DATA606 Lab 7

Source files: https://github.com/djlofland/DATA606_F2019/tree/master/Lab7

library(tidyverse)

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North Carolina births

In 2004, the state of North Carolina released a large data set containing information on births recorded in this state. This data set is useful to researchers studying the relation between habits and practices of expectant mothers and the birth of their children. We will work with a random sample of observations from this data set.

Exploratory analysis

Load the nc data set into our workspace.

load("more/nc.RData")

We have observations on 13 different variables, some categorical and some numerical. The meaning of each variable is as follows.

variable	description
`fage`	father’s age in years.
`mage`	mother’s age in years.
`mature`	maturity status of mother.
`weeks`	length of pregnancy in weeks.
`premie`	whether the birth was classified as premature (premie) or full-term.
`visits`	number of hospital visits during pregnancy.
`marital`	whether mother is `married` or `not married` at birth.
`gained`	weight gained by mother during pregnancy in pounds.
`weight`	weight of the baby at birth in pounds.
`lowbirthweight`	whether baby was classified as low birthweight (`low`) or not (`not low`).
`gender`	gender of the baby, `female` or `male`.
`habit`	status of the mother as a `nonsmoker` or a `smoker`.
`whitemom`	whether mom is `white` or `not white`.

Exercise 1

What are the cases in this data set? How many cases are there in our sample?

Each case in the dataset (row) is a single birth event. There are 1000 cases in the dataset.

As a first step in the analysis, we should consider summaries of the data. This can be done using the summary command:

summary(nc)

##       fage            mage            mature        weeks      
##  Min.   :14.00   Min.   :13   mature mom :133   Min.   :20.00  
##  1st Qu.:25.00   1st Qu.:22   younger mom:867   1st Qu.:37.00  
##  Median :30.00   Median :27                     Median :39.00  
##  Mean   :30.26   Mean   :27                     Mean   :38.33  
##  3rd Qu.:35.00   3rd Qu.:32                     3rd Qu.:40.00  
##  Max.   :55.00   Max.   :50                     Max.   :45.00  
##  NA's   :171                                    NA's   :2      
##        premie        visits            marital        gained     
##  full term:846   Min.   : 0.0   married    :386   Min.   : 0.00  
##  premie   :152   1st Qu.:10.0   not married:613   1st Qu.:20.00  
##  NA's     :  2   Median :12.0   NA's       :  1   Median :30.00  
##                  Mean   :12.1                     Mean   :30.33  
##                  3rd Qu.:15.0                     3rd Qu.:38.00  
##                  Max.   :30.0                     Max.   :85.00  
##                  NA's   :9                        NA's   :27     
##      weight       lowbirthweight    gender          habit    
##  Min.   : 1.000   low    :111    female:503   nonsmoker:873  
##  1st Qu.: 6.380   not low:889    male  :497   smoker   :126  
##  Median : 7.310                               NA's     :  1  
##  Mean   : 7.101                                              
##  3rd Qu.: 8.060                                              
##  Max.   :11.750                                              
##                                                              
##       whitemom  
##  not white:284  
##  white    :714  
##  NA's     :  2  
##                 
##                 
##                 
##

As you review the variable summaries, consider which variables are categorical and which are numerical. For numerical variables, are there outliers? If you aren’t sure or want to take a closer look at the data, make a graph.

Categorical: mature, premie, marital, lowbirthweight, gender, habit, whitemom

Numerical: fage, mage, weeks, visits, gained, weight

boxplot(nc$fage, nc$mage, nc$weeks, nc$visits, nc$gained, nc$weight)

fage as 2 high outliers, mage has 1 high outlier, weeks has a number of low outliers and 1 high outlier and has a clear right-skew, visits has outliers both above and below the interquartile range with a lisght left skew towards fewer visits, gained has a number of high outliers but those aside, looks fairly “normal”, and weight has a number of outliers.

Consider the possible relationship between a mother’s smoking habit and the weight of her baby. Plotting the data is a useful first step because it helps us quickly visualize trends, identify strong associations, and develop research questions.

Exercise 2

Make a side-by-side boxplot of habit and weight. What does the plot highlight about the relationship between these two variables?

boxplot(nc$weight~nc$habit)

Nonsmoker baby weight has a much wider range of values wit more outliers above and below the IQR. Non-smokers baby weights appear to be slightly higher on average. Smokers’ baby weights appear to be slightly lower with a narrower range of values.

The box plots show how the medians of the two distributions compare, but we can also compare the means of the distributions using the following function to split the weight variable into the habit groups, then take the mean of each using the mean function.

by(nc$weight, nc$habit, mean)

## nc$habit: nonsmoker
## [1] 7.144273
## -------------------------------------------------------- 
## nc$habit: smoker
## [1] 6.82873

There is an observed difference, but is this difference statistically significant? In order to answer this question we will conduct a hypothesis test.

