dplyr Example #1
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Hadley Wickam released the dplyr package in January 2014. Since then I have been itching to give it a try as it has been suggested to speed up some data manipulations and, more important to me, provide a singular framework for a variety of common data manipulations. Recently, I gave it a try with some simple common manipulations for fisheries work. Below are my examples.
First, the dplyr package, plotrix (for the plot at the end), and the FSAdata package (for the data file) must be loaded.
library(dplyr) library(FSAdata) library(plotrix)
The RuffeSLRH92 data frame is then loaded.
data(RuffeSLRH92) str(RuffeSLRH92) ## 'data.frame': 738 obs. of 11 variables: ## $ fish.id : num 1992 1992 1992 1992 1992 ... ## $ month : int 4 4 4 4 4 4 4 4 4 4 ... ## $ day : int 23 23 23 23 23 23 23 23 23 23 ... ## $ year : int 1992 1992 1992 1992 1992 1992 1992 1992 1992 1992 ... ## $ species : int 1 2 3 4 5 6 7 8 9 10 ... ## $ location: int 160170 160170 160170 160170 160170 160170 160170 160170 160170 160170 ... ## $ length : int 90 128 112 68 56 58 111 111 115 65 ... ## $ weight : num 9.3 32.5 19 4.4 2.1 2.8 16.1 17.9 22.7 3.4 ... ## $ sex : Factor w/ 3 levels "female","male",..: 2 1 2 2 3 2 2 2 2 1 ... ## $ maturity: Factor w/ 11 levels "developing","immature",..: 7 7 7 7 10 7 7 7 7 2 ... ## $ age : int NA NA NA NA NA NA NA NA NA 1 ...
Select (columns) Example
Columns can be selected from a data.frame with select(), given the original data.frame as the first argument and the variables to select, or include, as further arguments. The following creates a data.frame without the fish.id, species, day and year variables (they are not very useful in this context and will make the output further below easier to read).
RuffeSLRH92 <- select(RuffeSLRH92,-fish.id,-species,-day,-year) head(RuffeSLRH92) ## month location length weight sex maturity age ## 1 4 160170 90 9.3 male ripe NA ## 2 4 160170 128 32.5 female ripe NA ## 3 4 160170 112 19.0 male ripe NA ## 4 4 160170 68 4.4 male ripe NA ## 5 4 160170 56 2.1 unknown unknown NA ## 6 4 160170 58 2.8 male ripe NA
The following creates a data.frame of just the length and weight variables.
ruffeLW <- select(RuffeSLRH92,length,weight) head(ruffeLW) ## length weight ## 1 90 9.3 ## 2 128 32.5 ## 3 112 19.0 ## 4 68 4.4 ## 5 56 2.1 ## 6 58 2.8
The dplyr package contains a variety of helpers for selecting. As one example, the following will select all variables that contains the letter “l”.
ruffeL <- select(RuffeSLRH92,contains("l"))
str(ruffeL)
## 'data.frame': 738 obs. of 2 variables:
## $ location: int 160170 160170 160170 160170 160170 160170 160170 160170 160170 160170 ...
## $ length : int 90 128 112 68 56 58 111 111 115 65 ...
Filtering Example
The filter() function can be used similarly to subset() to select a set of rows from an original data.frame according to some conditioning statement. As with subset(), filter() returns an object that maintains a list of the original levels whether those levels exist in the new data.frame or not. Use droplevels() to restrict the levels to only those that exist in the data.frame. The example below finds just the males from the original data.frame.
male <- filter(RuffeSLRH92,sex=="male") xtabs(~sex,data=male) ## sex ## female male unknown ## 0 201 0 male <- droplevels(male) xtabs(~sex,data=male) ## sex ## male ## 201
Multiple conditioning statements can be strung together as additional arguments to filter(). The example below finds males that are also ripe.
maleripe <- filter(RuffeSLRH92,sex=="male",maturity=="ripe") xtabs(~sex+maturity,data=maleripe) ## maturity ## sex developing immature mature nearly.ripe nearly.spent recovering ## female 0 0 0 0 0 0 ## male 0 0 0 0 0 0 ## unknown 0 0 0 0 0 0 ## maturity ## sex ripe running spent unknown yoy ## female 0 0 0 0 0 ## male 63 0 0 0 0 ## unknown 0 0 0 0 0
So far, it seems that an “or” needs to be completed as with subset(). For example, the following selects those fish that are male or are ripe.
