Homework 5
Key
2026-03-09
Instructions
Answer the following questions and/or complete the exercises in
RMarkdown. Please embed all of your code and push the final work to your
repository. Your report should be organized, clean, and run free from
errors. Remember, you must remove the # for any included
code chunks to run. Any plots must have appropriate titles and
aesthetics.
Load the tidyverse
library("tidyverse")## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.2.0 ✔ readr 2.2.0
## ✔ forcats 1.0.1 ✔ stringr 1.6.0
## ✔ ggplot2 4.0.2 ✔ tibble 3.3.1
## ✔ lubridate 1.9.5 ✔ tidyr 1.3.2
## ✔ purrr 1.2.1
## ── 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 errorsoptions(scipen=999) #turn off scientific notationData
Database of vertebrate home range sizes. Reference:
Tamburello N, Cote IM, Dulvy NK (2015) Energy and the scaling of animal
space use. The American Naturalist 186(2):196-211. http://dx.doi.org/10.1086/682070.
Data: http://datadryad.org/resource/doi:10.5061/dryad.q5j65/1
1. Load the data into a new object called
homerange.
homerange <- read_csv("data/Tamburelloetal_HomeRangeDatabase.csv")## Rows: 569 Columns: 24
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (16): taxon, common.name, class, order, family, genus, species, primarym...
## dbl (8): mean.mass.g, log10.mass, mean.hra.m2, log10.hra, dimension, preyma...
##
## 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.2. What is the structure of the homerange data?
Does it have any NA’s? Do a quick exploratory analysis of your choice
below.
glimpse(homerange)## Rows: 569
## Columns: 24
## $ taxon <chr> "lake fishes", "river fishes", "river fishe…
## $ common.name <chr> "american eel", "blacktail redhorse", "cent…
## $ class <chr> "actinopterygii", "actinopterygii", "actino…
## $ order <chr> "anguilliformes", "cypriniformes", "cyprini…
## $ family <chr> "anguillidae", "catostomidae", "cyprinidae"…
## $ genus <chr> "anguilla", "moxostoma", "campostoma", "cli…
## $ species <chr> "rostrata", "poecilura", "anomalum", "fundu…
## $ primarymethod <chr> "telemetry", "mark-recapture", "mark-recapt…
## $ N <chr> "16", NA, "20", "26", "17", "5", "2", "2", …
## $ mean.mass.g <dbl> 887.00, 562.00, 34.00, 4.00, 4.00, 3525.00,…
## $ log10.mass <dbl> 2.9479236, 2.7497363, 1.5314789, 0.6020600,…
## $ alternative.mass.reference <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,…
## $ mean.hra.m2 <dbl> 282750.00, 282.10, 116.11, 125.50, 87.10, 3…
## $ log10.hra <dbl> 5.4514026, 2.4504031, 2.0648696, 2.0986437,…
## $ hra.reference <chr> "Minns, C. K. 1995. Allometry of home range…
## $ realm <chr> "aquatic", "aquatic", "aquatic", "aquatic",…
## $ thermoregulation <chr> "ectotherm", "ectotherm", "ectotherm", "ect…
## $ locomotion <chr> "swimming", "swimming", "swimming", "swimmi…
## $ trophic.guild <chr> "carnivore", "carnivore", "carnivore", "car…
## $ dimension <dbl> 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3…
## $ preymass <dbl> NA, NA, NA, NA, NA, NA, 1.39, NA, NA, NA, N…
## $ log10.preymass <dbl> NA, NA, NA, NA, NA, NA, 0.1430148, NA, NA, …
## $ PPMR <dbl> NA, NA, NA, NA, NA, NA, 530, NA, NA, NA, NA…
## $ prey.size.reference <chr> NA, NA, NA, NA, NA, NA, "Brose U, et al. 20…names(homerange)## [1] "taxon" "common.name"
## [3] "class" "order"
## [5] "family" "genus"
## [7] "species" "primarymethod"
## [9] "N" "mean.mass.g"
## [11] "log10.mass" "alternative.mass.reference"
## [13] "mean.hra.m2" "log10.hra"
## [15] "hra.reference" "realm"
## [17] "thermoregulation" "locomotion"
## [19] "trophic.guild" "dimension"
## [21] "preymass" "log10.preymass"
## [23] "PPMR" "prey.size.reference"3. Which animal groups are represented in the data? Make a plot that shows the number in each class.
