H10 The normally distribution Normal distribution Continuous porbability distribution describing a bell-shaped curve.

It is a good approximation to the frequency distributions of many biological variables. It is a continuous distribution, so probability is measured by the area under the curve rather than the height of the curve It is symmetric around its mean. It has a single mode. The probability density is highest exactly at the mean.

With a normally distributed variable, about two-thirds of individuals are within one standard deviation of the mean, and about 95% are within two standard deviations of the mean. Standard normal distribution A normal distribution with mean=0 and standard deviation=1 Standard normal deviate, or Z Tells us how many standard deviations a particular value is from the mean. Z= (Y-mu)/sigma normalcdf(Z,E9) If a variable Y has a normal distribution in a population, then the distribution of sample means Ystreep(mean) is also normal. Central Limit Theorem The sum or mean of a large number of measurements randomly sampled froma anon-normal population is approximately normally distributed. As n increases, the distribution of sample means starts to resemble a normal distribution, until at some point it becomes indistinguishable from the normal distribution. When the number of trials n is large, the binomial probability distribution for the number of scucesses is approximated by a normal distribution having mean n*p and standard deviation sqrt (np(1-p))

Interleaf 6 Controls in medical studies Placebo effect, the knowledge of being treated may be sufcient to improve a patients condition, an improvement in a medical condition that results from the psychological effects of medical treatment. The goal of careful experimental design is to make all else equal. H11 Inference for a normal population The difference between the sample mean and the true mean (Y-mean - mu) divided by the estimated standard error (SEy-mean), has a Students t-distribution with n-1 degrees of freedom. t=(Y-mean - mu)/SEy-mean df = n - 1 As the sample size increases, t becomes more like Z.

In 95% of random sample from a normal distribution, the interval from Y-mean[t0.05(2),df] SEymean to Ymean+[t0.05(2),df]SEymean will bracket the population mean. This interval is the 95% condence interval of the mean. Assumptions: Random sample, normal distribution. Method is not robust to departures from this assumption. The one-sample t-test compares the mean of a random sample from a normal population with the population mean proposed in a null hypothesis. Assumptions: Random sample, normal distribution in the population. A method is robust if the answer it gives is not sensitive to modest departures from the assumptions. H12 Comparing two means Study designs - paired: both treatments have been applied to every sampled unit, such as a subject or a plot, at different times or on different sides. two-sample: each group constitutes an independent random sample of individuals. In both cases, we make us of the t-distribution to calculate condence intervals for the mean difference and test hypotheses about means. In the paired design, both treatments are applied to every sampled unit. In the two-sample design, each treatment group is composed of an independent random sample of units. Paired measurements are converted to a single measurement by taking the difference between them. Paired t-test is used to test a null hypothesis that the mean difference of paired measurements equals a specied value. The method tests differences when both treatments have been applied to every samping unit and the data are therefore paired. The paired t-test is straightforward once we reduce the two measurements made on each pair down to a single number: the difference between the two measurements. This difference is then analyzed in the same way as a regular one-sample t-test. In the two-sample design, the two treatments are applied to separate, independent sampling units. Manipulated subjects are different individuals than control subjects. Pooled sample variance S2p is the average of the variances of the samples weighted by their degrees of freedom. Two-sample t-test is the simplest method to compare the means of a numerical variable between two independent groups. Its most common use is to test the null hypothesis that the means of two populations are equal (zero difference). Welchs t-test compares the means of two groups and can be used even when the variances of the two groups are not equal. Correct sampling units If multiple measurements have been taken on each sampling unit, the measurements arent independent, they require special handling. One solution is to summarize the data for each sampling unit by a single measurement. Comparisons between two groups should always be made directly, not indirectly by comparing both to the same null hypothesized value. Interpreting overlap of condence intervals