maleripe2 <- filter(RuffeSLRH92,sex=="male" | maturity=="ripe") xtabs(~sex+maturity,data=maleripe2) ## maturity ## sex developing immature mature nearly.ripe nearly.spent recovering ## female 0 0 0 0 0 0 ## male 29 5 5 21 14 10 ## unknown 0 0 0 0 0 0 ## maturity ## sex ripe running spent unknown yoy ## female 107 0 0 0 0 ## male 63 17 34 3 0 ## unknown 0 0 0 0 0
Arrange Example
The arrange() function can be used to order individuals. The first argument is the data.frame and the following arguments are the variables to sort by. The following sorts, in ascending order, the male data.frame created above by length.
malea <- arrange(male,length) head(malea) ## month location length weight sex maturity age ## 1 5 330040 45 1.4 male unknown NA ## 2 10 190170 47 1.3 male immature NA ## 3 9 120070 56 2.3 male developing NA ## 4 4 370010 57 2.5 male ripe NA ## 5 4 160170 58 2.8 male ripe NA ## 6 5 340050 58 2.9 male mature NA tail(malea) ## month location length weight sex maturity age ## 196 6 18007 153 43.4 male nearly.spent NA ## 197 4 15011 154 48.7 male ripe NA ## 198 9 10060 155 41.0 male nearly.ripe NA ## 199 4 90060 161 54.0 male mature NA ## 200 10 60010 163 51.0 male mature NA ## 201 4 15011 183 82.8 male ripe NA
The following does the same but in descending order.
maled <- arrange(male,desc(length)) head(maled) ## month location length weight sex maturity age ## 1 4 15011 183 82.8 male ripe NA ## 2 10 60010 163 51.0 male mature NA ## 3 4 90060 161 54.0 male mature NA ## 4 9 10060 155 41.0 male nearly.ripe NA ## 5 4 15011 154 48.7 male ripe NA ## 6 6 18007 153 43.4 male nearly.spent NA tail(maled) ## month location length weight sex maturity age ## 196 4 160170 58 2.8 male ripe NA ## 197 5 340050 58 2.9 male mature NA ## 198 4 370010 57 2.5 male ripe NA ## 199 9 120070 56 2.3 male developing NA ## 200 10 190170 47 1.3 male immature NA ## 201 5 330040 45 1.4 male unknown NA
Multiple levels of ordering can be completed by including multiple variables as arguments to arrange(). The following sorts the data by ascending length and then ascending weight.
ruffe2 <- arrange(RuffeSLRH92,length,weight) head(ruffe2) ## month location length weight sex maturity age ## 1 7 360020 13 0.1 unknown yoy NA ## 2 8 170160 14 0.1 unknown yoy NA ## 3 7 160190 15 0.1 unknown yoy NA ## 4 7 320060 16 0.1 unknown yoy NA ## 5 7 170160 16 0.1 unknown yoy NA ## 6 7 300070 17 0.1 unknown yoy NA tail(ruffe2) ## month location length weight sex maturity age ## 733 6 50090 178 57.4 female ripe NA ## 734 6 60070 180 55.1 female running NA ## 735 7 80090 180 63.3 female nearly.spent NA ## 736 7 50030 180 72.6 female spent NA ## 737 4 15011 183 82.8 male ripe NA ## 738 7 320060 192 93.1 female nearly.spent NA
Add new variables (i.e., columns) Example
The mutate() function can be used to add new variables to a data.frame. It requires the original data.frame as the first argument and then arguments to create new variables as the remaining arguments. The example below adds the natural log of length and weight to the data.frame created above that contains just the length and weight variables.
ruffeLW <- mutate(ruffeLW,logL=log(length),logW=log(weight)) head(ruffeLW) ## length weight logL logW ## 1 90 9.3 4.500 2.2300 ## 2 128 32.5 4.852 3.4812 ## 3 112 19.0 4.718 2.9444 ## 4 68 4.4 4.220 1.4816 ## 5 56 2.1 4.025 0.7419 ## 6 58 2.8 4.060 1.0296
Aggregation and Summarization Example
The dplyr package also provides functions that allow for simple aggregation of results. The group_by() function first sets up how you want to group your data. In the code below, the byMon data.frame is going to create groups by the month variable. The summarize() function will then summarize a data.frame by the functions after the first argument. The package also provides n() to count the number of individuals. Thus, the example below will count the number of ruffe in the original data.frame by each month.
