LANGUAGE, READING, & GENES Timothy C. Bates [email protected] .
+ Refresher in inferential statistics [email protected] stats.
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+ Refresher in inferential statistics [email protected] http://www.psy.ed.ac.uk/events/ research_seminars/psychstats
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Transcript of + Refresher in inferential statistics [email protected] stats.
+
Refresher in inferential [email protected]
http://www.psy.ed.ac.uk/events/research_seminars/psychstats
+Our basic question…
Did something occur?
Importantly, did what we predicted would occur, transpire?, i.e., is the world as we predicted?
Why does this require statistics?
+Is Breastfeeding good for Baby’s brains?
The association between breastfeeding and IQ is moderated by a genetic polymorphism (rs174575) in the FADS2 gene
Caspi A et al. PNAS 2007;104:18860-18865
©2007 by National Academy of Sciences
+Overview
Hypothesis testing p-values Type I vs. Type II errors Power Correlation Fisher’s exact test T-test Linear regression Non-parametric statistics (mostly for you to
go over in your own time)
+Hypothesis testing
1.Propose a null and an experimental hypothesis.
Mistakes here may make the experiment un-analysable
2.Consider the assumptions of the test: Are they met?
Statistical independence of observations
Distributions of the observations.
Student's t distribution, normal distribution etc.
3.Compute the relevant test statistic.
1.Student’s t-test-> t ; ANOVA F; Chi2
4.Compute likelihood of the test-statistic:
1.Does it exceed your chosen threshold?
2.Either reject (or fail to reject) the null hypothesis
+What mistakes can we make?
“The World”
Yes No
Your Decision
Yes correct detection
false positive
No false negative correct rejection
+Starting to make inferences…the Binomial
Toss a coin
+Dropping lots of coins...
Pachinko
+Normal compared to Binomial
n = 6
p = .5
+Distributions
normal (µ, ∂) binomial (p, n)
+Distributions
Poisson (lambda) Power
Accidents in a period of time; Publication rates
+Testing what distribution you have
+Why are things normal?
+Central limit theorem
The mean of a large number of independent random variables is distributed approximately normally.
+Hypothesis testing
Making statistical decisions using experimental data.
Need to form a null hypothesis
(we can reject, but not confirm hypotheses)
A result is “significant” if it is unlikely to have occurred by chance.
Ronald Fisher “We may discover whether a second sample is or is not significantly different from the first”.
+What mistakes can we make?
“The World”
Yes No
Your Decision
Yes correct detection
false positive
No false negative correct rejection
+Error
Type-I error: False Alarm, a bogus effect reject the null hypothesis when it is really
true Much of published science is Type-I error
(Ioannides, 2008)
Type-II error: Miss a real effect Fail to reject our null hypothesis when it is
false Many small projects have this problem
Type-III error: :-) lazy, incompetent, or willful ignorance of the
truth
+p-values
Almost any difference (a count, a difference in means, a difference in variances) can be found with some probability, irrespective of the true situation.
All we can do is to set a threshold likelihood for deciding that an event occurred by chance.
p=.05 = 1 time in 20, the result would be as large by chance when the null hypothesis is true.
+Type I vs. Type II errors
Type I: False positive Likelihood of type 1 = α p=.05 = setting α to .05
Type II: False negative Likelihood of type 2 = β Power = 1-β
World
Yes No
You
Yes Correct detection(power)
Type I (α)
No Type II (β) Correct rejection
+P-values
p-value is the likelihood of mean differences as large or larger than those observed in the data occurring by chance
p-value criteria (alpha ) allow us a binary answer to our questions
Questions – is a smaller p-value:
“More” significant?
Indicate a “Bigger” effect? (if so when?)
and how could we measure” effect”?
+Compare these two statements
It’s ‘significant’, but how big is the effect?
I can see it’s big: but what is the p-value?
+Confidence Intervals
Range of values within a given likelihood threshold (for instance 95%)
Closely related to p-values. p = 1-CI i.e., if p<.05, 95% CI will not include 0 (no difference) Would you rather have a CI or a p-value? Why?
What is an effect size?
+P and CI
You can’t go from p to CI!
You can go from CI to p At a p=.05, 95%CIs will overlap less than 25% At p= .01, the 95% CI bars just touch
+Units of a Confidence Interval
Unlike p, CIs are given in the units of the DV Cumming and Finch (2005) BMI in people on a low carb diet might be19-23 kg/m2
Cumming, G. and Finch S.(2005). Inference by eye: confidence intervals and how to read pictures of data. American Psychologist. 60:170-80. PMID: 15740449
+Standard Errors and Standard Deviations
SE is (typically) the standard error of the mean The precision with which we have estimated the population
mean based on our sample Computationally, it is ∂/sqrt(n)
A 95% confidence interval is ± 1.96 SE
+Example: coin toss
Random sample of 100 coin tosses, of a coin believed to be fair
We observed number of 45 heads, and 55 tails: Is the coin fair?
