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Your R-Journal should be a list of function or techniques that you've used to complete labs and in class assignments. It will be useful to include worked examples in code. I have inserted an entry for a simple function (mean()).
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mean(someData):This function computes the mean of a R object. It computes:
\[ \bar{x} = \frac{\sum_{i=1}^N x_i}{N} \]
The equation above is an example of latex math, a widely use, and convient way to write equations.
An example of using the function mean():
## Create a small dataset to demonstrate the use of mean()
someData <- c(1, 3, 5, 7, 9)
## Compute the mean of the object someData
mean(someData)
## [1] 5
# “<-” is called assignment operator # using “<-” assigns a value to a variable
CO2 <- read.csv("C:/Users/Hallie/Dropbox/GEOG 5023 - Spring 2013/Data/CO2.csv",
sep = ",", header = T)
## Warning: cannot open file 'C:/Users/Hallie/Dropbox/GEOG 5023 - Spring
## 2013/Data/CO2.csv': No such file or directory
## Error: cannot open the connection
names(CO2)
## [1] "Plant" "Type" "Treatment" "conc" "uptake"
CO2$conc # select a column
## [1] 95 175 250 350 500 675 1000 95 175 250 350 500 675 1000
## [15] 95 175 250 350 500 675 1000 95 175 250 350 500 675 1000
## [29] 95 175 250 350 500 675 1000 95 175 250 350 500 675 1000
## [43] 95 175 250 350 500 675 1000 95 175 250 350 500 675 1000
## [57] 95 175 250 350 500 675 1000 95 175 250 350 500 675 1000
## [71] 95 175 250 350 500 675 1000 95 175 250 350 500 675 1000
CO2$Type
## [1] Quebec Quebec Quebec Quebec Quebec
## [6] Quebec Quebec Quebec Quebec Quebec
## [11] Quebec Quebec Quebec Quebec Quebec
## [16] Quebec Quebec Quebec Quebec Quebec
## [21] Quebec Quebec Quebec Quebec Quebec
## [26] Quebec Quebec Quebec Quebec Quebec
## [31] Quebec Quebec Quebec Quebec Quebec
## [36] Quebec Quebec Quebec Quebec Quebec
## [41] Quebec Quebec Mississippi Mississippi Mississippi
## [46] Mississippi Mississippi Mississippi Mississippi Mississippi
## [51] Mississippi Mississippi Mississippi Mississippi Mississippi
## [56] Mississippi Mississippi Mississippi Mississippi Mississippi
## [61] Mississippi Mississippi Mississippi Mississippi Mississippi
## [66] Mississippi Mississippi Mississippi Mississippi Mississippi
## [71] Mississippi Mississippi Mississippi Mississippi Mississippi
## [76] Mississippi Mississippi Mississippi Mississippi Mississippi
## [81] Mississippi Mississippi Mississippi Mississippi
## Levels: Quebec Mississippi
CO2[CO2$Type == "Quebec", ]
## Plant Type Treatment conc uptake
## 1 Qn1 Quebec nonchilled 95 16.0
## 2 Qn1 Quebec nonchilled 175 30.4
## 3 Qn1 Quebec nonchilled 250 34.8
## 4 Qn1 Quebec nonchilled 350 37.2
## 5 Qn1 Quebec nonchilled 500 35.3
## 6 Qn1 Quebec nonchilled 675 39.2
## 7 Qn1 Quebec nonchilled 1000 39.7
## 8 Qn2 Quebec nonchilled 95 13.6
## 9 Qn2 Quebec nonchilled 175 27.3
## 10 Qn2 Quebec nonchilled 250 37.1
## 11 Qn2 Quebec nonchilled 350 41.8
## 12 Qn2 Quebec nonchilled 500 40.6
## 13 Qn2 Quebec nonchilled 675 41.4
## 14 Qn2 Quebec nonchilled 1000 44.3
## 15 Qn3 Quebec nonchilled 95 16.2
## 16 Qn3 Quebec nonchilled 175 32.4
## 17 Qn3 Quebec nonchilled 250 40.3
## 18 Qn3 Quebec nonchilled 350 42.1
## 19 Qn3 Quebec nonchilled 500 42.9
## 20 Qn3 Quebec nonchilled 675 43.9
## 21 Qn3 Quebec nonchilled 1000 45.5
## 22 Qc1 Quebec chilled 95 14.2
## 23 Qc1 Quebec chilled 175 24.1
## 24 Qc1 Quebec chilled 250 30.3
## 25 Qc1 Quebec chilled 350 34.6
## 26 Qc1 Quebec chilled 500 32.5
## 27 Qc1 Quebec chilled 675 35.4
## 28 Qc1 Quebec chilled 