homerange %>%
ggplot(mapping=aes(x=class))+
geom_bar(mapping=aes(fill=class))+
labs(title="Number of Species by Class",
x="Class",
y="Number of Species")
4. Are there more carnivores or herbivores represented in the data? Make a plot that shows the number in each trophic guild.
homerange %>%
ggplot(mapping=aes(x=trophic.guild))+
geom_bar(mapping=aes(fill=trophic.guild))+
labs(title="Number of Species by Trophic Guild",
x="Trophic Guild",
y="Number of Species")
5. Which herbivorous mammals have homeranges greater than 1,000,000 m²? Show only the common name, order, mean homerange size, and mean body mass. Arrange the data in descending order by homerange size and show only the top 10 species.
homerange %>%
filter(class == "mammalia",
trophic.guild == "herbivore",
mean.hra.m2 > 1000000) %>%
select(common.name, order, mean.hra.m2, mean.mass.g) %>%
arrange(desc(mean.hra.m2)) %>%
slice_head(n = 10)## # A tibble: 10 × 4
## common.name order mean.hra.m2 mean.mass.g
## <chr> <chr> <dbl> <dbl>
## 1 reindeer artiodactyla 3550830977 102059.
## 2 African bush elephant proboscidea 1753759352 4000000.
## 3 greater kudu artiodactyla 1070039969 197315.
## 4 American bison artiodactyla 265778594. 629999.
## 5 giraffe artiodactyla 136536888 1339985.
## 6 Asian elephant proboscidea 109999320. 4000000.
## 7 moose artiodactyla 93825308. 307227.
## 8 red deer artiodactyla 74865202. 234758.
## 9 goat artiodactyla 64528267. 51000.
## 10 common eland artiodactyla 52399845. 635038.6. Which two species have the largest and smallest homerange sizes?
homerange %>%
select(common.name, mean.hra.m2) %>%
arrange(desc(mean.hra.m2)) %>%
slice_head()## # A tibble: 1 × 2
## common.name mean.hra.m2
## <chr> <dbl>
## 1 reindeer 3550830977homerange %>%
select(common.name, mean.hra.m2) %>%
arrange(desc(mean.hra.m2)) %>%
slice_tail()## # A tibble: 1 × 2
## common.name mean.hra.m2
## <chr> <dbl>
## 1 rusty goby 0.037. Which carnivorous mammals have the largest homeranges?
homerange %>%
select(common.name, class, trophic.guild, mean.hra.m2) %>%
filter(class=="mammalia", trophic.guild=="carnivore") %>%
arrange(desc(mean.hra.m2))## # A tibble: 80 × 4
## common.name class trophic.guild mean.hra.m2
## <chr> <chr> <chr> <dbl>
## 1 cheetah mammalia carnivore 815060788.
## 2 leopard mammalia carnivore 504940261.
## 3 caracal mammalia carnivore 376634414
## 4 wolverine mammalia carnivore 361917847.
## 5 cougar mammalia carnivore 312003884.
## 6 Eurasian lynx mammalia carnivore 181042276.
## 7 Canada lynx mammalia carnivore 82748475.
## 8 jaguar mammalia carnivore 82735139.
## 9 jaguarundi mammalia carnivore 67079528.
## 10 tiger mammalia carnivore 53583367.
## # ℹ 70 more rows8. Is there a relationship between body mass and homerange size? Make a scatterplot to show this relationship. Be sure to include appropriate labels and a title.
homerange %>%
ggplot(mapping=aes(x=log10.mass, y=log10.hra))+
geom_point(mapping=aes(color=class))+
geom_smooth(method="lm", se=FALSE)+
labs(title="Relationship between Body Mass and Homerange Size",
x="Body Mass (g)",
y="Mean Homerange Size (m^2)")## `geom_smooth()` using formula = 'y ~ x'
9. Use filter to extract the data for only birds and mammals. Then make a plot that compares the homerange sizes of these two groups. Be sure to include appropriate labels and a title.
homerange %>%
filter(class == "aves" | class == "mammalia") %>%
ggplot(aes(x = class, y = log10.hra)) +
geom_boxplot(mapping=aes(fill=class)) +
labs(title = "Home Range Size for Birds vs Mammals",
x = "Class",
y = "log10(Home Range Area)")
10. Do one additional exploratory analysis of your choice.
Before writing the code, write the question you are trying to answer.
The question should be biologically meaningful and appropriate for the
data. It must include at least one filter(),
select(), and arrange().
Knit and Upload
Please knit your work as an .html file and upload to Canvas. Homework is due before the start of the next lab. No late work is accepted. Make sure to use the formatting conventions of RMarkdown to make your report neat and clean!