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This number, 0.030, is the *P* value. It is defined as the probability of getting the observed result, or a more extreme result, if the null hypothesis is true. So "*P*=0.030" is a shorthand way of saying "The probability of getting 17 or fewer male chickens out of 48 total chickens, *IF* the null hypothesis is true that 50% of chickens are male, is 0.030."

After you do a statistical test, you are either going to reject or accept the null hypothesis. Rejecting the null hypothesis means that you conclude that the null hypothesis is not true; in our chicken sex example, you would conclude that the true proportion of male chicks, if you gave chocolate to an infinite number of chicken mothers, would be less than 50%.

It is important to distinguish between *biological* null and alternative hypotheses and *statistical* null and alternative hypotheses. "Sexual selection by females has caused male chickens to evolve bigger feet than females" is a biological alternative hypothesis; it says something about biological processes, in this case sexual selection. "Male chickens have a different average foot size than females" is a statistical alternative hypothesis; it says something about the numbers, but nothing about what caused those numbers to be different. The biological null and alternative hypotheses are the first that you should think of, as they describe something interesting about biology; they are two possible answers to the biological question you are interested in ("What affects foot size in chickens?"). The statistical null and alternative hypotheses are statements about the data that should follow from the biological hypotheses: if sexual selection favors bigger feet in male chickens (a biological hypothesis), then the average foot size in male chickens should be larger than the average in females (a statistical hypothesis). If you reject the statistical null hypothesis, you then have to decide whether that's enough evidence that you can reject your biological null hypothesis. For example, if you don't find a significant difference in foot size between male and female chickens, you could conclude "There is no significant evidence that sexual selection has caused male chickens to have bigger feet." If you do find a statistically significant difference in foot size, that might not be enough for you to conclude that sexual selection caused the bigger feet; it might be that males eat more, or that the bigger feet are a developmental byproduct of the roosters' combs, or that males run around more and the exercise makes their feet bigger. When there are multiple biological interpretations of a statistical result, you need to think of additional experiments to test the different possibilities.

Usually, the null hypothesis is boring and the alternative hypothesis is interesting. For example, let's say you feed chocolate to a bunch of chickens, then look at the sex ratio in their offspring. If you get more females than males, it would be a tremendously exciting discovery: it would be a fundamental discovery about the mechanism of sex determination, female chickens are more valuable than male chickens in egg-laying breeds, and you'd be able to publish your result in *Science* or *Nature*. Lots of people have spent a lot of time and money trying to change the sex ratio in chickens, and if you're successful, you'll be rich and famous. But if the chocolate doesn't change the sex ratio, it would be an extremely boring result, and you'd have a hard time getting it published in the *Eastern Delaware Journal of Chickenology*. It's therefore tempting to look for patterns in your data that support the exciting alternative hypothesis. For example, you might look at 48 offspring of chocolate-fed chickens and see 31 females and only 17 males. This looks promising, but before you get all happy and start buying formal wear for the Nobel Prize ceremony, you need to ask "What's the probability of getting a deviation from the null expectation that large, just by chance, if the boring null hypothesis is really true?" Only when that probability is low can you reject the null hypothesis. The goal of statistical hypothesis testing is to estimate the probability of getting your observed results under the null hypothesis.

The primary goal of a statistical test is to determine whether an observed data set is so different from what you would expect under the null hypothesis that you should reject the null hypothesis. For example, let's say you are studying sex determination in chickens. For breeds of chickens that are bred to lay lots of eggs, female chicks are more valuable than male chicks, so if you could figure out a way to manipulate the sex ratio, you could make a lot of chicken farmers very happy. You've fed chocolate to a bunch of female chickens (in birds, unlike mammals, the female parent determines the sex of the offspring), and you get 25 female chicks and 23 male chicks. Anyone would look at those numbers and see that they could easily result from chance; there would be no reason to reject the null hypothesis of a 1:1 ratio of females to males. If you got 47 females and 1 male, most people would look at those numbers and see that they would be extremely unlikely to happen due to luck, if the null hypothesis were true; you would reject the null hypothesis and conclude that chocolate really changed the sex ratio. However, what if you had 31 females and 17 males? That's definitely more females than males, but is it really so unlikely to occur due to chance that you can reject the null hypothesis? To answer that, you need more than common sense, you need to calculate the probability of getting a deviation that large due to chance.

How do you know which hypothesis to put in H_{0} and which one to put in H_{a}? Typically, the null hypothesis says that nothing new is happening; the previous result is the same now as it was before, or the groups have the same average (their difference is equal to zero). In general, you assume that people’s claims are true until proven otherwise. So the question becomes: Can you prove otherwise? In other words, can you show sufficient evidence to reject H_{0}?

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If you only want to see whether the time turns out to be greater than what the company claims (that is, whether the company is falsely advertising its quick prep time), you use the greater-than alternative, and your two hypotheses are

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.

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.

For example, if you want to test whether a company is correct in claiming its pie takes five minutes to make and it doesn’t matter whether the actual average time is more or less than that, you use the not-equal-to alternative. Your hypotheses for that test would be

The null hypothesis is a statement that you want to test. In general, the null hypothesis is that things are the same as each other, or the same as a theoretical expectation. For example, if you measure the size of the feet of male and female chickens, the null hypothesis could be that the average foot size in male chickens is the same as the average foot size in female chickens. If you count the number of male and female chickens born to a set of hens, the null hypothesis could be that the ratio of males to females is equal to a theoretical expectation of a 1:1 ratio.

The alternative hypothesis is that things are different from each other, or different from a theoretical expectation. For example, one alternative hypothesis would be that male chickens have a different average foot size than female chickens; another would be that the sex ratio is different from 1:1.

In the figure above, I used the to calculate the probability of getting each possible number of males, from 0 to 48, under the null hypothesis that 0.5 are male. As you can see, the probability of getting 17 males out of 48 total chickens is about 0.015. That seems like a pretty small probability, doesn't it? However, that's the probability of getting *exactly* 17 males. What you want to know is the probability of getting 17 *or fewer* males. If you were going to accept 17 males as evidence that the sex ratio was biased, you would also have accepted 16, or 15, or 14,… males as evidence for a biased sex ratio. You therefore need to add together the probabilities of all these outcomes. The probability of getting 17 or fewer males out of 48, under the null hypothesis, is 0.030. That means that if you had an infinite number of chickens, half males and half females, and you took a bunch of random samples of 48 chickens, 3.0% of the samples would have 17 or fewer males.

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