byMon <- group_by(RuffeSLRH92,month) ( sumMon <- summarize(byMon,count=n()) ) ## Source: local data frame [7 x 2] ## ## month count ## 1 4 62 ## 2 5 66 ## 3 6 154 ## 4 7 182 ## 5 8 79 ## 6 9 126 ## 7 10 69
The following counts the number of ruffe by each month and sex.
byMonSex <- group_by(RuffeSLRH92,month,sex) ( sumMonSex <- summarize(byMonSex,count=n())) ## Source: local data frame [20 x 3] ## Groups: month ## ## month sex count ## 1 4 female 30 ## 2 4 male 30 ## 3 4 unknown 2 ## 4 5 female 35 ## 5 5 male 31 ## 6 6 female 114 ## 7 6 male 38 ## 8 6 unknown 2 ## 9 7 female 96 ## 10 7 male 20 ## 11 7 unknown 66 ## 12 8 female 28 ## 13 8 male 18 ## 14 8 unknown 33 ## 15 9 female 68 ## 16 9 male 39 ## 17 9 unknown 19 ## 18 10 female 36 ## 19 10 male 25 ## 20 10 unknown 8
Multiple functions can be used to create multiple summaries at once. The following summarizes the number of fish and the mean and standard deviation of length by month.
( LenSumMon <- summarize(byMon,n=n(),mn=mean(length),sd=sd(length)) ) ## Source: local data frame [7 x 4] ## ## month n mn sd ## 1 4 62 111.37 35.42 ## 2 5 66 112.41 35.60 ## 3 6 154 113.62 31.61 ## 4 7 182 93.55 50.55 ## 5 8 79 82.22 40.80 ## 6 9 126 98.76 39.15 ## 7 10 69 98.72 39.16
Putting It All Together
Finally, all of the functions described above can be strung together with the %.% operator. This is best shown with an example. The following set of code will compute the proportion of all captured fish captured in each month by (1) grouping the data by month, (2) summarizing the number per month, (3) adding a new variable that is the proportion of the total catch in each month, and then (4) sorting the results such that the month with the largest catch is listed first.
fnl1 <- RuffeSLRH92 %.% group_by(month) %.% summarize(n=n()) %.% mutate(prop.catch=n/sum(n)) %.% arrange(desc(prop.catch)) fnl1 ## Source: local data frame [7 x 3] ## ## month n prop.catch ## 1 7 182 0.24661 ## 2 6 154 0.20867 ## 3 9 126 0.17073 ## 4 8 79 0.10705 ## 5 10 69 0.09350 ## 6 5 66 0.08943 ## 7 4 62 0.08401
The following example constructs a data.frame (that is then used to construct a plot) that contains the mean, sd, se, and approximate 95% confidence interval for length by month.
fnl2 <- RuffeSLRH92 %.% group_by(month) %.% summarize(n=n(),mn=mean(length),sd=sd(length)) %.% mutate(se=sd/sqrt(n),LCI=mn+qnorm(0.025)*se,UCI=mn+qnorm(0.975)*se) fnl2 ## Source: local data frame [7 x 7] ## ## month n mn sd se LCI UCI ## 1 4 62 111.37 35.42 4.498 102.55 120.19 ## 2 5 66 112.41 35.60 4.382 103.82 121.00 ## 3 6 154 113.62 31.61 2.547 108.63 118.62 ## 4 7 182 93.55 50.55 3.747 86.21 100.90 ## 5 8 79 82.22 40.80 4.590 73.22 91.21 ## 6 9 126 98.76 39.15 3.488 91.93 105.60 ## 7 10 69 98.72 39.16 4.714 89.48 107.96 with(fnl2,plotCI(month,mn,ui=UCI,li=LCI,pch=16,ylab="Length (mm)",xlab="Month"))
Final Thoughts
The dplyr package appears to have many more useful functions. This first foray suggests to me that it is going to be a useful “grammar” for simplifying data manipulations. I will post more as I explore it more. In the meantime, let me know what your experience with dplyr is.
Filed under: Fisheries Science, R Tagged: Data, Manipulation, R
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