Re: [R] for loop with multiple conditions in R (e.g. for(i in x j in y)
Hi,
May be this helps:
res.i - NULL
for(i in seq_along(x)){ res.i - c(res.i,x[i]-y[i])}
#or using your nested loop:
res.ij - NULL
for(i in seq_along(x)){
for(j in seq_along(y)){
if(i==j){
res.ij - c(res.ij,x[i]-y[j])
}
}}
identical(x-y,res.i)
#[1] TRUE
identical(res.i,res.ij)
#[1] TRUE
A.K.
I need a for loop that pulls data from two different vectors. For example,
suppose that my vectors were
x - c(1,2,3)
y - c(4,5,6)
and I wanted a loop that woul take i in x and subtract it from j in y
how would I do it? (i.e. 1-4,2-5,3-6). Note: I realize that for this
silly example there are much better ways to do this than using a for
loop, but the actual script that I am working with is much more
complicated and really does needs to be a for loop, so if you would
humor me and tell me how to write a loop for this example rather than
recommending a better way to solve the example, I would appreciate it.
I've tried the following line of code, but, as expected, it
subtract each value of i from each value of j, which is not what I want,
I want the first value of i subtracted from the first value of j, the
second value of i from the second value of j, etc.
res.i - c(NULL)
for(i in x){
for(j in y){
sol.i - i-j
res.i - c(res.i,sol.i)}
print(res.i)}
thanks!
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[R] Help: Split-Split model nested in a nested structure
Dear list members. We are trying see effect of N on yield of three wheat genotypes under late and early planting conditions in saline and non-saline environments. Our experimental structure as follows: Districts (2: DIST01 and DIST02) - Not randomly selected ENV (Saline and Non-Saline) - One saline and non-saline environment (eg. village) were selected in each district (not random). *SOWING Time (Late and Early):* 8 farmers' fields were selected randomly in each environment or village. These are spatially distributed in a village. Among them, 4 were grouped as early and 4 were grouped as a late sowing group. *N_TREAT (N0 and N100)* - Then, each farmer field was splitted into two main plots where two N-treatment were assigned randomly. *GENOTYPE ( G1, G2, G3*) - Then, N-main plots were further splited into three subplots here 3 wheat varieties were assigned randomly. This experiment was repeated for two years. Farmers' fields in Year 1 and Year 2 were not same. We are not interested to see the District effect on wheat yield here. Rather, we like to see the effect of saline environment, sowing time, N and genotype and their interaction on wheat yield for year 1 and year 2 separately. We are using the following ANOVA model. We do not know whether we are missing something here. Help will be highly arreciated. Regards Zia Ahmed, CIMMYT model-aov(YIELD~ENV*SOWING*N_RATE*GEN+Error(FARMERS/N_RATE/GEN), data=mydata) summary(model) # District: two DIST-as.factor(rep(c(DIST01,DIST02),each=96)) # ENV: Saline and Non-saline environment ENV-as.factor(rep(rep(c(Saline,Non-saline),each=48),2)) # Farmers 16 FARMERS-as.factor(rep(c(F1,F2,F3,F4,F5,F6,F7,F8, F9,F10,F11, F12,F13,F14,F15,F16),each=12)) # Showing Date: two SOWING-as.factor(rep(rep(c(Early,Late),each=6),16)) # Nitrogen treatments: N0 and N100 N_RATE-as.factor(rep(rep(c(N0,N100),each=3),32)) # Genotype GEN-as.factor(rep(rep(c(V1,V2,V3),each=1),64)) # Response: Wheat Yield set.seed(1234) YIELD - rnorm(n=192, mean=3.0, sd=0.5) # Create Data Frame mydata-data.frame(DIST,ENV, FARMERS,SOWING,N_RATE,GEN,YIELD) mydata [[alternative HTML version deleted]] __ R-help@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.
