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Distributions, Iteration, Simulation. Why R will rock your world (if it hasn’t already). Simulation. Sampling Calculation Iteration Data storage Summation. General structure of common functions on distributions. There are many distributions in R (e.g. norm is Gaussian) - PowerPoint PPT Presentation
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Distributions, Iteration, Simulation
Why R will rock your world
(if it hasn’t already)
Simulation
Sampling Calculation Iteration Data storage Summation
General structure of common functions on distributions There are many distributions in R (e.g. norm is Gaussian) For every statistical distribution in R, there are 4 related functions
d: density p: probability distribution q: quantile r: random number generation
e.g. rnorm(10) draws ten values randomly from a standard normal distribution
Like most R functions, one can alter the defaults by specifying additional parameters. What parameters can be altered varies by distrubution
> dnorm(0) <-default mean=0, sd=1[1] 0.3989423
input
output
> pnorm(2) <-default mean=0, sd=1[1] 0.9772499
input
output
> qnorm(.40)[1] -0.2533471
input
output> rnorm(100, mean=0,sd=1) [1] 0.66075674 -0.55118652 0.08139252 0.46958450 -0.05435657 -0.86266560 1.07616374 [8] 0.16302857 -0.89804740 -0.78564903 0.29835536 -0.71735186 -1.51407253 0.89670212 [15] 1.18914054 0.48275543 -0.07937962 -0.79158265 0.66515914 0.91851769 -0.46559128 [22] 0.73002690 0.28342742 -1.15366595 1.22958479 0.50383209 -0.42909720 -0.69166003 [29] 0.16479583 1.15306943 -0.34162134 -1.10417420 0.74769236 1.09840855 -0.51784452 [36] 0.70605966 0.28660515 -0.62594167 -0.20681508 -0.69174153 -0.85814328 -0.23921311 [43] -0.13501255 -0.26683858 -1.67594580 1.19625453 -1.46812625 0.65995661 -0.79434250 [50] 0.51520368 -0.63391224 -0.16388674 -1.19557850 0.57594851 -0.32403622 -0.69371174 [57] -1.12080737 -0.28248934 1.40289924 0.82057604 -0.78505396 -0.05197960 -1.04549759 [64] -0.01334230 1.46494433 -0.18540372 -1.80950468 -0.18717730 -0.20780014 -0.07233845 [71] 0.11554796 0.83534676 -1.28519697 0.41796046 -1.48320795 -0.37269167 1.33504531 [78] 2.89549729 1.19711458 -0.11064494 1.23430822 0.42402993 -0.70746642 -1.01444881 [85] 1.19138047 -0.24913786 -0.29479432 0.21643338 0.50766542 0.69286785 -1.58078913 [92] -0.10119364 -0.44138704 -0.81407226 -1.57577525 2.83165289 -0.55277727 -1.50489032 [99] 0.09719564 0.75148485
Simulating random variables in R
rnorm(): uni normal mvrnorm(): multi normal rbinom(): binomial runif(): uniform rpois(): poisson rchisq(): 2
rnbinom(): neg. binomial
rlogis(): logistic rbeta(): beta rgamma(): gamma rgeom(): geometric rlnorm(): log normal rweibull(): Weibull rt(): t rf(): F …
loops for() and while() are the most commonly used others (e.g. repeat) are less useful
for(i in [vector]){
do something
}
while([some condition is true]){
do something else
}
for loop{for (i in 10:1){+ cat("Matt is here for ", i, " more days \n")+ }cat(“Matt is gone”)}
Matt is here for 10 more days Matt is here for 9 more days Matt is here for 8 more days Matt is here for 7 more days Matt is here for 6 more days Matt is here for 5 more days Matt is here for 4 more days Matt is here for 3 more days Matt is here for 2 more days Matt is here for 1 more days Matt is gone
The Elementary Conditional if
if([condition is true]){do this}
if([condition is true]){do this}else{do this instead}
ifelse([condition is true],do this ,do this instead)
Conditional operators
== : is equal to (NOT THE SAME as ‘=‘)! : not!= : not equalinequalities (>,<,>=,<=)& : and by element (if a vector)| : or by element&& : and total object || : y total objectxor(x,y): x or y true by not both
Other useful functions:
sample(): sample elements from a vector, either with or without replacement and weights
subset(): extract subset of a data frame based on logical criteria
Time to get your hands dirty
Open up the R file sim.R Different scripts separated by lines of “#”
Two approaches to the CLT Exercise #1 Simple ACE Simulator Simple Factor model/IRT simulator Exercise #2
“solutions” to exercises at the bottom
Exercise #1: Create a simple genetic drift simulator for a biallelic locus
The frequency of an allele at t+1 is dependent on its frequency at t.
The binomial distribution might come in handy
There are many ways to model this phenomenon, more or less close to reality
(source: wikipedia)
N=100
N=1000
Simulating Path Diagrams Simulating data based on a path model is usually fairly
easy Latent variables are sources of variance, and usually
standard normal path coefficients represent strength of effect from
causal variable to effect variable. Drawing simulations using path diagrams (or
something similar) can help formalize the structure of your simulation
ACE Model 2 measured variables 6 sources of variance 3 levels of correlation
1, .5, or 0 Standard normal latent
variables
Effect of latent variable on phenotype
= factor score * path coefficient
Phenotype #1 Phenotype #2
mvrnorm()
part of MASS library Allows generation of n-dimensional matrices
of multivariate normal distributions Also useful for simulating data for unrelated
random normal variablesefficient code and less work
mvrnorm() == simplicity
mvrnorm(n,mu,Sigma,…) n = number of samples mu = vector of means for some number of
variables Sigma = covariance matrix for these variables Example:
mu<- rep(0,3) Sigma<-matrix(c(1,.5,.25,.5,1,.25,.25,.25,1),3,3) ex<-mvrnorm(n=500,mu=mu,Sigma=Sigma) pairs(ex)
output
Back to R script
Factor Models
Similar principles In a simple model, each
observed variable has 2 sources of variance (factor + “error”)
Psychometric models often require binary/ordinal data
Back to R script
Exercise #2: Generate a simulator for measuring the accuracy of Falconer estimation in predicting variance components
MZ
DZ
Hints: Simulation:
The EEAsim6.R script contains a twin simulator that will speed things up. source(“EEAsim6.R”) will load it. function is twinsim() “zyg” variable encodes zygosity; MZ=0, DZ=1 Variables required here are numsubs, a2, c2,and e2
Calculation: cor(x,y): calculate the Pearson correlation between x and y Falconer Estimates
a2 = 2*(corMZ-corDZ) c2 = (2*corDZ)-corMZ) e2=1-a2-c2
Iteration: a “for” loop will work just fine data storage: perhaps a nsim x nestimates matrix? visualization: prior graph used plot and boxplot, do whatever you want