Inference

Exercise 3

Check if the conditions necessary for inference are satisfied. Note that you will need to obtain sample sizes to check the conditions. You can compute the group size using the same by command above but replacing mean with length.

by(nc$weight, nc$habit, length)

## nc$habit: nonsmoker
## [1] 873
## -------------------------------------------------------- 
## nc$habit: smoker
## [1] 126

Conditions: cases were randomly sampled. We have > 10 cases in each group, smoker and nonsmoker

Exercise 4

Write the hypotheses for testing if the average weights of babies born to smoking and non-smoking mothers are different.

$H_{0}$: There is no difference between baby weights based on mom smoking habit

$H_{A}$: There is as differnce between the baby weights of moms who smoke vs those who don’t

Next, we introduce a new function, inference, that we will use for conducting hypothesis tests and constructing confidence intervals.

inference(y = nc$weight, x = nc$habit, est = "mean", type = "ht", null = 0, 
          alternative = "twosided", method = "theoretical")

## Response variable: numerical, Explanatory variable: categorical
## Difference between two means
## Summary statistics:
## n_nonsmoker = 873, mean_nonsmoker = 7.1443, sd_nonsmoker = 1.5187
## n_smoker = 126, mean_smoker = 6.8287, sd_smoker = 1.3862

## Observed difference between means (nonsmoker-smoker) = 0.3155
## 
## H0: mu_nonsmoker - mu_smoker = 0 
## HA: mu_nonsmoker - mu_smoker != 0 
## Standard error = 0.134 
## Test statistic: Z =  2.359 
## p-value =  0.0184

Let’s pause for a moment to go through the arguments of this custom function. The first argument is y, which is the response variable that we are interested in: nc$weight. The second argument is the explanatory variable, x, which is the variable that splits the data into two groups, smokers and non-smokers: nc$habit. The third argument, est, is the parameter we’re interested in: "mean" (other options are "median", or "proportion".) Next we decide on the type of inference we want: a hypothesis test ("ht") or a confidence interval ("ci"). When performing a hypothesis test, we also need to supply the null value, which in this case is 0, since the null hypothesis sets the two population means equal to each other. The alternative hypothesis can be "less", "greater", or "twosided". Lastly, the method of inference can be "theoretical" or "simulation" based.

Exercise 5

Change the type argument to "ci" to construct and record a confidence interval for the difference between the weights of babies born to smoking and non-smoking mothers.

By default the function reports an interval for ($\mu_{nonsmoker} - \mu_{smoker}$) . We can easily change this order by using the order argument:

inference(y = nc$weight, x = nc$habit, est = "mean", type = "ci", null = 0, 
          alternative = "twosided", method = "theoretical", 
          order = c("smoker","nonsmoker"))

## Response variable: numerical, Explanatory variable: categorical
## Difference between two means
## Summary statistics:
## n_smoker = 126, mean_smoker = 6.8287, sd_smoker = 1.3862
## n_nonsmoker = 873, mean_nonsmoker = 7.1443, sd_nonsmoker = 1.5187

## Observed difference between means (smoker-nonsmoker) = -0.3155
## 
## Standard error = 0.1338 
## 95 % Confidence interval = ( -0.5777 , -0.0534 )

On your own

Problem 1

Calculate a 95% confidence interval for the average length of pregnancies (weeks) and interpret it in context. Note that since you’re doing inference on a single population parameter, there is no explanatory variable, so you can omit the x variable from the function.

inference(y = nc$weeks, est = "mean", type = "ci", null = 0, 
          alternative = "twosided", method = "theoretical")

## Single mean 
## Summary statistics:

## mean = 38.3347 ;  sd = 2.9316 ;  n = 998 
## Standard error = 0.0928 
## 95 % Confidence interval = ( 38.1528 , 38.5165 )

( 38.1528 , 38.5165 )

Problem 2

Calculate a new confidence interval for the same parameter at the 90% confidence level. You can change the confidence level by adding a new argument to the function: conflevel = 0.90.

inference(y = nc$weeks, est = "mean", type = "ci", null = 0, 
          alternative = "twosided", method = "theoretical",
          conflevel = 0.90)

## Single mean 
## Summary statistics:

## mean = 38.3347 ;  sd = 2.9316 ;  n = 998 
## Standard error = 0.0928 
## 90 % Confidence interval = ( 38.182 , 38.4873 )

( 38.182 , 38.4873 )

Problem 3

Conduct a hypothesis test evaluating whether the average weight gained by younger mothers is different than the average weight gained by mature mothers.

