# Reevaluating my sleep experiments

### 2019-02-09

Way back in 2015, I was just learning R and produced a simple analysis of my sleep patterns when I experimented with taking potato starch.

What happens when I re-evaluate the data using better R skills? This post will show how I write the code. Check the Personal Science Guide to the Microbiome for a summary of the conclusions.

To start, I load the original data into the variable `track_data`

, which is derived from an Excel spreadsheet with rows representing my self-tracking results from each day of the year. The sheet has columns like `Date`

, `Vitamin D`

, `Fish Oil`

and many other variables representing what I did that day and, if relevant, the quantity. For purposes below, I’ll especially use the columns related to sleep:

`Z`

: Total amount of sleep that night (hours)`REM`

: Time spent in REM sleep (hours)`Deep`

: Time spent in deep sleep (hours)`Potato Starch`

: Quantity of potato starch consumed the previous day (tablespoons)

Let’s do a super-dumb t-test to compare the days with and without potato starch. A t-test is a quick way to compare two lists of numbers to see the likelihood that any differences between them are due to chance. R makes this super-easy with the function `t.test()`

: you simply give it two vectors of numbers and it will calculate the means, the deviation from those means, and some summary information that includes a `p-value`

. You shouldn’t rely on p-values for hard-and-fast confirmation that something is statistically significant, but for an initial guesstimate, statisticians use the convention that `p < 0.05`

is worthy of further investigation, while values greater than that are generally simply due to chance.

R Note: Please see the handy`cut()`

function, which lets me chop a vector into an arbitrary number of factors. Because I have so many different amounts of potato starch, the analysis is easier if I can divide the amounts into more qualitative buckets (None/Low/High).

```
experiment_days <- track_data %>% dplyr::filter(Date < as.Date("2015-04-10")) %>%
dplyr::filter(!is.na(`Potato Starch`) & !is.na(Z)) %>%
select(Date,PS = `Potato Starch`, Z, REM, Alcohol, Deep, `Vitamin D`) %>%
group_by(Week = cut(Date, "1 week")) %>%
mutate(MeanZ = mean(Z),
Date = as.Date(Date),
`Potato Starch` = cut(PS,breaks = c(0,.2,2,8), include.lowest = TRUE, labels =c("None", "Low", "High")),
REM = as.numeric(REM) * 24,
Deep = as.numeric(Deep) * 24)
t.test(experiment_days %>% dplyr::filter(PS>0 ) %>% pull(Z),
experiment_days %>% dplyr::filter(PS == 0) %>% pull(Z))
```

```
##
## Welch Two Sample t-test
##
## data: experiment_days %>% dplyr::filter(PS > 0) %>% pull(Z) and experiment_days %>% dplyr::filter(PS == 0) %>% pull(Z)
## t = 1.04, df = 61.824, p-value = 0.3024
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.1419544 0.4498331
## sample estimates:
## mean of x mean of y
## 6.482676 6.328737
```

`with(experiment_days,table(cut(PS,breaks = c(0,.2,2,8), include.lowest = TRUE, labels =c("None", "Low", "High")))) %>% knitr::kable(col.names = c("PS","Days"))`

PS | Days |
---|---|

None | 124 |

Low | 24 |

High | 12 |

Here’s a more detailed breakdown of the number of days involved:

`with(experiment_days, table(PS, cut(Z,4))) %>% knitr::kable()# %>% as.matrix() %>% prop.table() * 100`