If the 95% condence intervals of two estimates do not overlap at all, then the null hypothesis of equal means would be rejected at the alpha=0.05 level. If the value of one of the sample means is included within the 95% condence interval of the other mean, the the null hypothesis of equal means would not be rejected at alpha=0.05. Between these two extremes, where the condence intervals overlap, but neither interval includes the sample mean of the other group, we cannot be sure what the outcome of a hypothesis test would be from a simple inspection of the overlap in condence intervals. Comparing variances F-test of equal variances The F-test evaluates whether two population variances are equal. H0: sigma12=sigma22 HA: sigma12sigma22 F=S12/S22 df=(n1-1, n2-1) Levenes test for homogeneity of variances Test the null hypothesis that the variances of two or more groups are equal. More robust than Ftest. H13 Handling violations of assumptions Three alternative options: 1. Ignore the violations of assumptions. 2. Transform the data. 3. Use a nonparametric method. Detecting deviations from normality Look at histograms. The normal quantile plot compares each observation in the sample with its quantile expected from teh standard normal distribution. Points should paff roughly along a straight line if the data comes from a normal distribution. Formal test of normality A Shapiro-Wilk test evaluates the goodness of t of a normal distribution to a set of data randomly sampled from a population. When to ignore violations of assumptions A statistical procedure is robust if the answer it gives is not sensitive to violations of the assumptions of the method. Violations of normality may be ignored if the sample size is large enough (n>=30). The distributions of two groups should be roughly the same, if they both differ from normality in different ways, then even subtle deviations from normality can cause erros in the analysis. Unequal standard deviations can be ignored if the sample size is large enough (n>30), the two sample methods for estimation and hypothesis testing using the t-distribution will still perform, as long as the sample sizes of the two groups are apporximately equal. If sample sizes are not approximately equal, or if the difference in standard deviations is more than three-fold, then the Welchs t-test should be used, assuming that the assumption of normality is met. Data transformations A data transformation changes each measurement by the same mathematical formula. Log tansformation

lnY=Y useful for ratios or products of variables frequency distribution is skewed right (long tail on the right) larger mean has higher standard deviation the data span several orders of magnitude Arcsine transformation p=arcsin[sqrt(p)] useful for almost exclusively used on proportions Square-root transformation Y=sqrt(Y+1/2) useful for often used on counts (number of mates acquired, number of eggs laid etc.) sometimes helps equalize standard deviations if higher mean has higher standard deviation. similiair effect as log transformation. Other transformations Square transformation Y=Y2 used if frequency distribution of the data is skewed left antilog transformation Y=eY also used if frequency distribution of the data is skewed left reciprocal transformation Y=1/Y used if frequency distribution of the data is skewed right. only usable if all the data points in all samples have the same sign. After transforming for meeting assumptions of condence intervals its usually best to backtransform the lower and upper limits of the condence interval once computed with the transformed data. Multiple testing with transformations increases Type I error rate. Nonparametric alternatives to one-sample and paired t-tests If ignoring violations of assumptions and transforming the data fails. A nonparametric method makes fewer assumptions tan standard parametric methods about the distributions of the variable. They are usually based on the ranks of the data points rather than the actual values of the data. The sign test compares the median of a sample to a constant specied in the null hypothesis. It makes no assumptions about the distribution of the measurement in the population. Very little power compared with the t-test. The Wilcoxon signed-rank test is an improvement on the sign test for evaluating whether hte median of a population is equal to a null-hypothesized constant. It assumes that the distribution of measurements in the population is symmetric around the median; no skew is present. Nearly as restrictive as the normality assumption. [Boek gaat verder niet in op berekening hiervan] Comparing two groups: the Mann-Whitney U-test