1000 38.7
## 29 Qc2 Quebec chilled 95 9.3
## 30 Qc2 Quebec chilled 175 27.3
## 31 Qc2 Quebec chilled 250 35.0
## 32 Qc2 Quebec chilled 350 38.8
## 33 Qc2 Quebec chilled 500 38.6
## 34 Qc2 Quebec chilled 675 37.5
## 35 Qc2 Quebec chilled 1000 42.4
## 36 Qc3 Quebec chilled 95 15.1
## 37 Qc3 Quebec chilled 175 21.0
## 38 Qc3 Quebec chilled 250 38.1
## 39 Qc3 Quebec chilled 350 34.0
## 40 Qc3 Quebec chilled 500 38.9
## 41 Qc3 Quebec chilled 675 39.6
## 42 Qc3 Quebec chilled 1000 41.4
CO2.Q <- CO2[CO2$Type == "Quebec", ] # creates new dataset
CO2$concat[CO2$conc <= 200] <- 1 # can create a new variable by assignment
CO2$concat[CO2$conc > 200 & CO2$conc <= 400] <- 2 # can create a new variable by assignment
CO2$new <- CO2$conc * CO2$uptake # can create a new variable by arithmetic
CO2$new <- CO2$uptake/1000 # can create a new variable by arithmetic
hist(CO2$uptake, col = "blue", breaks = seq(0, 60, by = 2), xlab = "Rate (umol/m^2 sec)",
main = "CO2 Uptake Rates")
# parameter 'breaks' allows you to bin data -- number of categories to
# plot, breakpoints for each category # xlab: x axis label # ylab: y axis
# label # col: color
boxplot(CO2$uptake ~ CO2$Type, main = "CO2 Uptake Rates", ylab = "Rate (umol/m^2 sec)",
col = rainbow(2)) # can also plot by categories
plot(CO2$conc, CO2$uptake, xlab = "CO2 Concentration", ylab = "CO2 Uptake Rate",
pch = 2, col = "red")
# Other Parameters: # ylim - range for y axis # xlim - range for x axis # main - provides title
# good for time series data # consider flow gauge data for 2 Thames tributaries
thames2 <- read.csv("C:/Users/Hallie/Dropbox/GEOG 5023 - Spring 2013/Data/thames.csv",
sep = ",", header = T)
## Warning: cannot open file 'C:/Users/Hallie/Dropbox/GEOG 5023 - Spring
## 2013/Data/thames.csv': No such file or directory
## Error: cannot open the connection
names(thames2)
## Error: object 'thames2' not found
t1 <- 1:nrow(thames2)
## Error: object 'thames2' not found
plot(t1, thames2$Feildes, xlab = "Time", ylab = "Flow Rate", main = "Flow Rate for Feildes") #scatter plot
## Error: object 't1' not found
plot(t1, thames2$Feildes, xlab = "Time", ylab = "Flow Rate", main = "Flow Rate for Feildes",
type = "l", ylim = c(-1, 100)) # line plot of scatter plot basically
## Error: object 't1' not found
lines(t1, thames2$Redbridge, lty = 2, col = "red") # add another line to the graph
## Error: object 't1' not found
legend(5, 8, c("Feildes", "Redbridge"), lty = c(1, 2), col = c("black", "red")) # adding a legend
## Error: plot.new has not been called yet
# legend(x, y, names, line types, colors) # x: x coordinate # y: y coordinate # names: names of series in column format # line type: corresponding line types # colors: corresponding colors
# More than one graphic on a panel # Can partition garphics panel to yield a framework in which to panel our plots # example code: par(mfrow = c( nrow, ncol)) # nrow is number of rows ## ncol is number of columns
par(mfrow = c(2, 2))
hist(CO2$uptake, col = "blue", breaks = seq(0, 50, by = 5), xlab = "Rate (umol/m^2 sec)",
main = "CO2 Uptake Rates")
plot(CO2$conc, CO2$uptake, xlab = "CO2 Concentration", ylab = "CO2 Uptake Rate",
pch = 2, col = "red")
boxplot(CO2$uptake ~ CO2$Type, main = "CO2 Uptake Rates", ylab = "Rate (umol/m^2 sec)",
col = rainbow(2))
plot(t1, thames2$Feildes, xlab = "Time", ylab = "Flow Rate", main = "Flow Rate for Thames Tributaries",
type = "l")
## Error: object 't1' not found
lines(t1, thames2$Redbridge, lty = 2, col = "red")
## Error: object 't1' not found
legend(5, 8, c("Feildes", "Redbridge"), lty = c(1, 2), col = c("black", "red"))