(2.99,4.38] | (4.38,5.75] | (5.75,7.12] | (7.12,8.51] | |
---|---|---|---|---|

0 | 2 | 25 | 79 | 18 |

1 | 0 | 1 | 11 | 4 |

1.5 | 0 | 0 | 1 | 0 |

2 | 0 | 1 | 6 | 0 |

2.5 | 0 | 1 | 0 | 0 |

3 | 0 | 0 | 4 | 1 |

4 | 0 | 1 | 3 | 1 |

8 | 0 | 0 | 1 | 0 |

Let’s look at *Bifidobacterium* levels during this period

```
bifido <- mhg_taxa(subset_samples(sprague.genus.norm,Site == "gut" &
Date > as.Date("2014-5-15") &
Date < as.Date("2015-05-01")),
"Bifidobacterium") %>% mutate(Date = date, bifido = abundance/10000) %>%
select(Date,bifido)
# insert one new row (not in my current uBiome Explorer results for some reason, but for which I have JSON data)
bifido <- rbind(bifido,
c("2015-01-19",bifido = as.numeric(6.6516)))
bifido$bifido <- as.numeric(bifido$bifido)
j <- full_join(bifido, experiment_days) %>% as_tibble()
j[is.na(j$`Potato Starch`),]$`Potato Starch` <- "None"
ggplot(data = j ) +
geom_point(aes(x=as.Date(Date),y=Z, color = `Potato Starch`)) +
geom_smooth(inherit.aes = FALSE, data = j %>% dplyr::filter(`Potato Starch` %in% c("Low","None")),
aes(x=as.Date(Date),y=Z, color = `Potato Starch`),
method = "lm", se = FALSE) +
geom_bar( data = j, stat = "identity", aes(x = as.Date(Date), y = bifido),
color = "black") +
scale_y_continuous(sec.axis = sec_axis(~.,
name = "Bifidobacterium (%)")) +
scale_x_date(date_labels = "%b", date_breaks = "1 month", date_minor_breaks = "2 weeks") +
xlim(as.Date("2014-10-04"),as.Date("2015-04-01")) +
labs(title = "Total Sleep Per Night", x = "Date")
```

During the period when I was rigorously testing this, I only sampled myself three times, so the microbiome data isn’t as useful as for my other experiments. Still, note that my long-term typical levels of *Bifidobacterium* are around 1 % – about what you see in this chart for the February sample, which was taken after several weeks of no potato starch.

Of course, *Bifidobacterium* levels are not the main point of this experiment. We want to know if potato starch affected my sleep. So how does the t-test look when comparing days with or without potato starch?

```
t.test(experiment_days %>% dplyr::filter(`Potato Starch` == "None") %>% pull(Z),
experiment_days %>% dplyr::filter(`Potato Starch` != "None") %>% pull(Z))
```

```
##
## Welch Two Sample t-test
##
## data: experiment_days %>% dplyr::filter(`Potato Starch` == "None") %>% and experiment_days %>% dplyr::filter(`Potato Starch` != "None") %>% pull(Z) and pull(Z)
## t = -1.04, df = 61.824, p-value = 0.3024
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.4498331 0.1419544
## sample estimates:
## mean of x mean of y
## 6.328737 6.482676
```

Sadly, that p-value is much greater than 0.05, which tells me that, at least in this experiment, there’s not much reason to think the potato starch really helped one way or another.

## Does alcohol affect my sleep?

Incidentally, I have data for several other variables. It turns out that none of the other things I tried had much impact on sleep either. Here’s my sleep on nights after drinking alcohol, compared to nights when I had none:

```
t.test(experiment_days %>% dplyr::filter(Alcohol == 0 ) %>% pull(Z),
experiment_days %>% dplyr::filter(Alcohol !=0 & !is.na(Alcohol)) %>% pull(Z))
```

```
##
## Welch Two Sample t-test
##
## data: experiment_days %>% dplyr::filter(Alcohol == 0) %>% pull(Z) and experiment_days %>% dplyr::filter(Alcohol != 0 & !is.na(Alcohol)) %>% experiment_days %>% dplyr::filter(Alcohol == 0) %>% pull(Z) and pull(Z)
## t = -0.022903, df = 157.77, p-value = 0.9818
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.2613462 0.2553548
## sample estimates:
## mean of x mean of y
## 6.361838 6.364833
```

Here’s the total number of days I drank, and how much:

`with(experiment_days,table(cut(Alcohol,breaks = c(0,.2,1,8), include.lowest = TRUE, labels =c("None", "One", "More than One")))) %>% knitr::kable(col.names = c("Drinks","Days"))`

Drinks | Days |
---|---|

None | 78 |

One | 67 |

More than One | 15 |

In this case I can test my numbers against a much longer data set where I recorded alcohol consumption and sleep. Over the course of nearly two years of data, I found that my nighly sleep average is slightly higher when I’ve had no alcohol, but the difference isn’t statistically significant. I tried to find correlations between sleep and the *amount* of alcohol, comparing the nights when I’d had several drinks, but I found nothing. Alcohol seems not to affect the number of hours I sleep.

```
# grab all dates where I had some alcohol the day/night before
ad <- rikStats %>% dplyr::filter(Alcohol !=0 & !is.na(Alcohol)) %>% pull(Date) + lubridate::days(1)
# and dates following no-alcohol days
nad <- rikStats %>% dplyr::filter(Alcohol == 0 ) %>% pull(Date) + lubridate::days(1)
t.test(rikStats %>% dplyr::filter(Date %in% ad) %>% pull(Z),
rikStats %>% dplyr::filter(Date %in% nad) %>% pull(Z))
```

```
##
## Welch Two Sample t-test
##
## data: rikStats %>% dplyr::filter(Date %in% ad) %>% pull(Z) and rikStats %>% dplyr::filter(Date %in% nad) %>% pull(Z)
## t = -2.2871, df = 1107.7, p-value = 0.02238
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.22394033 -0.01712889
## sample estimates:
## mean of x mean of y
## 6.534975 6.655510
```