Compares the distributions of two groups. It does not require as many assumptions as the twosample t-test. Nonparametric tests are typically less powerful than parametric tests. When assumptions of a parametric test are not met, then the Type I error (rejecting a true H0) rate can become larger than the stated alpha-value. When using a nonparametric test, the type II error (failing to reject a false H0) rate can become larger. H14 Designing experiments Confounding variable A variable that masks or distorts the causual relationship between measured variables in a study. Can be minimized by randomization. Experimental artifact A bias in a measurement produced by unintended consequences of experimental procedures. Clinical trial Experimental study in which two or more treatments are applied to human subjects. A good experiment is designed with two objectives in mind: To reduce bias in estimating an testing treatment effects To reduce the effects of sampling error The goal of experimental design is to eliminate bias and to reduce sampling error when estimating and testing the effects of one variable on another. How to reduce bias Control group Group of subjects who do not receive the treatment of interest but who otherwise experience similar conditions as the treated subjects. Randomization The random assignment of treatments to units in an experimental study. Blinding The process of concealing information from participants (sometimes including researchers) about which subjects receive which treatment. Single-blind experiment Subjects are unaware of the treatment to which they have been assigned. Double blind experiments the researchers administering the treatments and measuring the response are also unaware of which subjects are receiving which treatments. How to reduce the inuence of sampling error Replication The application of every treatment to multiple, independent experimental units. More replication is always better. Balanced experimental design All treatments have equal sample size. Blocking Blocking is an experimental design strategy used to account for extraneous variation by dividing the experimental units into groups, called blocksor strata, taht share common features.

Blocking The grouping of experimental units that have similar properties. Within each block, treatments are randomly assigned to experimental units. Paired design for two treatments is an example of blocking. Randomized block design Same as paired design but for more than two treatments. Experiments with more than one factor Factor A single treatment variable whose effects are of interest to the researcher. Factorial design An experiment having this design investigates all treatment combinations of two or more variables. A factorial design can measure interactions between treatment variables. Interaction Interaction between two or more explanatory variables means that the effect of one variable depends upon the state of the other variable. What if you can't do experiments? (Observational instead of experimental) Matching With matching, every individual in the treatment group is paired with a control individual having the same or closely similar values for the suspected confounding variables. In a weaker version of this approach, a comparison group is chosen that has a frequency distribution of measurements for each confounding variable that is similar to that of the treatment group, but no pairing takes place. Choosing a sample size An important part of planning an experiment or observational study is choosing a sample size that will give sufcient power or precision. Plan for precision A frequent goal of studies in biology is to estimate the magnitude of the treatment effect as precisely as possible. Planning for precision involves choosing a sample size that yields a condence interval of expected width. Typically, we hope to set the bounds as narrowly as we can afford. Plan for power Next we consider choosing a sample size based on a desired probabilty of rejecting a false null hypothesis - that is, planning a sample based on a desired power. Plan for data loss The previous plans for sample sizes refer to sample sizes still available at the end of the experiment. But some experimental individuals may die, leave the study, or be lost between the start and the end of the study. The starting sample sizes should be made even larger to compensate. Interleaf 8 Data dredging Data dredging is the carrying out of many statistical tests in hope of nding at least one statistically signicant result. The problem is that the probability of making at least one Type I error (false positive) is greater than the signicance level alpha when amny tests are conducted, if the null hypothesis is true. If you admit that you dredged the data, your results can still be useful (exploring data). Most common correction for multiple comparisons is the Bonferroni correction.

alpha*=alpha/number of tests Another increasingly popular approach to correct for multiple comparisons is called the false discovery rate (FDR)(Is niet uitgelegd bij college, zie boek, maar ik snap het niet goed genoeg) H15 Comparing means of more than two groups (ANOVA =ANalysis Of VAriance) Rejecting Hnull in ANOVA indicates that the mean of at least one group is different from the others. ANOVA in a nutshell The job of ANOVA is to determine whether the variaon among the group sample means is greater than expected by chance. Error mean square The pooled sample variance, a measure of the variability of groups. Group mean square Represents variation among individuals belonging to different gropus. It should be similar to the error mean square if population means are equal. The nal outcome of ANOVA is a test that compares these two mean squares. Zie formulekaart voor formules MSgroups, MSerror. The variance ratio, F tg=F=MSgroups/MSerror P=Fcdf(tg,df) df=n1+n2+n3.. etc -k R^2 measures the fraction of the variation in Y that is explained by group differences. SStotal=SSgroups+SSerror R^2=SSgroups/SStotal Assumptions and alternatives Assumptions: - The measurements in every group represent a random sample form the correcsponding population - The variable is normally distributed in each of the k populations - The variance is the same in all k populations The ANOVA is robust to deviations from the assumptions of normality, particularly when the sample sizes are large. The ANOVA is also robust to departures from the assumption of equal variance in the k populations, but only if the samples are all about the same size. Nonparametric alternatives If the normality isn't met and transformations are unsuccessful, there is a nonparametric alternative to the single-factor ANOVA. Kruskal-Wallis test A nonparametric method based on ranks, equivalent of the Mann-Whitney U-test. (ANOVA based on ranks) Assumptions: - All group samples are random samples from the corresponding populations. - To use Kruska-Wallis as a test of differences among populations in means or medians, the distribution of the variable must have the same shape in every population. The Kruskal-Wallis test has little power when sample sizes are very small. Planned comparison

