[R] [R-pkgs] mosaic 0.4 on CRAN

Wed Apr 11 14:31:41 CEST 2012

One of the products of Project MOSAIC (funded by an NSF CCLI grant)
has been the development of an R package with the goal of making it
easier to use R, especially in teaching situations.  We're not quite
ready to declare that we've reached version 1.0, but version 0.4 does
represent a fairly large step in that direction.  You can find out
more about the package on CRAN or by installing it, but here are some
of the highlights (some example code appears at the end of this
message):

   * extensions of syntax to promote consistency across functions and
make wider use of the formula interface

   * simplified ways of creating and plotting functions, including
extracting model fits as functions

   * a tally() function that combines features of table() and xtabs()
and more in a common syntax

   * expanded syntax for summary functions like mean(), median(),
max(), sd(), var(), etc. that accepts formulas and data frames

   * a do() function that simplifies resampling-based statistical
analysis

   * numerical integration and differentiation to support using
calculus techniques in R

   * first drafts of vignettes on teaching resampling and calculus in R

   * some functions that add extra features to familiar functions
(e.g., xchisq.test(), xhistogram(), xpnorm(), ...)

   * some data sets

If you are using mosaic and discover bugs, or have suggestions for
future development, consider submitting an issue on our github
development site:

	http://github.com/rpruim/mosaic/issues/

You can also look there to see what's already on our to-do list.

---rjp (on behalf of the development team that includes Danny Kaplan
         and Nick Horton)

========================================================================
   Randall Pruim                        phone:  616.526.7113
   Dept. of Mathematics and Statistics  email:  rpruim at calvin.edu
   Calvin College                      office:  NH 284
   1740 Knollcrest Circle SE              URL:  http://www.calvin.edu/~rpruim/
   Grand Rapids, MI 49546-4403            FAX:  616.526.6501
                ---------------------------------------------

Here are the promised code examples to give you a feel for what mosaic
makes possible:

> mean(age, data=HELPrct)
[1] 35.65342

> mean(~age, data=HELPrct)
[1] 35.65342

> mean(age ~ sex, data=HELPrct)
   female     male
36.25234 35.46821

> mean(age ~ sex & treat, data=HELPrct)
  female.no    male.no female.yes   male.yes
   37.56364   35.90173   34.86538   35.03468

> interval(binom.test( ~ eruptions > 3, faithful))
probability of success                  lower                  upper
              0.6433824              0.5832982              0.7003038

> pval(binom.test( ~ eruptions > 3, faithful))
      p.value
2.608528e-06

> xchisq.test(phs) # physicians health study example (data entry  
> omitted)

	Pearson's Chi-squared test with Yates' continuity correction

data:  phs
X-squared = 24.4291, df = 1, p-value = 7.71e-07

    104.00   10933.00
(  146.52) (10890.48)
[12.34]  [ 0.17]
<-3.51>  < 0.41>

    189.00   10845.00
(  146.48) (10887.52)
[12.34]  [ 0.17]
< 3.51>  <-0.41>

key:
	observed
	(expected)
	[contribution to X-squared]
	<residual>

> model <- lm(length ~ width + sex, KidsFeet)

> L <- makeFun(model)

> L( 9.0, 'B')
        1
24.80017

> L( 9.0, 'B', interval='confidence')
        fit      lwr      upr
1 24.80017 24.30979 25.29055

> xyplot( length ~ width, groups= sex, KidsFeet )  # scatter plot   
> with different symbols for boys and girls

> plotFun(L(x,'B') ~ x, add=TRUE)  # add model fit (for boys) to plot

> plotFun(L(x,'G') ~ x, add=TRUE, lty=2)  # add model fit (for girls)   
> to plot

> rflip(10)  # flip a coin 10 times

Flipping 10 coins [ Prob(Heads) = 0.5 ] ...

T H T H H H T H H T

Result: 6 heads.

> do(2) * rflip(10) # do that twice; notice that do() extracts   
> interesting info
    n heads tails
1 10     4     6
2 10     6     4

> ladyTastingTea <- do(5000) * rflip(10)  # simulate 5000 ladies
tasting tea

> tally(~heads, ladyTastingTea)

     0     1     2     3     4     5     6     7     8     9    10 Total
     5    52   221   573  1032  1227  1027   606   198    52     7  5000

> tally(~heads, ladyTastingTea, format='proportion')

      0      1      2      3      4      5      6      7      8        
9     10  Total
0.0010 0.0104 0.0442 0.1146 0.2064 0.2454 0.2054 0.1212 0.0396 0.0104   
0.0014 1.0000

# do() extracts useful information from lm objects so that  
randomization tests are easy.
> do(2) * lm( length ~ width + shuffle(sex), data=KidsFeet )
   Intercept    width       sexG    sigma r-squared
1  9.646822 1.693137 -0.3057453 1.026824 0.4246224
2 11.416739 1.453416  0.4860068 1.013323 0.4396534

> tally( ~ sex & substance, HELPrct )
         substance
sex      alcohol cocaine heroin Total
   female      36      41     30   107
   male       141     111     94   346
   Total      177     152    124   453

> tally( ~ sex | substance, HELPrct )  # auto switch to proportions  
> for conditional distributions
         substance
sex        alcohol   cocaine    heroin
   female 0.2033898 0.2697368 0.2419355
   male   0.7966102 0.7302632 0.7580645
   Total  1.0000000 1.0000000 1.0000000

> favstats(age ~ sex & substance, data=HELPrct)
                min Q1 median Q3 max     mean       sd   n missing
female.alcohol  23 33   37.0 45  58 39.16667 7.980333  36       0
male.alcohol    20 32   38.0 42  58 37.95035 7.575644 141       0
female.cocaine  24 31   34.0 38  49 34.85366 6.195002  41       0
male.cocaine    23 30   33.0 37  60 34.36036 6.889772 111       0
female.heroin   21 29   34.0 39  55 34.66667 8.035839  30       0
male.heroin     19 27   32.5 39  53 33.05319 7.973568  94       0

> D(sin(a*x) ~ x)  # return derivative as a function with parameter a
function (x, a)
cos(a * x) * a

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