Re: [R] shapiro.test
Hello, Inline Em 21-02-2014 23:13, Rolf Turner escreveu: On 22/02/14 11:04, Rui Barradas wrote: Hello, Not answering directly to your question, if the sample size is a documented problem with shapiro.test and you want a normality test, why don't you use ?ks.test? m - mean(HP_TrinityK25$V2) s - sd(HP_TrinityK25$V2) ks.test(HP_TrinityK25$V2, pnorm, m, s) Strictly speaking this is not a valid test. The KS test is used for testing against a *completely specified* distribution. If there are parameters to be estimated, the null distribution is no longer applicable. This may not be a real problem if the parameters are *well* estimated, as they would be in this instance (given that the sample size is over-large). I'm not sure about this. Yes, you're right. I hesitated before posting my answer precisely because of this, the parameters must be pre-determined constants, not computed from the data. Like Greg pointed out in his reply, the help page for ?ks.test also explicitly refers to it (which I had missed). The chi-squared gof test seems to be a good choice, given the sample size. Rui Barradas The Lilliefors test is theoretically available in this context when mu and sigma are estimated, but according to the Wikipedia article, the Lilliefors distribution is not known analytically and the critical values must be determined by Monte Carlo methods. There is a LillieTest function in the DescTools package which makes use of some approximations to get p-values. However I think that a better approach would be to use a chi-squared goodness of fit test whereby you can adjust for estimated parameters simply by reducing the degrees of freedom. I believe that the chi-squared test is somewhat low in power, but with a very large sample this should not be a problem. The difficulty with the chi-squared test is that the choice of bins is somewhat arbitrary. I believe the best approach is to take the bin boundaries to be the quantiles of the normal distribution (with parameters m and s) corresponding to equispaced probabilities on [0,1], with the number of such probabilities being k+1 where k = floor(n/5), n being the sample size. This makes the expected counts all equal to n/k = 5 so that the chi-squared test is valid. The degrees of freedom are then k-3 (k - 1 - #estimated parameters). One last comment: I believe that it is generally considered that testing for normality is a waste of time and a pseudo-intellectual exercise of academic interest at best. cheers, Rolf Turner Hope this helps, Rui Barradas Em 21-02-2014 15:59, Gonzalo Villarino Pizarro escreveu: Dear R users, Please help with with this maybe basic question. I am trying to see if my data is normal but is a large file and the test does not work. I keep getting the message : Error in shapiro.test(x = HP_TrinityK25$V2) : sample size must be between 3 and 5000 thanks! shapiro.test(x=HP_TrinityK25$V2) Error in shapiro.test(x = HP_TrinityK25$V2) : sample size must be between 3 and 5000 ##Note: HP_TrinityK25= my file HP_TrinityK25$V2= data in my file [[alternative HTML version deleted]] __ R-help@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. __ R-help@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. __ R-help@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.
Re: [R] shapiro.test
Second. Rui Barradas Em 21-02-2014 23:44, Rolf Turner escreveu: On 22/02/14 11:53, Greg Snow wrote: SNIP Why are you testing your data for normality? For large sample sizes the normality tests often give a meaningful answer to a meaningless question (for small samples they give a meaningless answer to a meaningful question). SNIP Fortune!!! cheers, Rolf __ R-help@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. __ R-help@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.
[R] Math symbols in ggplot facets
Hello,
I would like to show in my facet labels the equivalent in LaTex of
$\sigma_{0}= \sqrt{2}$. I think I'm close below, but not yet as it shows
$(\sigma_{0}, \sqrt{2})$
m - mpg
levels(m$drv) - c(sigma[0]=sqrt(2), sigma[0]=2 * sqrt(2), sigma[0]= 3
* sqrt(2))
ggplot(m, aes(x = displ, y = cty)) + geom_point() +
facet_grid(. ~ drv, labeller = label_parsed)
Thanks,
Lars.