A comparison between means planned during the design of the study, before the data are examined. Higher precision. Unplanned comparison Some sort of data dredging. Tukey-Kramer test The probability of making at least one type I error throughout the course of testing all pairs of means is no greater than the signicance level alpha. Fixed and random effects An explanatory variable is called a exed effect if the groups are predened and are of direct interest. An explanatory variable is called a random effect if the groups are randomly sampled from a population of possible groups. ANOVA with randomly chosen groups Variance components In a random-effects ANOVO these components make up all the variance in the response variable: variance within gropus (sigma^2_ and variance among groups (sigmaA^2). SA^2=(MSgroups-MSerror)/n Repeatabilityis the fraction of summed variance that is among groups = SA^2/(SA^2+MSerror) Random-effects ANOVA makes all of the same assumptions as xed-effectsANOVA, but adds two more. It assumes that groups are randomly sampled. ALso random-effects ANOVA assumes that the grou means have a normal distribution in the population. H16 Correlation between numerical variables Correlation When two numerical variables are associated we say that they are correlated. Estimating a linear correlation coefcient Correlation coefcient Measures the strength and direction of the linear association between two numerical variables. The most common use of hypothesis testing in correlation analysis is to test the null hypothesis that the population correlation rho is exactly zero. Assumptions Random sample Bivariate normal distribution A bivariate normal distribution is a bell-shaped probability distribution in three dimensions rather than two. - The relationship between X and Y is linear. - The cloud of points in a scatter plot of X and Y has a circular or elliptical shape. - The frequency distributions of X and Y separately are normal. departures: - Cloud of points that is funnel shaped. - presence of outliers. - non-linear relationship between X and Y. If the assumption of bivariate normality isn't met Transformations or nonparametric methods Log, square root, arcsine.

Spearman's rank correlation Correlation coefcient depends on the range The correlation is weaker when a smaller range of X-values is present. because the other factors that affect Y become relatively more important. The correlation coefcient between the same two variables is not comparable between separate studies unless the studies use the same range of values for the X-variable. Spearman's rank correlation Measures the strength and direction of the linear association between the ranks of two variables. Assumes random sample, linear relationship between ranks. Measurement error When a variable isn't measured correctly. Attenuation Underestimation of the magnitude of rho by r. Interleaf 10Publication bias The difference between the true effect and the average effect published in journals is called publications bias. Journals tend to publish the more interesting papers, papers that reject the null hypothesis, papers describing larger effects. H17 Regression Regression is the method used to predcit the value of one numerical variable from that of another. Linear regression Draws a straight lilne through a scatter plot to predict the response variable from the explanatory variable, assuming the relationship between the two variables really is linear. Least squares regression Ideally we would nd a line that leads to the smallest possible squared deviations in Y, between the data points and the regression line. Formula for the line Y=a+bX Coefcient a is the Y-intercept Coefcient b is the slopeof the regression line. It's the rate of change in Y per unit of X. Predicted values Predicted values of Y from a regression line estimate the mean value of Y for all individuals that have a given value of X. Residuals Measure the scatter of points above and below the least squares regression line. Condence bands Measure the precision of the predicted mean Y for each value of X. Prediction intervals Measure the precision of the predicted single Y-values for each X. Extrapolation The prediction of the value of a response variable outside the range of X-vales in the data. Regression toward the mean