+Binomial test
binom.test(x=45, n=100, p=.5, alternative="two.sided”)
number of successes = 45, number of trials = 100
p-value = 0.3682
alternative hypothesis: true probability of success != 0.5
95 percent confidence interval: 0.3503 0.5527
sample estimates: probability of success: 0.45
+Categorical Data
Fisher’s Exact Test
Categorical data resulting from classifying objects in one of two ways
Tests significance of the observed "contingency" of the two outcomes. Fisher, R. A. (1922). On the interpretation of χ2 from
contingency tables, and the calculation of P. Journal of the Royal Statistical Society, 85(1), 87-94.
+The Lady Drinking Tea
Question: Does Tea taste better if the milk is added to the tea, or vice versa?
Null Hypothesis: The drinker cannot tell
Subjects: Ms Bristol
Experiment: 8 "trials" (cups): 4 in each way, in random order
DV: Milk versus Milk second discrimination
Enter data into 2 x 2 contingency table
+Fisher Contingency Table
A = c(1, 1, 1, 0, 1, 0, 0, 0) # vector of guesses
B = c(1, 1, 1, 1, 0, 0, 0, 0) # vector of Teas
guessTable <- table(A,B) # contingency table
labels = list(Guess = c("Milk", "Tea"), Truth = c("Milk", "Tea")) # make labels
dimnames(guessTable)= labels # add label
fisher.test(guessTable, alternative = "greater") # test
GuessMilk Tea
TruthMilk 3 1
Tea 1 3
+Can she tell?
Fisher's Exact Test for Count Data
p-value = 0.24 # association could not be established
Alternative hypothesis: true odds ratio is greater than 1
95% confidence interval: 0.313 – Inf
Sample odds ratio: 6.40
+What if we have two continuous variables?
Are they related
Q: If you have continuous depression scores and cut-off scores, which is more powerful?
+Correlation of two continuous variables: Pearson’s r
All variables continuous
Pearson
+Correlation: what are the maximum and minimum correlations?
+Power (1-β)
Probability that a test will correctly reject the null hypothesis.
Complement of the false negative rate, β False negative = missing a real effect 1-β = p (correctly reject a false null hypothesis)
+Power and how to get it
Probability of rejecting the null hypothesis when it is false
Whence comes power?
+Power applied to a correlation
Samples of n=30 from a population in which two normal traits correlate 0.3
r=0.3
xy = mvrnorm (n=30, mu=rep(0,2), Sigma= matrix(c(1,r,r,1) ,nrow=2, ncol=2));
xy = data.frame(xy);
names(xy) <- c("x", "y");
qplot(x, y, data = xy, geom = c("point" , "smooth"), method=lm)
+Power of a correlation test
library(pwr)
pwr.r.test(n = 30, r = .3, sig.level = 0.05)
n = 30
r = 0.3
sig.level = 0.05
power = 0.359
alternative = two.sided
+Power: r = .3
+ t-test
When we wish to compare means in a sample, we must estimate the standard deviation from the sample
Student's t-distribution is the distribution of small samples from normally varying populations
+t-distribution function
t is defined as the ratio:
Z/sqrt(V/v) Z is normally distributed with expected value 0 and
variance 1; V has a chi-square distribution with ν degrees of
freedom;
+Normal and t-distributions
Normal is in blue
Green = t with df = 1
Red = t with df = 3 (far right = df increasing to 30)
+Power of t-test
power.t.test(n=15, delta=.5)
Two-sample t test power calculation
n = 15 ; delta = 0.5 ; sd = 1; sig.level = 0.05
power = 0.26
alternative = two.sided
NOTE: n is number in *each* group
+Linear regression
+Linear regression
fit = lm(y ~ x1 + x2 + x3, data=mydata)
summary(fit) # show results
anova(fit) # anova table
coefficients(fit) # model coefficients
confint(fit, level=0.95) # CIs for model parameters
fitted(fit) # predicted values
residuals(fit) # residuals
influence(fit) # regression diagnostics
+Bootstrapping: Kurtosis differences
kurtosisDiff <- function(x, y, B = 1000){
kx <- replicate(B, kurtosi(sample(x, replace = TRUE)))
ky <- replicate(B, kurtosi(sample(y, replace = TRUE)))
return(kx - ky)
}
kurtDiff <- kurtosisDiff(x, y, B = 10000); mean(kurtDiff > 0) # p= 0.205 NS
+Parametric Statistics 1
Assume data are drawn from samples with a certain distribution (usually normal)
Compute the likelihood that groups are related/unrelated or same/different given that underlying model
t-test, Pearson’s correlation, ANOVA…
+Parametric Statistics 2
Assumptions of Parametric statistics1. Observations are independent
2. Your data are normally distributed
3. Variances are equal across groups Can be modified to cope with unequal ∂2
+Non-parametric Statistics?
