Broken line questions
Hi,
You may also replace the NAs using ?na.approx() from library(zoo).
library(zoo)
?mydata2<- mydata
?mydata2$MW01<-na.approx(mydata2$MW01)
?plot(MW01~Year,data=mydata2,col=ifelse(D_MW01,"black","red"),ylab="END (mg/L)",pch=ifelse(D_MW01,19,24),cex=1)
with(mydata2,lines(Year,MW01,lty=c(1),col="black"))
plx<-predict(loess(MW01 ~ Year, data=mydata2), se=T)
lines(mydata2$Year,plx$fit+2*plx$s, lty=2)
lines(mydata2$Year,plx$fit-2*plx$s, lty=2)
y.loess <- loess(y ~ x, span=0.8, data.frame(x=mydata2$Year,y=mydata2$MW01))
y.predict <- predict(y.loess, data.frame(x=mydata2$Year))
lines(mydata2$Year,y.predict, lty=2, lwd=2)
legend ("topleft",
c("Smoothing Curve","Detect","Non-Detect"),
col = c(1,1,1),
cex = 1,
text.col = "black",
lty = c(2,-1,-1),
lwd = c(2,-1,-1),
pch = c(-1,19,24),
merge = TRUE, bg = 'gray90')
A.K.
----- Original Message -----
From: arun <smartpink111 at yahoo.com>
To: David Doyle <kydaviddoyle at gmail.com>
Cc: R help <r-help at r-project.org>
Sent: Tuesday, May 14, 2013 11:52 PM
Subject: Re: [R] Broken line questions
Hi,
It is because of the unequal lengths of x and y.
I was able to plot without the errors.? But, not sure if this is what you wanted.
mydata <- read.table("TestData.csv", header=TRUE, sep="\t")
reg1<-lm(MW01~Year,data=mydata)
?plot(MW01~Year,data=mydata[!is.na(mydata$MW01),],col=ifelse(D_MW01,"black","red"),ylab="END (mg/L)",pch=ifelse(D_MW01,19,24),cex=1)
with(mydata[!is.na(mydata$MW01),],lines(Year,MW01,lty=c(1),col="black"))
plx1<-predict(loess(MW01 ~ Year, data=mydata[!is.na(mydata$MW01),]), se=T)
#rough & ready CI by adding and subtracting 2 times the standard error to the mean
lines(mydata[!is.na(mydata$MW01),"Year"],plx1$fit+2*plx1$s, lty=2)
lines(mydata[!is.na(mydata$MW01),"Year"],plx1$fit-2*plx1$s, lty=2)
mydata1<-mydata[!is.na(mydata$MW01),2:3]
y.loess <- loess(y ~ x, span=0.8, data.frame(x=mydata1$Year,y=mydata1$MW01))
# Compute loess smoothed values for all points along the curve
y.predict <- predict(y.loess, data.frame(x=mydata1$Year))
# Plots the curve.
lines(mydata1$Year,y.predict, lty=2, lwd=2)
BTW,? "Non-detect" in the legend is not clear.
A.K.
#Add line between the points
lines(mydata1$Year,mydata1$MW01)
From: David Doyle <kydaviddoyle at gmail.com>
To: arun <smartpink111 at yahoo.com>
Sent: Tuesday, May 14, 2013 11:10 PM
Subject: Re: [R] Broken line questions
To: arun <smartpink111 at yahoo.com>
Sent: Tuesday, May 14, 2013 11:10 PM
Subject: Re: [R] Broken line questions
Hi, I'm trying to do something very?similar?to the graph before and I got the broken line problem fixed with your example. On this one I'm trying to add 2 times the standard error (approxmating a 10% confidence) onto the LOESS curve. The data is at https://docs.google.com/file/d/0B0CqEkyKWiq9SjFwemRhZnV4aTA/edit?usp=sharing (sorry I don't have access to my FTP right now.) When I use the code below, I get? "Error in xy.coords(x, y) : 'x' and 'y' lengths differ" I assume this is because there are blanks in the data. ? Any?suggestions??? The code I'm ?using is: #set the dir to where you data is setwd("c:/R") #Load your data. ?The data is in a spreadsheet named nd-spreadsheet and we are going to call it data in R mydata <- read.table("TestData.csv", header=TRUE, sep=",",) attach(mydata) reg1 <- lm(MW01~Year) par(cex=1) #Plots the data but makes nondetects a different color and type based on column D_MW01 being a 0 for ND and 1 for detect. plot(MW01~Year,data=mydata[!is.na(mydata$MW01),], col=ifelse (D_MW01, "black", "red"),ylab = "EMD (mg/L)", pch=ifelse(D_MW01, 19, 24), cex = 1) with(mydata[!is.na(mydata$MW01),],lines(Year,MW01,lty=c(1),col="black")) plx<-predict(loess(MW01 ~ Year, data=mydata), se=T) #rough & ready CI by adding and subtracting 2 times the standard error to the mean