`with(rikStats,table(cut(Alcohol,breaks = c(0,.2,1,8), include.lowest = TRUE, labels =c("None", "One", "More than One")))) %>% knitr::kable(col.names = c("Drinks","Days"))`

Drinks | Days |
---|---|

None | 682 |

One | 440 |

More than One | 134 |

But maybe alcohol affects my REM or deep sleep? The answer appears to be no.

```
# grab all dates where I had some alcohol the day/night before
ad <- experiment_days %>% dplyr::filter(Alcohol !=0 & !is.na(Alcohol)) %>% pull(Date) #+ lubridate::days(1)
# and dates following no-alcohol days
nad <- experiment_days %>% dplyr::filter(Alcohol == 0 ) %>% pull(Date) #+ lubridate::days(1)
t.test(experiment_days %>% dplyr::filter(Date %in% ad & !is.na(REM)) %>% pull(REM),
experiment_days %>% dplyr::filter(Date %in% nad & !is.na(REM)) %>% pull(REM))
```

```
##
## Welch Two Sample t-test
##
## data: experiment_days %>% dplyr::filter(Date %in% ad & !is.na(REM)) %>% and experiment_days %>% dplyr::filter(Date %in% nad & !is.na(REM)) %>% pull(REM) and pull(REM)
## t = -0.48131, df = 118.25, p-value = 0.6312
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.1760789 0.1072209
## sample estimates:
## mean of x mean of y
## 1.811616 1.846045
```

```
t.test(experiment_days %>% dplyr::filter(Date %in% ad & !is.na(Deep)) %>% pull(Deep),
experiment_days %>% dplyr::filter(Date %in% nad & !is.na(Deep)) %>% pull(Deep))
```

```
##
## Welch Two Sample t-test
##
## data: experiment_days %>% dplyr::filter(Date %in% ad & !is.na(Deep)) %>% and experiment_days %>% dplyr::filter(Date %in% nad & !is.na(Deep)) %>% pull(Deep) and pull(Deep)
## t = -0.2844, df = 122.95, p-value = 0.7766
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.07853084 0.05879962
## sample estimates:
## mean of x mean of y
## 1.059343 1.069209
```

## Vitamin D supplementation and sleep

There *did* seem to be one effect worth noting. I seem to sleep better on days after I’ve taken a Vitamin D supplement:

```
# grab all dates where I had some Vitamin D the day/night before
ad <- experiment_days %>% dplyr::filter(`Vitamin D` > 0 & !is.na(`Vitamin D`)) %>% pull(Date)# + lubridate::days(1)
# and dates following no `Vitamin D` days
nad <- experiment_days %>% dplyr::filter(`Vitamin D` == 0 ) %>% pull(Date)# + lubridate::days(1)
t.test(experiment_days %>% dplyr::filter(Date %in% ad & !is.na(`Vitamin D`)) %>% pull(REM),
experiment_days %>% dplyr::filter(Date %in% nad & !is.na(`Vitamin D`)) %>% pull(REM))
```

```
##
## Welch Two Sample t-test
##
## data: experiment_days %>% dplyr::filter(Date %in% ad & !is.na(`Vitamin D`)) %>% and experiment_days %>% dplyr::filter(Date %in% nad & !is.na(`Vitamin D`)) %>% pull(REM) and pull(REM)
## t = 1.995, df = 71.758, p-value = 0.04984
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## 0.0001122644 0.3138701523
## sample estimates:
## mean of x mean of y
## 1.883128 1.726136
```

`with(experiment_days,table(`Vitamin D`)) %>% knitr::kable(col.names = c("3K IUs", "Days"))`

3K IUs | Days |
---|---|

0 | 75 |

1 | 53 |

2 | 32 |

But when I looked closer, the effect disappeared if I had more than 3000 IUs. Either Vitamin D helps sleep only in a narrow band of quantity, or it has no real effect. My money is on the “no effect”, though it would be interesting to do a more rigorous study.