Results when two variables have a correlation less than one. Individuals that are far from the mean for one of the measurements will, on avarage, lie closer to the mean for the other measurement. Regression fallacy Interpreting improvement due to regression toward the mean as if it were a response to the treatment, instead of a mathematical fact of regression, is called the regression fallacy. Assumptions - At each value of X, there is a population of possible Y-values whose mean lies on the true regression line - At each value of X, the distribution of possible Y-values is normal. - The variance of Y-values is the same at all values of X. - At each value of X, the Y-measurements represent a random sample from the population of possible Y-values. Detecting non-normality and unequal variance through visual inspecition of a residual plot - A roughly symmetric cloud of points above and below the horizontal line at zer, with a higher density of points close to the line than away from the line - little noticeable curvature as we move from left to right along the X-axis - approximately equal variance of points above and below the line at all values of X Residual plot A scatter plot of the residuals (Yi-Yhati) against the Xi, the values of the explanatory variable. Transformations can help making non-linear relationships linear. Onderstaande lijst is INCOMPLEET gebruik formulekaart Formula summary Z-standardization Converts values from any normal distribution with known mean mu and known variance sigma into standard normal deviates Assumptions: The original distribution is normal with known parameters. Formula: Z = (Y-mu)/sigma Normal approximation to the binomial distribution Approximates the binomial distribution using the normal distribution. Assumptions: That np and n(1-p) are both ve or greater. Formula: Pr[X>=Observed] = Pr[Z>(Observed - np)/(sqrt(np(1-p))], where n is the number of trials, p is the probability of succes for each trial, and Observed is the number of successes in the data. Continuity correction for the normal approximation to the binomial distribution Impvroves the match between the normal and binomial distributions. The binomial distribution is discrete, and the normal distribution is continuous. By adding or substracting 1/2 from the desired value, we can match the normal and binomial distributions better. Formula: Pr[X>=Observed] = Pr[Z>(Observed - 1/2 -np)/(sqrt(np(1-p))] and Pr[X<=Observed] = Pr[Z<{Observed + 1/2 - np)/(sqrt(np(1-p))], where n is the number of trials, p is the probability of success for each trial, and Observed is the number of successes in the data. Condence interval for a mean Assumptions: Individuals are chosen as a random sample from a population that is normally distributed. Estimate: Ymean

Parameter: mu Degrees of freedom: n-1 Formula: Ymean - t[alpha](2),df SEymean <= mu <= Ymean + t[alpha](2),df SEymean This formula calculates the 1- alpha condence interval. One-sample t-test Compares the sample mean of a numerical variable to a hypothesized value, mu0. Assumptions: Individuals are randomly sampled from a a population that is normally distributed. Test statistic: t Distribution under H0: The t-distribution with n-1 degrees of freedom. Formula: t = (Ymean-m0)/(s/sqrt(n)) Condence interval for variance Assumptions: Individuals are chosen as a random sample from a normally distributed population. Estimate: s^2 Parameter: sigma^2 Degrees of freedom: df = n - 1 Formula: (df s^2)/(X^2 a/2,df)=<sigma^2=< (df s^2)/(X^2 1-a/2,df) Condence interval for the mean difference (paired data) Assumptions: Pairs are a random sample. The difference between paired measurements is normally distributed. Parameter: mud Statistic: dmean Degrees of freedom: n - 1 Formula: dmean - t SEdmean<mud<dmean + t SEdmean Where dmean is the mean of the differences between members of each of the pairs, SEdmean=sd/ sqrt(n), sd is the sample standard deviation of the differences, and n is the number of pairs Paired t-test To test whether the mean difference in a population equals a null hypothesized value, mud0 Assumptions: Pairs are randomly sampled from a population. The differences are normally distributed. Test statistic: t Distribution under H0: The t-distribution with n-1 degrees of freedom, where n is the number of pairs. Formula: t=(dmean-mudmean)/SEdmean Standard error of difference between two means
2 Formula: SEymean1-ymean2=sqrt(s p((1/n1)+(1/n2))) where s2p is the pooled sample variance:

s2p=(df1s12+df2s22)/(df1+df2)) the degrees of freedom df1=n1-1 and df2=n2-1 Condence interval for the difference between two means (two samples)