lines(mydata$Year,plx$fit+2*plx$s, lty=2)? lines(mydata$Year,plx$fit-2*plx$s, lty=2) # Apply loess smoothing using the default span value of 0.8. ?You can change the curve by changing the span value. y.loess <- loess(y ~ x, span=0.8, data.frame(x=Year, y=MW01)) # Compute loess smoothed values for all points along the curve y.predict <- predict(y.loess, data.frame(x=Year)) # Plots the curve. lines(Year,y.predict, lty=2, lwd=2) #Add line between the points lines(Year,MW01) #Add Legend to MW01. ?You can change the size of the box by changing cex = 0.75 ?Large # makes it larger. legend ("topleft",? c("Smoothing Curve","Detect","Non-Detect"),? col = c(1,1,1), cex = 1,? text.col = "black",? lty = c(2,-1,-1),? lwd = c(2,-1,-1), pch = c(-1,19,24),? merge = TRUE, bg = 'gray90') #Add title title(main="MW01") # Done Thanks again David On Sun, May 12, 2013 at 10:11 AM, arun <smartpink111 at yahoo.com> wrote: No problem, >Regards, >Arun > > > > > > > >________________________________ >From: David Doyle <kydaviddoyle at gmail.com> >To: arun <smartpink111 at yahoo.com> >Sent: Sunday, May 12, 2013 8:03 AM >Subject: Re: [R] Broken line questions > > > > >Thanks! > >That took care of it. > > > >On Sat, May 11, 2013 at 10:01 PM, arun <smartpink111 at yahoo.com> wrote: > >Hi, >>May be this helps: >>plot(dataset1~Date,data=mydata[!is.na(mydata$dataset1),],ylim=range(5.7,8),pch=10,cex=0.8,col="black",xlab="Date",ylab="pH") >>?with(mydata[!is.na(mydata$dataset2),],points(Date,dataset2,col="blue",pch=2,cex=0.8)) >>?with(mydata[!is.na(mydata$dataset3),],points(Date,dataset3,col="red",pch=2,cex=0.8)) >>?with(mydata[!is.na(mydata$dataset1),],lines(Date,dataset1,lty=c(1),col="black")) >>?with(mydata[!is.na(mydata$dataset2),],lines(Date,dataset2,lty=c(1),col="blue")) >>?with(mydata[!is.na(mydata$dataset3),],lines(Date,dataset3,lty=c(1),col="red")) >> >> >> >>A.K. >> >> >> >> >>----- Original Message ----- >>From: David Doyle <kydaviddoyle at gmail.com> >>To: r-help at r-project.org >>Cc: >>Sent: Saturday, May 11, 2013 10:22 PM >>Subject: [R] Broken line questions >> >>Hello Everyone, >> >>I have some data that like most real world data isn't complete.? I'm trying >>to plot all of it together with lines connecting the data points.? Because >>I have breaks in the data I have breaks in the lines. >> >>Is there a way that the lines will connect all the markers???? ?Below is >>the code. >> >>Thanks in advance. >>David >> >>#Load your data.? The data is in a spreadsheet named KW-spreadsheet and we >>are going to call it "data" in R >>mydata <- read.csv("http://doylesdartden.com/example-smoothing-data.csv";;, >>sep=",") >>attach(mydata) >> >>#Plots the Y and X axis >>plot( Date, dataset1, >> >>#sets the range of the y axis >>ylim=range(5.7,8), >> >>#sets the symbol type, size, and color for the 1st series >>pch=10,cex=0.8, col='black', xlab="Date ", ylab="pH") >> >>#Plots the second series >>points( Date, dataset2, col='blue',pch=2, cex=0.8) >> >>#Plots the 3rd series >>points( Date, dataset3, col='red',pch=3, cex=0.8) >> >>#Lines >>lines(Date, dataset1, lty = c(1),col='black') >>lines(Date, dataset2, lty = c(2),col='blue') >>lines(Date, dataset3, lty = c(3),col='red') >> >>#Add Legend to graph.? You can change the size of the box by changing cex = >>0.75? Large # makes it larger. >>legend("bottomleft",c("Dataset1","Dataset2", "Dataset3"), >>col = c("black","blue", "red"), >>cex = 0.7,text.col = "black",lty = c(1,2,3),lwd=c(2),pch = c(10,2,3), >>merge = TRUE, bg = 'gray90') >> >>#Add title >>title(main="Time Series Plot") >>#done >> >>??? [[alternative HTML version deleted]] >> >>______________________________________________ >>R-help at r-project.org mailing list >>https://stat.ethz.ch/mailman/listinfo/r-help >>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>and provide commented, minimal, self-contained, reproducible code. >> >> >