Let’s look at my longer data set.

```
vd <- rikStats %>% dplyr::filter(`Vitamin D` !=0 & !is.na(`Vitamin D`)) %>% pull(Date) + lubridate::days(1)
nvd <- rikStats %>% dplyr::filter(`Vitamin D` == 0 & !is.na(`Vitamin D`)) %>% pull(Date) + lubridate::days(1)
with(rikStats, table(`Vitamin D`)) %>% knitr::kable(col.names = c("3K IUs", "Days"))
```

3K IUs | Days |
---|---|

0 | 435 |

0.5 | 3 |

1 | 147 |

2 | 182 |

3 | 9 |

4 | 5 |

5 | 16 |

6 | 2 |

13 | 1 |

```
t.test(rikStats %>% dplyr::filter(Date %in% vd) %>% pull(Z),
rikStats %>% dplyr::filter(Date %in% nvd) %>% pull(Z))
```

```
##
## Welch Two Sample t-test
##
## data: rikStats %>% dplyr::filter(Date %in% vd) %>% pull(Z) and rikStats %>% dplyr::filter(Date %in% nvd) %>% pull(Z)
## t = 0.92771, df = 710.22, p-value = 0.3539
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.06598338 0.18420195
## sample estimates:
## mean of x mean of y
## 6.581159 6.522050
```

Here, indeed, I slept slightly better on nights after taking Vitamin D (6.6 hrs vs 6.5) and this is with a lot of observations, but that p-value indicates that this is likely just a coincidence. Still, it’s intriguing that two separate data sets gave results in the same direction.

More generally, can I make a table of *all* possible P-values?

```
experiment_days %>% ungroup() %>% dplyr::filter(Date >= "2014-10-05" & Date <= "2015-03-18") %>% select(Z,REM, Deep) %>%
apply(2,function (x) c(mean(x, na.rm = TRUE),
median(x, na.rm = TRUE),
sd(x, na.rm = TRUE)) ) %>% knitr::kable(digits = 3)
```

Z | REM | Deep |
---|---|---|

6.377 | 1.856 | 1.086 |

6.500 | 1.883 | 1.067 |

0.859 | 0.372 | 0.193 |

```
# t.test(experiment_days %>% dplyr::filter(`Potato Starch` == "None") %>% pull(Z),
# experiment_days %>% dplyr::filter(`Potato Starch` != "None") %>% pull(Z))$p.value
#
# t.test(experiment_days %>% dplyr::filter(`Potato Starch` == "None") %>% pull(REM),
# experiment_days %>% dplyr::filter(`Potato Starch` != "None") %>% pull(REM))$p.value
#
# t.test(experiment_days %>% dplyr::filter(`Potato Starch` == "None") %>% pull(Deep),
# experiment_days %>% dplyr::filter(`Potato Starch` != "None") %>% pull(Deep))$p.value
# compare the null case with the non-null case. Returns the T-Test showing X=NULL, y= hypothesis
compare_treatment<- function (data=experiment_days,treatment=experiment_days$PS,wrt="Deep"){
x = t.test(data[[wrt]][treatment>0], data[[wrt]][treatment==0])
x$p.value
}
# P values while taking Potato Starch
# sapply(c("REM","Z","Deep"),function(x,y) {compare_treatment(treatment = experiment_days[[y]], wrt = x)},
# c("PS"))
#
# sapply(c("REM","Z","Deep"),function(x,y) {compare_treatment(treatment = experiment_days[[y]], wrt = x)},
# c("Alcohol"))
#
# sapply(c("REM","Z","Deep"),function(x,y) {compare_treatment(treatment = experiment_days[[y]], wrt = x)},
# c("Vitamin D"))
sapply(c("PS","Alcohol","Vitamin D"),
function (m) {sapply(c("REM","Z","Deep"),
function(x,y) {compare_treatment(treatment = experiment_days[[y]], wrt = x)},m)}) %>% knitr::kable(digits = 3)
```

PS | Alcohol | Vitamin D | |
---|---|---|---|

REM | 0.635 | 0.631 | 0.050 |

Z | 0.302 | 0.982 | 0.508 |

Deep | 0.785 | 0.777 | 0.064 |

Like I said, I’m still exploring my data and will write this up in a prettier format. For now, consider this a tutorial on how to study the data in R.