[[alternative HTML version deleted]]
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Re: [R] dependent column(s) in data frame
Many thanks David, I will have a look on logistic regression for my case. Do you know about a good example regarding logistic regression ? I was thinking also of using Multiple Factor Analysis too (MFA - like in FactoMineR). However I am not sure how successful this is going to be. Best, P. -- View this message in context: http://r.789695.n4.nabble.com/dependent-column-s-in-data-frame-tp4685561p4685684.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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.
[R] Exposures in bernoulli glm()
Hi, is it possible to add exposures to a glm with family=binomial()? It's easy to do it for a Poisson/negative binomial: just multiply the mean by the exposure, that is, offset(log(exposure)): but this obviously wrong for a binomial/Bernoulli since the mean must be no bigger than 1. My goal was do it it with pscl::zeroinfl and pscl::hurdle, but answering for binomial/Bernoulli would already help. __ R-help@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.
[R] Learn R in a Day - new ebook
Dear all, I'd like to make you aware of my new ebook - Learn R in a Day - which provides the reader with key programming skills through an examples-oriented approach and is ideally suited for academics, scientists, mathematicians and engineers. Amazon.com: http://www.amazon.com/Learn-R-Day-Steven-Murray-ebook/dp/B00GC2LKOK/ref=sr_1_1?s=digital-textie=UTF8qid=1393005750sr=1-1keywords=learn+r+in+a+day Amazon UK: http://www.amazon.co.uk/Learn-R-Day-Steven-Murray-ebook/dp/B00GC2LKOK The book assumes no prior knowledge of computer programming and progressively covers all the essential steps needed to become confident and proficient in using R within a day. Topics include how to input, manipulate, format, iterate (loop), query, perform basic statistics on, and plot data, via a step-by-step technique and demonstrations using in-built datasets which the reader is encouraged to replicate on their computer. Each chapter also includes exercises (with solutions) to practice key skills and empower the reader to build on the essentials gained during this introductory course. Steve Murray [[alternative HTML version deleted]] __ R-help@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.
[R] Hi everybody, your help would be very appreciate, thanks !
Hi everybody, I have realized a multiple linear regression. To know how well my model does in terms of prediction, I can compute prediction intervals bands and decide if they are narrow enough to be of use. If they are too wide, then they probably are not useful. Using R, I have written these R codes. LinearModel.1 - lm(GDP.per.head ~ Competitivness.score + Quality.score, data=Dataset) summary(LinearModel.1) predict(LinearModel.1, se.fit = FALSE, scale = NULL, df = Inf,interval = c(none, confidence, prediction),level = 0.95, type = c(response, terms),terms = NULL) Now, I am trying to draw one graph / plot, where I can have the straight regression line and the prediction interval bands in the same graph / plot to see if the bands are narrow enough to be of use. Could you please help me with my R codes ? Thanks for your precious help, [[alternative HTML version deleted]] __ R-help@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.
[R] hist: argument '...' is not made use of
Hi: When converting some code to use plot = F in a call to hist(), I received the following warning (with a much simplified example). moo-1:10 hist(moo, las=1, plot=F) Warning message: In hist.default(moo, las = 1, plot = F) : argument '...' is not made use of From the help page, I was able to figure out that it was the las=1 argument, which is not needed with plot = F that was my issue. My question is whether this was the intended warning (instead of mentioning las = 1 explicitly, which might be hard to implement) and if so if there might be some more direct way to figure out what was wrong from say args(hist), since I initially thought I'd in some way unintentionally passed ... as an argument? sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks! Jen [[alternative HTML version deleted]] __ R-help@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.
[R] create video?
Hello: Might someone have experience with video production? The animation package in R can produce video clips. These could presumably be merged and synced with audio using something like Avidemux. I have not done this, but it looks like it might be a relatively easy way for an R user to create a video from audio and slides. I'd like something that would give me more control than screencasting. For this, I'm thinking of recording the audio, then measuring each phrase with something like Audacity. I'd then use that with R and Avidemux as outlined above. Can anyone suggest something different or provide details on ways to make this easy? Thanks, Spencer Graves __ R-help@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.
