull_for_do . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
deg2rad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
derivedVariable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
design_plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
diffmean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
do . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
docFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
dotPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
dpqrdist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
expandFun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
factorize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
fav_stats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
fetchData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
findZeros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
findZerosMult . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
fitModel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
fitSpline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
fortify.hclust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Rtopics documented:3

fortify.summary.lm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
freqpoly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
freqpolygon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
FunctionsFromData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
getVarFormula . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
googleMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
inferArgs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
is.wholenumber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
ladd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
leaflet_map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
linear.algebra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
MAD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
MAD_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
maggregate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
makeColorscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
makeMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
mean_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
mid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
mosaic.options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
mPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
mplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
mUSMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Mustangs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
mWorldMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
ntiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
orrr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
panel.levelcontourplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
panel.lmbands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
panel.plotFun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
panel.plotFun1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
pdist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
plotCumfreq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
plotDist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
plotFun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
plotModel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
plotPoints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
prop.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
prop_test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
qdata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
qdata_v . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
qdist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
rand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
read.file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
relm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
repeater-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
resample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
rescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112

4mosaic-package

rflip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
rfun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
rlatlon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
rspin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
rsquared . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
rstudio_is_available . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
set.rseed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Sleep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
sp2df . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
standardName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
statTally . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
surround . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
swap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
theme.mosaic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
theme_map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
TukeyHSD.lm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
t_test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
update_ci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
xchisq.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
xhistogramBreaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
xpnorm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
xqqmath . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
xyz2latlon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
zscore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Index138mosaic-packagemosaic: the Project MOSAIC packageDescription mosaic

Details

Data sets and utilities from Project MOSAIC (mosaic-web.org) used to teach mathematics, statis- tics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineer-

ing and mathematics will need in their professional lives, but which are usually taught in isolation,

if at all.

Author(s)

Randall Pruim (), Daniel Kaplan (), Nicholas

Horton ()

adapt_seq5

References

http://www.mosaic-web.orgadapt_seqAdaptively generate sequences in an intervalDescription adapt_seqis similar toseqexcept that instead of selecting points equally spaced along an interval,

it selects points such that the values of a function applied at those points are (very) roughly equally

spaced. This can be useful for sampling a function in such a way that it can be plotted more smoothly, for example. Usage adapt_seq( from, to, length.out = 200, f = function(x, ...) { 1 args = list(), quiet = FALSE

Arguments

fromstart of interval toend of interval length.outdesired length of sequence fa function argsarguments passed tof quietsuppress warnings about NaNs, etc. Value a numerical vector

Examples

adapt_seq(0, pi, 25, sin)

6aggregatingFunction1aggregatingFunction11-ary Aggregating functionsDescription

aggregatinFuntion1creates statistical summaries of one numerical vector that are formula aware. Usage aggregatingFunction1( fun, output.multiple = FALSE, envir = parent.frame(), na.rm = getOption("na.rm", FALSE), style = c("formula1st", "formula", "flexible")

Arguments

funa function that takes a numeric vector and computes a summary statistic, return- ing a numeric vector. output.multiple a boolean indicating whetherfunreturns multiple values enviran environment in which evaluation takes place. na.rmthe default value for na.rm in the resulting function. styleone of"formula1st","formula2nd"or"flexible". In the first two cases, the first argument must be a formula or evaluate to an object. In the latter case, bare names will be converted into formulas.

Details

The logic of the resulting function is this: 1) If the first argument is a formula, use that formula and

datato create the necessary call(s) tofun; (2) Else simply pass everything tofunfor evaluation. Value a function that generalizesfunto handle a formula/data frame interface. Note Earlier versions of this function supported a "bare name + data frame" interface. This functionality has been removed since it was (a) ambiguous in some cases, (b) unnecessary, and (c) difficult to maintain. aggregatingFunction1or27

Examples

if (require(mosaicData)) { foo <- aggregatingFunction1(base::mean) foo( ~ length, data = KidsFeet) base::mean(KidsFeet$length) foo(length ~ sex, data = KidsFeet) }aggregatingFunction1or2

1- or 2-ary aggregating functionsDescription

aggregatingFunction1or2()creates statistical summaries for functions likevar()that can have either 1 or 2 numeric vector inputs. Usage aggregatingFunction1or2( fun, output.multiple = FALSE, na.rm = getOption("na.rm", FALSE)

Arguments

funa function that takes 1 or 2 numeric vectors and computes a summary statistic, returning a numeric vector of length 1. output.multiple a boolean indicating whetherfunreturns multiple values na.rmthe default value for na.rm in the resulting function.

