This is problem set #4, in which we want you to integrate your knowledge of data wrangling with some basic simulation skills. It’s a short problem set to help consolidate your ggplot2 skills and then help you get your feet wet in testing statistical concepts through “making up data” rather than consulting a textbook or doing math.
For ease of reading, please separate your answers from our text by marking our text with the > character (indicating quotes).
Part 1: ggplot practice
This part is a warmup, it should be relatively straightforward ggplot2 practice.
Load data from Frank, Vul, Saxe (2011, Infancy), a study in which we measured infants’ looking to hands in moving scenes. There were infants from 3 months all the way to about two years, and there were two movie conditions (Faces_Medium, in which kids played on a white background, and Faces_Plus, in which the backgrounds were more complex and the people in the videos were both kids and adults). An eye-tracker measured children’s attention to faces. This version of the dataset only gives two conditions and only shows the amount of looking at hands (other variables were measured as well).
library(tidyverse)
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.3 ✔ readr 2.1.4
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.3 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.0
✔ purrr 1.0.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
fvs <-read_csv("data/FVS2011-hands.csv")
Rows: 232 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (1): condition
dbl (3): subid, age, hand.look
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
First, use ggplot to plot a histogram of the ages of children in the study. NOTE: this is a repeated measures design, so you can’t just take a histogram of every measurement.
ggplot(fvs, aes(age, fill =factor(condition))) +geom_histogram() +facet_wrap(~condition)
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Second, make a scatter plot showing hand looking as a function of age and condition. Add appropriate smoothing lines. Take the time to fix the axis labels and make the plot look nice.
ggplot(fvs, aes(x = age, y = hand.look, color = condition)) +geom_point() +geom_smooth(method ='lm') +labs(title ="Scatter Plot of Proportion of Hand Looking vs Age ", x ="Age (Months)", y ="Proportion of Hand Looking")
`geom_smooth()` using formula = 'y ~ x'
What do you conclude from this pattern of data?
ANSWER HERE: Infants that are older seem to look at hands more than younger infants (around 10 months and lesser in age). Further, the slope is higher for the Faces_Plus condition (complex actions and backgrounds) in comparison to the Faces_Medium condition (with a simple white background)
What statistical analyses would you perform here to quantify these differences?
ANSWER HERE: A Repeated Measures Analysis of Variance or an ANOVA can be performed initially to determine statistical difference and further a t-test to quantify the differences.
Part 2: Simulation
library(tidyverse)
Let’s start by convincing ourselves that t-tests have the appropriate false positive rate. Run 10,000 t-tests with standard, normally-distributed data from a made up 30-person, single-measurement experiment (the command for sampling from a normal distribution is rnorm).
The goal of these t-tests are to determine, based on 30 observations, whether the underlying distribution (in this case a normal distribution with mean 0 and standard deviation 1) has a mean that is different from 0. In reality, the mean is not different from 0 (we sampled it using rnorm), but sometimes the 30 observations we get in our experiment will suggest that the mean is higher or lower. In this case, we’ll get a “significant” result and incorrectly reject the null hypothesis of mean 0.
What’s the proportion of “significant” results (\(p < .05\)) that you see?
First do this using a for loop.
p_values <-0for (x in1:10000){ res <-t.test(rnorm(30)) p_values[x] <- res$p.value}# Proportion of significant resultsmean(p_values<0.05)
[1] 0.0519
Next, do this using the replicate function:
p_val <-replicate(10000, {t.test(rnorm(30))$p.value})# Proportion of significant resultsmean(p_val<0.05)
[1] 0.0483
How does this compare to the intended false-positive rate of \(\alpha=0.05\)?
ANSWER: Proportion of significant results is lesser than intended false positive rate. The observed proportion is 0.0499.
Ok, that was a bit boring. Let’s try something more interesting - let’s implement a p-value sniffing simulation, in the style of Simons, Nelson, & Simonsohn (2011).
Consider this scenario: you have done an experiment, again with 30 participants (one observation each, just for simplicity). The question is whether the true mean is different from 0. You aren’t going to check the p-value every trial, but let’s say you run 30 - then if the p-value is within the range p < .25 and p > .05, you optionally run 30 more and add those data, then test again. But if the original p value is < .05, you call it a day, and if the original is > .25, you also stop.
First, write a function that implements this sampling regime.
double.sample <-function(u_p) { sim_data <-rnorm(30) t_res <-t.test(sim_data) p <- t_res$p.valuewhile (p >0.05& p < u_p){ new_sim <-rnorm(30) sim_data <-c(sim_data,new_sim) new_res <-t.test(sim_data) p <- new_res$p.value }return(p)}
Now call this function 10k times and find out what happens.
p_sam <-replicate(10000, {double.sample(0.25)})# Proportion of significant resultsmean(p_sam<0.05)
[1] 0.0876
Is there an inflation of false positives? How bad is it?
ANSWER: The observed proportion of false positives has now increased to 0.0858.
Now modify this code so that you can investigate this “double the sample” rule in a bit more depth. In the previous question, the researcher doubles the sample only when they think they got “close” to a significant result, i.e. when their not-significant p is less than 0.25. What if the researcher was more optimistic? See what happens in these 3 other scenarios:
The researcher doubles the sample whenever their pvalue is not significant, but it’s less than 0.5.
The researcher doubles the sample whenever their pvalue is not significant, but it’s less than 0.75.
The research doubles their sample whenever they get ANY pvalue that is not significant.
How do these choices affect the false positive rate?
HINT: Try to do this by making the function double.sample take the upper p value as an argument, so that you can pass this through dplyr.
HINT 2: You may need more samples. Find out by looking at how the results change from run to run.
What do you conclude on the basis of this simulation? How bad is this kind of data-dependent policy?
ANSWER: There false positives are highly inflated (For example, observed proportions are 0.1249 for scenario 1,and 0.1803 for scenario 2 for 10,000 repetitions for one run) depending on the upper threshold. Lesser the false positives obtained for smaller upper thresholds. Scenario 3 almost means doubling the sample always and will highly inflate the false positives. Due to this, regardless of the sample size, the code continued to loop infinitely. If not understood well, such data-dependent policies can lead to inflated false positives .