Non-parametric statistics do not assume any underlying distribution
They compute the likelihood that your groups are the same or different by comparing the ranks of subjects across the range of scores.
+Non-parametric Statistics
Assumptions of non-parametric statistics1. Observations are independent
+Non-parametric Statistics?
Non-parametric statistics do not assume any underlying distribution
Estimating or modeling this distribution reduces their power to detect effects…
So don’t use them unless you have to
+Why use a Non-parametric Statistic?
Very small samples Leads to Type-1 (false alarm) errors
Outliers more often lead to spurious Type-1 (false alarm) errors in parametric statistics. Nonparametric statistics reduce data to an
ordinal rank, which reduces the impact or leverage of outliers.
+Non-parametric Choices
Data type?
χ2
discrete
Question?
continuous
Number of groups?
Spearman’s Rank
association
Different central value
Mann-Whitney UWilcoxon’s Rank Sums
Kruskal-Wallis test
two-groups
more than 2
Brown-Forsythe
Difference in ∂2
+Non-parametric Choices
Data type?
χ2
discrete
Question?
continuous
Number of groups?
Spearman’s Rank
Like a Pearson’s R
Mann-Whitney UWilcoxon’s Rank Sums
Kruskal-Wallis test
two-groups
more than 2 Like ANOVA
Like Student’s t
No alternative
Different central value
Brown-Forsythe
Difference in ∂2
Like F-test
association
+Binomial test
binom.test(45, 100, .5, alternative="two.sided”)
number of successes = 45, number of trials = 100,
p-value = 0.3682
alternative hypothesis: true probability of success is not equal to 0.5
95 percent confidence interval: 0.350 0.5527
Sample estimates: probability of success 0.45
binom.test(51,235,(1/6),alternative="greater")
+Spearman Rank test (ρ (rho))
Named after Charles Spearman,
Non-parametric measure of correlation Assesses how well an arbitrary monotonic function
describes the relationship between two variables,
Does not require the relationship be linear
Does not require interval measurement
+Spearman Rank (ρ rho)
d = difference in rank of a given pair n = number of pairs
Alternative test = Kendall's Tau (Kendall's τ)
+Mann-Whitney U
AKA: “Wilcoxon rank-sum test Mann & Whitney, 1947; Wilcoxon, 1945
Non-parametric test for difference in the medians of two independent samples Assumptions:
Samples are independent Observations can be ranked (ordinal or better)
+Mann-Whitney U
U tests the difference in the medians of two independent samples
n1 = number of obs in sample 1
n2 = number of obs in sample 2
R = sum of ranks of the lower-ranked sample
+Mann-Whitney U or t?
Should you use it over the t-test? Yes if you have a very small sample (<20)
(central limit assumptions not met) If your data are really ordinal Otherwise, probably not.
It is less prone to type-I error (spurious significance) due to outliers.
But does not in fact handle comparisons of samples whose variances differ very well (Use unequal variance t-test with rank data)
+Wilcoxon signed-rank test (related samples)
Same idea as Mann-U, generalized to matched samples
Equivalent to non-independent sample t-test
+Kruskall-Wallis
Non-parametric one-way analysis of variance by ranks (named after William Kruskal and W. Allen Wallis)
tests equality of medians across groups.
It is an extension of the Mann-Whitney U test to 3 or more groups.
Does not assume a normal population,
Assumes population variances among groups are equal.
+Aesop: Mann-Whitney U Example
Suppose that Aesop is dissatisfied with his classic experiment in which one tortoise was found to beat one hare in a race.
He decides to carry out a significance test to discover whether the results could be extended to tortoises and hares in general…
+Aesop 2: Mann-Whitney U
He collects a sample of 6 tortoises and 6 hares, and makes them all run his race. The order in which they reach the finishing post (their rank order) is as follows:
tort = c(1, 7, 8, 9, 10,11)
hare = c(2, 3, 4, 5, 6, 12) Original tortoise still goes at warp speed,
original hare is still lazy, but the others run truer to stereotype.
+Aesop 3: Mann-Whitney U
wilcox.test(tort, hare)
Wilcoxon = W = 25, p-value = 0.31 Tortoises and hares do not differ tort = c(1, 7, 8, 9, 10,11) (n2 = 6)
hare = c(2, 3, 4, 5, 6, 12) (n1 = 6, R1 =32)