Re: [R] how to plot a logarithmic regression line
HI, Try ?curve fit - lm(Mean_Percent_of_Range~log(No.ofPoints)) coef(fit) # (Intercept) log(No.ofPoints) # -74.52645 46.14392 plot(Mean_Percent_of_Range ~ No.ofPoints) curve(coef(fit)[[1]]+coef(fit)[[2]]*log(x),add=TRUE,col=2) A.K. I realize this is a stupid question, and I have honestly tried to find the answer online, but nothing I have tried has worked. I have two vectors of data: Mean_percent_of_range 10.9 17.5 21.86667 25.0 25.4 26.76667 29.5 32.36667 43.1 41.8 50.56667 49.26667 50.36667 51.9 59.7 63.96667 62.5 60.8 64.2 66.0 74.0 70.4 77.06667 76.46667 78.1 89.46667 88.9 90.0 91.6 94.3 95.5 96.2 96.5 91.4 98.2 96.6 97.4 99.0 100.0 and No.ofPoints 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 When I plot these, I get a logarithmic curve (as I should for this type of data) plot(Mean_Percent_of_Range ~ No.ofPoints) All that I want to do is plot best fit regression line for that curve. From what I have read online, it seems like the code to do that should be abline(lm(log(Mean_Percent_of_Range) ~ log(No.ofPoints))) but that gives me a straight line that isn't even close to fitting the data How do I plot the line and get the equation of that line and a correlation coefficient? Thanks __ R-help@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.
Re: [R] dependent column(s) in data frame
On Feb 22, 2014, at 4:28 AM, PQuery wrote: Many thanks David, I will have a look on logistic regression for my case. Do you know about a good example regarding logistic regression ? I was thinking also of using Multiple Factor Analysis too (MFA - like in FactoMineR). However I am not sure how successful this is going to be. Your data (exclusively 0/1 values) did not look like it would be suitable for factor analysis. Perhaps you mean to use that package's correspondence analysis methods? -- David Winsemius Alameda, CA, USA __ R-help@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.
Re: [R] how to plot a logarithmic regression line
On Feb 22, 2014, at 1:06 PM, arun wrote: HI, Try ?curve fit - lm(Mean_Percent_of_Range~log(No.ofPoints)) coef(fit) #(Intercept) log(No.ofPoints) # -74.52645 46.14392 plot(Mean_Percent_of_Range ~ No.ofPoints) curve(coef(fit)[[1]]+coef(fit)[[2]]*log(x),add=TRUE,col=2) A.K. I realize this is a stupid question, and I have honestly tried to find the answer online, but nothing I have tried has worked. I have two vectors of data: Mean_percent_of_range 10.9 17.5 21.86667 25.0 25.4 26.76667 29.5 32.36667 43.1 41.8 50.56667 49.26667 50.36667 51.9 59.7 63.96667 62.5 60.8 64.2 66.0 74.0 70.4 77.06667 76.46667 78.1 89.46667 88.9 90.0 91.6 94.3 95.5 96.2 96.5 91.4 98.2 96.6 97.4 99.0 100.0 and No.ofPoints 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 When I plot these, I get a logarithmic curve (as I should for this type of data) plot(Mean_Percent_of_Range ~ No.ofPoints) All that I want to do is plot best fit regression line for that curve. From what I have read online, it seems like the code to do that should be abline(lm(log(Mean_Percent_of_Range) ~ log(No.ofPoints))) but that gives me a straight line that isn't even close to fitting the data How do I plot the line and get the equation of that line and a correlation coefficient? The 'abline' function is not what you want. Use 'lines' to plot multiple points. Perhaps: mod - lm(log(Mean_percent_of_range) ~ log(No.ofPoints)) plot(log(Mean_percent_of_range), log(No.ofPoints)) lines( log(No.ofPoints), predict(mod)) # summary(mod) Call: lm(formula = log(Mean_percent_of_range) ~ log(No.ofPoints)) Residuals: Min 1Q Median 3Q Max -0.32617 -0.04839 0.00962 0.05316 0.17316 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 1.198400.08060 14.87 2e-16 *** log(No.ofPoints) 0.942280.02609 36.12 2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 0.09455 on 37 degrees of freedom Multiple R-squared: 0.9724,Adjusted R-squared: 0.9717 F-statistic: 1305 on 1 and 37 DF, p-value: 2.2e-16 David Winsemius Alameda, CA, USA __ R-help@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.
