Module 8 code and images
Code and results thereof for Module 08, which uses data from a pharmacological study.
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(ggplot2)
theoph = read.csv("theoph.csv")
str(theoph)
theoph$Subject = factor(theoph$Subject)Using select() make a new data frame containing only the subject ID, the Time and conc variables:
theoph_1 = select(theoph, Subject, Time, conc)
head(theoph_1)## Subject Time conc
## 1 1 0.00 0.74
## 2 1 0.25 2.84
## 3 1 0.57 6.57
## 4 1 1.12 10.50
## 5 1 2.02 9.66
## 6 1 3.82 8.58Using a combination of select() and distinct() make a new data frame containing a single row for each subject with the subject ID, their weight and the dose:
subject_info <- theoph %>%
select(Subject, Wt, Dose) %>%
distinct()
head(subject_info)## Subject Wt Dose
## 1 1 79.6 4.02
## 2 2 72.4 4.40
## 3 3 70.5 4.53
## 4 4 72.7 4.40
## 5 5 54.6 5.86
## 6 6 80.0 4.00Using filter() make a new data frame containing only the first subject:
filter(theoph, Subject == "1")## Subject Wt Dose Time conc
## 1 1 79.6 4.02 0.00 0.74
## 2 1 79.6 4.02 0.25 2.84
## 3 1 79.6 4.02 0.57 6.57
## 4 1 79.6 4.02 1.12 10.50
## 5 1 79.6 4.02 2.02 9.66
## 6 1 79.6 4.02 3.82 8.58
## 7 1 79.6 4.02 5.10 8.36
## 8 1 79.6 4.02 7.03 7.47
## 9 1 79.6 4.02 9.05 6.89
## 10 1 79.6 4.02 12.12 5.94
## 11 1 79.6 4.02 24.37 3.28Using filter() make a new data frame containing only the first four subjects:
theoph_1to4 <- theoph %>%
filter(Subject %in% c("1", "2", "3", "4"))
theoph_1to4## Subject Wt Dose Time conc
## 1 1 79.6 4.02 0.00 0.74
## 2 1 79.6 4.02 0.25 2.84
## 3 1 79.6 4.02 0.57 6.57
## 4 1 79.6 4.02 1.12 10.50
## 5 1 79.6 4.02 2.02 9.66
## 6 1 79.6 4.02 3.82 8.58
## 7 1 79.6 4.02 5.10 8.36
## 8 1 79.6 4.02 7.03 7.47
## 9 1 79.6 4.02 9.05 6.89
## 10 1 79.6 4.02 12.12 5.94
## 11 1 79.6 4.02 24.37 3.28
## 12 2 72.4 4.40 0.00 0.00
## 13 2 72.4 4.40 0.27 1.72
## 14 2 72.4 4.40 0.52 7.91
## 15 2 72.4 4.40 1.00 8.31
## 16 2 72.4 4.40 1.92 8.33
## 17 2 72.4 4.40 3.50 6.85
## 18 2 72.4 4.40 5.02 6.08
## 19 2 72.4 4.40 7.03 5.40
## 20 2 72.4 4.40 9.00 4.55
## 21 2 72.4 4.40 12.00 3.01
## 22 2 72.4 4.40 24.30 0.90
## 23 3 70.5 4.53 0.00 0.00
## 24 3 70.5 4.53 0.27 4.40
## 25 3 70.5 4.53 0.58 6.90
## 26 3 70.5 4.53 1.02 8.20
## 27 3 70.5 4.53 2.02 7.80
## 28 3 70.5 4.53 3.62 7.50
## 29 3 70.5 4.53 5.08 6.20
## 30 3 70.5 4.53 7.07 5.30
## 31 3 70.5 4.53 9.00 4.90
## 32 3 70.5 4.53 12.15 3.70
## 33 3 70.5 4.53 24.17 1.05
## 34 4 72.7 4.40 0.00 0.00
## 35 4 72.7 4.40 0.35 1.89
## 36 4 72.7 4.40 0.60 4.60
## 37 4 72.7 4.40 1.07 8.60
## 38 4 72.7 4.40 2.13 8.38
## 39 4 72.7 4.40 3.50 7.54
## 40 4 72.7 4.40 5.02 6.88
## 41 4 72.7 4.40 7.02 5.78
## 42 4 72.7 4.40 9.02 5.33
## 43 4 72.7 4.40 11.98 4.19
## 44 4 72.7 4.40 24.65 1.15Using group_by(), calculate the average concentration per subject (across all times):
theoph |>
group_by(Subject) |>
summarize(avgconc = mean(conc))## # A tibble: 12 × 2
## Subject avgconc
## <fct> <dbl>
## 1 1 6.44
## 2 2 4.82
## 3 3 5.09
## 4 4 4.94
## 5 5 5.78
## 6 6 3.53
## 7 7 3.91
## 8 8 4.27
## 9 9 4.89
## 10 10 5.93
## 11 11 4.51
## 12 12 5.41Using filter() make a new data frame containing only the first subject and pipe this to ggplot() to make a line plot with Time on the x-axis and conc on the y-axis:
theoph |>
filter(Subject == "1") |>
ggplot(aes(x = Time, y = conc)) +
geom_line() +
ggtitle("Concentration vs. Time for Subject 1")
Using select() to extract just the Subject, Time and conc variables and pipe this to ggplot() to make a line plot with Time on the x-axis, conc on the y-axis and the lines colored by subject:
theoph$Subject = factor(theoph$Subject)
theoph |>
select(Subject, Time, conc) |>
ggplot(aes(x = Time, y = conc, col= theoph$Subject, group = Subject)) +
geom_line() +
ggtitle("Concentration vs. Time, All Subjects")
Using select() to extract just the Subject, Time and conc variables and pipe this to ggplot to make a line plot with Time on the x-axis, conc on the y-axis and faceted by the subject ID:
theoph$Subject = factor(theoph$Subject)
theoph |>
select(Subject, Time, conc) |>
ggplot(aes(x = Time, y = conc)) +
geom_line() +
geom_line(color = "blueviolet") +
facet_wrap(~ Subject) +
ggtitle("Concentration vs. Time Faceted by Subject ID")
That is all, thank you.