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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.

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.

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 H_{a}. Here they are, along with their shorthand notations in the context of the pie example:

Hypotheses developers and testers usually hope that the null hypothesis is rejected and their alternative hypothesis supported – that the drug they’re testing is effective; the campaign they’re running is a success; that the light is bent by gravity as predicted by Newtonian physics and Einstein’s theory of relativity …

Which alternative hypothesis you choose in setting up your hypothesis test depends on what you’re interested in concluding, should you have enough evidence to refute the null hypothesis (the claim). The alternative hypothesis should be decided upon before collecting or looking at any data, so as not to influence the results.

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

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The significance level (also known as the "critical value" or "alpha") you should use depends on the costs of different kinds of errors. With a significance level of 0.05, you have a 5% chance of rejecting the null hypothesis, even if it is true. If you try 100 different treatments on your chickens, and none of them really change the sex ratio, 5% of your experiments will give you data that are significantly different from a 1:1 sex ratio, just by chance. In other words, 5% of your experiments will give you a false positive. If you use a higher significance level than the conventional 0.05, such as 0.10, you will increase your chance of a false positive to 0.10 (therefore increasing your chance of an embarrassingly wrong conclusion), but you will also decrease your chance of a false negative (increasing your chance of detecting a subtle effect). If you use a lower significance level than the conventional 0.05, such as 0.01, you decrease your chance of an embarrassing false positive, but you also make it less likely that you'll detect a real deviation from the null hypothesis if there is one.

You must choose your significance level before you collect the data, of course. If you choose to use a different significance level than the conventional 0.05, people will be skeptical; you must be able to justify your choice. **Throughout this handbook, I will always use P** If you are doing an experiment where the cost of a false positive is a lot greater or smaller than the cost of a false negative, or an experiment where you think it is unlikely that the alternative hypothesis will be true, you should consider using a different significance level.

Does a probability of 0.030 mean that you should reject the null hypothesis, and conclude that chocolate really caused a change in the sex ratio? The convention in most biological research is to use a significance level of 0.05. This means that if the *P* value is less than 0.05, you reject the null hypothesis; if *P* is greater than or equal to 0.05, you don't reject the null hypothesis. There is nothing mathematically magic about 0.05, it was chosen rather arbitrarily during the early days of statistics; people could have agreed upon 0.04, or 0.025, or 0.071 as the conventional significance level.

When you reject a null hypothesis, there's a chance that you're making a mistake. The null hypothesis might really be true, and it may be that your experimental results deviate from the null hypothesis purely as a result of chance. In a sample of 48 chickens, it's possible to get 17 male chickens purely by chance; it's even possible (although extremely unlikely) to get 0 male and 48 female chickens purely by chance, even though the true proportion is 50% males. This is why we never say we "prove" something in science; there's always a chance, however miniscule, that our data are fooling us and deviate from the null hypothesis purely due to chance. When your data fool you into rejecting the null hypothesis even though it's true, it's called a "false positive," or a "Type I error." So another way of defining the *P* value is the probability of getting a false positive like the one you've observed, *if* the null hypothesis is true.

The probability that was calculated above, 0.030, is the probability of getting 17 or fewer males out of 48. It would be significant, using the conventional *P**P*=0.03 value found by adding the probabilities of getting 17 or fewer males. This is called a one-tailed probability, because you are adding the probabilities in only one tail of the distribution shown in the figure. However, if your null hypothesis is "The proportion of males is 0.5", then your alternative hypothesis is "The proportion of males is different from 0.5." In that case, you should add the probability of getting 17 or fewer females to the probability of getting 17 or fewer males. This is called a two-tailed probability. If you do that with the chicken result, you get *P*=0.06, which is not quite significant.

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