Re: [R] Math symbols in ggplot facets
Hi:
You were close...
library(ggplot2)
m - mpg
# Set the factor labels with plotmath code (note the ==)
m$drv - factor(m$drv, labels = c(sigma[0] == sqrt(2),
sigma[0] == 2 * sqrt(2),
sigma[0] == 3 * sqrt(2)))
ggplot(m, aes(x = displ, y = cty)) + geom_point() +
facet_grid(. ~ drv, labeller = label_parsed)
Dennis
On Sat, Feb 22, 2014 at 3:24 AM, Lars Bishop lars...@gmail.com wrote:
Hello,
I would like to show in my facet labels the equivalent in LaTex of
$\sigma_{0}= \sqrt{2}$. I think I'm close below, but not yet as it shows
$(\sigma_{0}, \sqrt{2})$
m - mpg
levels(m$drv) - c(sigma[0]=sqrt(2), sigma[0]=2 * sqrt(2), sigma[0]= 3
* sqrt(2))
ggplot(m, aes(x = displ, y = cty)) + geom_point() +
facet_grid(. ~ drv, labeller = label_parsed)
Thanks,
Lars.
[[alternative HTML version deleted]]
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[R] equivalent of $\check Y$ in plotmath
Hi, I am trying to put the expression which in LaTeX would be $\check Y$ as a label on the axis of a plot. How does one get the \check part of the above to produce a similar symbol in plotmath in R? I looked around plotmath's help but could not see this in the documentation. Many thanks for any suggestions, and best wishes, Ranjan -- Important Notice: This mailbox is ignored: e-mails are set to be deleted on receipt. Please respond to the mailing list if appropriate. For those needing to send personal or professional e-mail, please use appropriate addresses. FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks orcas on your desktop! __ R-help@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.
[R] seeking alternative method to copy a large section of my R program
Is there any way I can insert markers at the beginning and end of a large section of R statements and then copy all text in between to clipboard? I have trouble scrolling to select long sections, so if there is another way I would like to know it! Julie (for husband Larry) [[alternative HTML version deleted]] __ R-help@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.
Re: [R] seeking alternative method to copy a large section of my R program
This is a function of the editor you use and the operating system you use, neither of which is on topic here. That said, many popular GUI editors allow you to select by holding the shift key down while moving the cursor with arrow keys. Note that in the long run using the source function to have R process a whole file is much easier to remember how to do later than remembering which chunks of code to copy and paste. In addition, sometimes the amount of text that the clipboard can hold will be less than you want to run, leading to mysterious error messages from R. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On February 22, 2014 1:57:14 PM PST, Julie Royster jsdroys...@nc.rr.com wrote: Is there any way I can insert markers at the beginning and end of a large section of R statements and then copy all text in between to clipboard? I have trouble scrolling to select long sections, so if there is another way I would like to know it! Julie (for husband Larry) [[alternative HTML version deleted]] __ R-help@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. __ R-help@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.
Re: [R] seeking alternative method to copy a large section of my R program
On Feb 22, 2014, at 1:57 PM, Julie Royster wrote: Is there any way I can insert markers at the beginning and end of a large section of R statements and then copy all text in between to clipboard? I have trouble scrolling to select long sections, so if there is another way I would like to know it! Each interface is going to be a bit different, but on both the Mac and Windoze I can position the cursor at one end , hold down the shift-key, scroll to the other end and release the shift-key and I will have the target ready for either an Edit/Cut or a cmd-C/ctrl-C. -- David Winsemius Alameda, CA, USA __ R-help@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.
