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How to Set Up a Hypothesis Test: Null versus Alternative

In the second experiment, you are going to put human volunteers with high blood pressure on a strict low-salt diet and see how much their blood pressure goes down. Everyone will be confined to a hospital for a month and fed either a normal diet, or the same foods with half as much salt. For this experiment, you wouldn't be very interested in the P value, as based on prior research in animals and humans, you are already quite certain that reducing salt intake will lower blood pressure; you're pretty sure that the null hypothesis that "Salt intake has no effect on blood pressure" is false. Instead, you are very interested to know how much the blood pressure goes down. Reducing salt intake in half is a big deal, and if it only reduces blood pressure by 1 mm Hg, the tiny gain in life expectancy wouldn't be worth a lifetime of bland food and obsessive label-reading. If it reduces blood pressure by 20 mm with a confidence interval of ±5 mm, it might be worth it. So you should estimate the effect size (the difference in blood pressure between the diets) and the confidence interval on the difference.

the null hypothesis is rejected when it is true b.
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There are different ways of doing statistics. The technique used by the vast majority of biologists, and the technique that most of this handbook describes, is sometimes called "frequentist" or "classical" statistics. It involves testing a null hypothesis by comparing the data you observe in your experiment with the predictions of a null hypothesis. You estimate what the probability would be of obtaining the observed results, or something more extreme, if the null hypothesis were true. If this estimated probability (the P value) is small enough (below the significance value), then you conclude that it is unlikely that the null hypothesis is true; you reject the null hypothesis and accept an alternative hypothesis.

the null hypothesis is not rejected when it is false c.

The hypothesis test that followed ended with a decision of "reject H(O)".
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If (that is, ), we say the data are consistent with a population mean difference of 0 (because has the sort of value we expect to see when the population value is 0) or "we fail to reject the hypothesis that the population mean difference is 0". For example, if t were 0.76, we would fail reject the hypothesis that the population mean difference is 0 because we've observed a value of t that is unremarkable if the hypothesis were true.

One of the main goals of statistical hypothesis testing is to estimate the P value, which is the probability of obtaining the observed results, or something more extreme, if the null hypothesis were true. If the observed results are unlikely under the null hypothesis, your reject the null hypothesis. Alternatives to this "frequentist" approach to statistics include Bayesian statistics and estimation of effect sizes and confidence intervals.

failing to reject the null hypothesis when it is false.

It is the point where the decision changes from reject to fail to reject.
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Now instead of testing 1000 plant extracts, imagine that you are testing just one. If you are testing it to see if it kills beetle larvae, you know (based on everything you know about plant and beetle biology) there's a pretty good chance it will work, so you can be pretty sure that a P value less than 0.05 is a true positive. But if you are testing that one plant extract to see if it grows hair, which you know is very unlikely (based on everything you know about plants and hair), a P value less than 0.05 is almost certainly a false positive. In other words, if you expect that the null hypothesis is probably true, a statistically significant result is probably a false positive. This is sad; the most exciting, amazing, unexpected results in your experiments are probably just your data trying to make you jump to ridiculous conclusions. You should require a much lower P value to reject a null hypothesis that you think is probably true.

A related criticism is that a significant rejection of a null hypothesis might not be biologically meaningful, if the difference is too small to matter. For example, in the chicken-sex experiment, having a treatment that produced 49.9% male chicks might be significantly different from 50%, but it wouldn't be enough to make farmers want to buy your treatment. These critics say you should estimate the effect size and put a on it, not estimate a P value. So the goal of your chicken-sex experiment should not be to say "Chocolate gives a proportion of males that is significantly less than 50% (P=0.015)" but to say "Chocolate produced 36.1% males with a 95% confidence interval of 25.9 to 47.4%." For the chicken-feet experiment, you would say something like "The difference between males and females in mean foot size is 2.45 mm, with a confidence interval on the difference of ±1.98 mm."

If we would reject a null hypothesis at the 5% level, we would also reject it at the 1% level.
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failing to reject the null hypothesis when it is true.

Before actually conducting a hypothesis test, you have to put two possible hypotheses on the table — the null hypothesis is one of them. But, if the null hypothesis is rejected (that is, there was sufficient evidence against it), what’s your alternative going to be? Actually, three possibilities exist for the second (or alternative) hypothesis, denoted Ha. Here they are, along with their shorthand notations in the context of the pie example:

rejecting the null hypothesis when it is true.

Every hypothesis test contains a set of two opposing statements, or hypotheses, about a population parameter. The first hypothesis is called the denoted H0. The null hypothesis always states that the population parameter is to the claimed value. For example, if the claim is that the average time to make a name-brand ready-mix pie is five minutes, the statistical shorthand notation for the null hypothesis in this case would be as follows:

rejecting the null hypothesis when it is false.

Here are three experiments to illustrate when the different approaches to statistics are appropriate. In the first experiment, you are testing a plant extract on rabbits to see if it will lower their blood pressure. You already know that the plant extract is a diuretic (makes the rabbits pee more) and you already know that diuretics tend to lower blood pressure, so you think there's a good chance it will work. If it does work, you'll do more low-cost animal tests on it before you do expensive, potentially risky human trials. Your prior expectation is that the null hypothesis (that the plant extract has no effect) has a good chance of being false, and the cost of a false positive is fairly low. So you should do frequentist hypothesis testing, with a significance level of 0.05.

rejecting the null hypothesis when the alternative is true.

When you set up a hypothesis test to determine the validity of a statistical claim, you need to define both a null hypothesis and an alternative hypothesis.

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