Details

This was designed primarily to supportvarwhich can be used to compute either the variance of

one variable or the covariance of two variables. The logic of the resulting function is this: 1) If the

first two arguments are both formulas, then those formulas are evaluated (withdata) to compute the covariance; (2) If the first argument is a formula, and the second isNULL, then the formula and dataare used to create the necessary call(s) tofun; (3) Else everything is simply passed tofunfor evaluation. Note Earlier versions of this function supported a "bare name + data frame" interface. This functionality has been removed since it was (a) ambiguous in some cases, (b) unnecessary, and (c) difficult to maintain.

8aggregatingFunction2aggregatingFunction22-ary aggregating functionsDescription

Usage aggregatingFunction2(fun)

Arguments

funa function that takes two numeric vectors and computes a summary statistic, returning a numeric vector of length 1.

Details

This was designed to support functions likecov()which can be used to compute numerical sum- maries from two numeric vectors. The logic of the resulting function is this: 1) If the first two arguments are both formulas, then those formulas are evaluated (withdata) to compute the covari-

ance; (2) If the first argument is a formula, and the second isNULL, then the left and ride sides of the

formula anddataare used to create the vectors passed tofun; (3) Else everything is simply passed tofunfor evaluation. Value a function that generalizesfunto handle a formula/data frame interface. Note Earlier versions of this function supported a "bare name + data frame" interface. This functionality has been removed since it was (a) ambiguous in some cases, (b) unnecessary, and (c) difficult to maintain.

Examples

if(require(mosaicData)) { foo <- aggregatingFunction2(stats::cor) foo(length ~ width, data = KidsFeet) stats::cor(KidsFeet$length, KidsFeet$width) as.xtabs9as.xtabsConvert objects to xtabs formatDescription Convert a data frame or a matrix into anxtabsobject. Usage as.xtabs(x, ...) ## S3 method for class?data.frame? as.xtabs(x, rowvar = NULL, colvar = NULL, labels = 1, ...) ## S3 method for class?matrix? as.xtabs(x, rowvar = NULL, colvar = NULL, ...)

Arguments

xobject (typically a data frame) to be converted toxtabsformat ...additional arguments to be passed to or from methods. rowvarname of the row variable as character string colvarname of the column variable as character string labelscolumn of data frame that contains the labels of the row variable.

Details

The intended use is to convert a two-way contingency table stored in a data frame or a matrix into anxtabsobject. Value

Anxtabsobject.

Examples

# example from example(fisher.test) df <- data.frame( X=c(?Tea?,?Milk?), Tea=c(3,1), Milk=c(1,3) ) xt <- as.xtabs(df, rowvar="Guess", colvar="Truth"); xt if (require(vcd)) { mosaic(xt) }

10ashplotashplotAverage Shifted HistogramsDescription

An ASH plot is the average over all histograms of a fixed bin width. Usage ashplot( x, data = data, width = NULL, adjust = NULL, panel = panel.ashplot, prepanel = prepanel.default.ashplot prepanel.default.ashplot(x, darg, groups = NULL, subscripts = TRUE, ...) panel.ashplot( x, darg = list(), plot.points = FALSE, ref = FALSE, groups = NULL, jitter.amount = 0.01 * diff(current.panel.limits()$ylim), type = "p", identifier = "ash"

Arguments

xA formula or numeric vector. dataA data frame. ...Additional arguments passed to panel and prepanel functions ordata, a data frame in which to find the variables used for the plot. widthThe histogram bin width. adjustA numeric adjustment towidth. Primarily useful whenwidthis not specified.

Increasingadjustmakes the plot smoother.

panelA panel function. prepanelA prepanel function. darga list of arguments for the function computing the ASH. bargraph11 groupsas in other lattice plots subscriptsas in other lattice prepanel functions plot.pointsOne ofTRUE,FALSE,"jitter", or"rug" refa logical indicating whether a reference line should be displayed jitter.amountwhenplot.points="jitter", the value to use as the amount argument to jitter(). typetype argument used to plot points, if requested. This is not expected to be useful, it is available mostly to protect atypeargument, if specified, from affecting the display of the ASH. identifierA character string that is prepended to the names of i grobs that are created by this panel function.

Examples

ashplot( ~age | substance, groups = sex, data = HELPrct)bargraphCreate bar graphs from raw dataDescription

lattice::barchart()from thelatticepackage makes bar graphs from pre-tabulated data. Raw data can be tabulated usingxtabs(), but the syntax is unusual compared to the other lattice plotting functions.bargraphprovides an interface that is consistent with the otherlatticefunctions.quotesdbs_dbs20.pdfusesText_26