Worksheet 6 - Data Exploration and Plotting with ggplot2 - Answers
One of the most challenging parts of R is reading in your data. For spreadsheet applications, I find that comma deliminated data, .csv is the most useful format. Try out your import skills by downloading the mammal data into excel: https://github.com/bw4sz/2013-10-09-canberra/tree/master/data. Easiest way is to right click on “raw”“, and hit ‘save as’ and save it locally. This file gives the ages of extinct mammal taxa.
Data Exploration
- Read in the file
dat <- read.csv("C:/Users/Mike/Desktop/Dropbox/R_course/data/mammals.csv")
- How many records are in the data
nrow(dat)## [1] 2022
- Using a contingency table, how many records are there for the family Cervidae
table(dat$Family)##
## Perdectidae Achaenodontidae Adapidae
## 1 1 7
## Agriochoeridae Ailuridae Alagomyidae
## 8 1 1
## Allomyidae Alphadontidae Amphicyonidae
## 13 11 19
## Amphilemuridae Amynodontidae Anthracotheriidae
## 11 6 5
## Antiacodontidae Antilocapridae Apatemyidae
## 1 12 12
## Aplodontidae Apternodontidae Aquiladelphidae
## 10 3 1
## Arctocyonidae Arctostylopidae Barbourofelidae
## 35 1 5
## Barylambdidae Bovidae Brontotheriidae
## 3 2 18
## Camelidae Camelidae Canidae
## 45 1 96
## Carpolestidae Castoridae Cervidae
## 7 30 3
## Chalicotheriidae Cimolestidae Cimolodontidae
## 3 11 4
## Cimolomyidae Coryphodontidae Cricetidae
## 7 5 144
## Cylindrodontidae Cylindrodontidae Dichobunidae
## 17 2 32
## Elephantidae Entelodontidae Eomyidae
## 1 7 49
## Epoicotheriidae Equidae Erethizontidae
## 2 95 4
## Erinaceidae Escavadodontidae Esthonychidae
## 17 1 11
## Eucosmodontidae Eutypomyidae Felidae
## 5 9 27
## Florentiamyidae Geolabididae Geomyidae
## 10 12 40
## Glasbiidae Gomphotheriidae Gypsonictopidae
## 1 9 2
## Hapalodectidae Helaletidae Helaletidae
## 2 1 2
## Heliscomyidae Helohyidae Herpetotheriidae
## 5 3 9
## Heteromyidae Hyaenidae Hyaenodontidae
## 64 1 28
## Hydrochoeridae Hyopsodontidae Hypertragulidae
## 2 45 10
## Hyrachyidae Hyracodontidae Incertae sedis
## 3 11 44
## Ischyromyidae Isectolophidae Leporidae
## 57 3 30
## Leptictidae Leptochoeridae Leptomerycidae
## 8 3 4
## Mammutidae Megalonychidae Mephitidae
## 3 5 2
## Merycoidodontidae Merycoidodontidae Mesonychidae
## 35 1 10
## Miacidae Microcosmodontidae Micromomyidae
## 15 4 5
## Micropternodontidae Microsyopidae Mixodectidae
## 3 19 3
## Moschidae Muridae Musteliade
## 4 3 1
## Mustelidae Mustelidae Mylagaulidae
## 43 3 7
## Neoplagiaulacidae Nimravidae Not known
## 29 7 1
## Notharctidae Nothrotheriidae Nyctitheriidae
## 9 1 14
## Ochotonidae Omomyidae Oromerycidae
## 12 58 9
## Oxyaenidae Oxyclaenidae Pachynolophidae
## 15 4 1
## Palaechthonidae Palaeomerycidae Palaeoryctidae
## 9 8 5
## Palaeotheriidae Pampatheriidae Pantolambdidae
## 5 2 4
## Pantolestidae Pantolestidae Paromomyidae
## 15 3 8
## Paromomyidae Pediomyidae Peradectidae
## 1 4 1
## Perdectidae Periptychidae Phenacodontidae
## 6 28 19
## Picrodontidae Picromomyidae Plagiomenidae
## 1 1 8
## Plagiomenidae Plesiadapidae Plesiosoricidae
## 1 18 3
## Procyonidae Prodinoceratidae Proscalopidae
## 10 3 3
## Protoceratidae Protoptychidae Ptilodontidae
## 20 1 8
## Reithroparamyidae Rhinocerotidae Rhinocerotidae
## 5 21 1
## Saxonellidae Sciuravidae Sciuridae
## 1 12 69
## Simimyidae Simimyidae Soricidae
## 2 1 35
## Soricidae Spalacotheriidae Stagodontidae
## 1 4 1
## Stylinodontidae Taeniolabididae Talpidae
## 5 8 18
## Tapiridae Tayassuidae Titanoideidae
## 17 12 4
## Triconodontidae Triisodontidae Ursidae
## 1 4 11
## Viverravidae Zapodidae Zhelestidae
## 21 13 3There are three extinct Cervidae species
- How many familes are in the data? Hint: use length and table.
length(table(dat$Family))## [1] 159Subsetting
- Create a smaller dataframe for just extinct beavers (Castoridae)
Cast <- dat[dat$Family=="Castoridae",]
- When was the first beaver species present in the fossil record?
d <- which.min(Cast$First_appearance_mya)
paste(d,"Million Years Ago")## [1] "26 Million Years Ago"Plotting
- Make a boxplot of the range of species Last appearance dates by Order (for your interest add + theme(axis.text.x = element_text(angle = 90)) to turn the names sideways)
require(ggplot2)## Loading required package: ggplot2ggplot(dat,aes(x=Order_or_higher,y=Last_appearance_mya)) + geom_boxplot() + theme(axis.text.x = element_text(angle = 90))
- Using your beaver subset data create a scatterplot showing the relationship between mass and first appearance in the fossil record.
ggplot(Cast,aes(x=Mass_ln_g,y=First_appearance_mya)) + geom_point()
- Add a smoothing line to this data using geom_smooth. Explore the method=“” arguments, what is the default? How would you make the smoothing line linear? Use the help screen and google.
ggplot(Cast,aes(x=Mass_ln_g,y=First_appearance_mya)) + geom_point() + geom_smooth()## geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.
ggplot(Cast,aes(x=Mass_ln_g,y=First_appearance_mya)) + geom_point() + geom_smooth(method="lm")
10 BONUS. Create a plot showing the time in existance (hint:ymin=?,ymax=?) for each species of extinct beaver. Color by mass. Make it legible using themes, scale_color_continious, and labels.
ggplot(Cast,aes(ymin=First_appearance_mya,ymax=Last_appearance_mya,x=Species,col=Mass_ln_g)) + geom_linerange(size=3) + scale_y_reverse() + coord_flip() + scale_color_continuous(high="red",low="blue") + ylab("Mya") + xlab("Species")