Conditions: 867 younger women and 133 mature women

$H_{0}$: Weight gained between young and mature women is the same

$H_{A}$: Weight gained between young and mature women is different.

inference(y = nc$gained, x=nc$mature, est = "mean", type = "ht", null = 0, 
          alternative = "twosided", method = "theoretical",
          )

## Response variable: numerical, Explanatory variable: categorical
## Difference between two means
## Summary statistics:
## n_mature mom = 129, mean_mature mom = 28.7907, sd_mature mom = 13.4824
## n_younger mom = 844, mean_younger mom = 30.5604, sd_younger mom = 14.3469

## Observed difference between means (mature mom-younger mom) = -1.7697
## 
## H0: mu_mature mom - mu_younger mom = 0 
## HA: mu_mature mom - mu_younger mom != 0 
## Standard error = 1.286 
## Test statistic: Z =  -1.376 
## p-value =  0.1686

inference(y = nc$gained, x=nc$mature, est = "mean", type = "ci", null = 0, 
          alternative = "twosided", method = "theoretical",
          )

## Response variable: numerical, Explanatory variable: categorical
## Difference between two means
## Summary statistics:
## n_mature mom = 129, mean_mature mom = 28.7907, sd_mature mom = 13.4824
## n_younger mom = 844, mean_younger mom = 30.5604, sd_younger mom = 14.3469

## Observed difference between means (mature mom-younger mom) = -1.7697
## 
## Standard error = 1.2857 
## 95 % Confidence interval = ( -4.2896 , 0.7502 )

While the mean weight is lower for mature women, it is not statistically significant at the 95% confidence. 0 lbs (our null hypothesis) falls within the 95% confidence interval (-4.2896 ,0.7502) so we cannot reject the null hypothesis.

Problem 4

Now, a non-inference task: Determine the age cutoff for younger and mature mothers. Use a method of your choice, and explain how your method works.

nc %>% group_by(mature) %>% summarize(min_age = min(mage), max_age=max(mage))

## # A tibble: 2 x 3
##   mature      min_age max_age
##   <fct>         <int>   <int>
## 1 mature mom       35      50
## 2 younger mom      13      34

youger women: 13-34 and mature women: 35-50 with the cuttoff at 35yro

Problem 5

Pick a pair of numerical and categorical variables and come up with a research question evaluating the relationship between these variables. Formulate the question in a way that it can be answered using a hypothesis test and/or a confidence interval. Answer your question using the inference function, report the statistical results, and also provide an explanation in plain language.

Question: Is there a difference in birth weights between male and female babies?

qqnorm(nc$weight[nc$gender=='male'])
qqline(nc$weight[nc$gender=='male'])

qqnorm(nc$weight[nc$gender=='female'])
qqline(nc$weight[nc$gender=='female'])

inference(y = nc$weight, x=nc$gender, est = "mean", type = "ht", null = 0, 
          alternative = "twosided", method = "theoretical",
          )

## Response variable: numerical, Explanatory variable: categorical
## Difference between two means
## Summary statistics:
## n_female = 503, mean_female = 6.9029, sd_female = 1.4759
## n_male = 497, mean_male = 7.3015, sd_male = 1.5168

## Observed difference between means (female-male) = -0.3986
## 
## H0: mu_female - mu_male = 0 
## HA: mu_female - mu_male != 0 
## Standard error = 0.095 
## Test statistic: Z =  -4.211 
## p-value =  0

inference(y = nc$weight, x=nc$gender, est = "mean", type = "ci", null = 0, 
          alternative = "twosided", method = "theoretical",
          )

## Response variable: numerical, Explanatory variable: categorical
## Difference between two means
## Summary statistics:
## n_female = 503, mean_female = 6.9029, sd_female = 1.4759
## n_male = 497, mean_male = 7.3015, sd_male = 1.5168

## Observed difference between means (female-male) = -0.3986
## 
## Standard error = 0.0947 
## 95 % Confidence interval = ( -0.5841 , -0.2131 )

The p-value, 0, from the hypotheis test suggest that we reject the null hypothesis (male and female babies have the same mean birth weight) and we should accept that the weights are different. Since the weights are both skewed from normal, I’d lke to also explore whether the median weights are different between male and female babies.

inference(y = nc$weight, x=nc$gender, est = "median", type = "ht", null = 0, 
          alternative = "twosided", method = "simulation",
          )

## Response variable: numerical, Explanatory variable: categorical
## Difference between two medians
## Summary statistics:
## n_female = 503, median_female = 7.13, n_male = 497, median_male = 7.44,

## Observed difference between medians (female-male) = -0.31
## 
## H0: median_female - median_male = 0 
## HA: median_female - median_male != 0

## p-value =  0.0026

inference(y = nc$weight, x=nc$gender, est = "median", type = "ci", null = 0, 
          alternative = "twosided", method = "simulation",
          )

## Response variable: numerical, Explanatory variable: categorical
## Difference between two medians
## Summary statistics:
## n_female = 503, median_female = 7.13, n_male = 497, median_male = 7.44,

## Observed difference between medians (female-male) = -0.31

## 95 % Bootstrap interval = ( -0.56 , -0.19 )

Looking at median weights, we also see a clear difference in the same direction with male babies weighting more at birth (p=0.0026).