[R-sig-eco] Organizing Data for Bootstrap ANOVA
How would you go about using boot() and boot.ci() to perform a one-way ANOVA? I have a hand-coded, bootstrap-based function, but my main question concerns organizing the raw data, so the problem may be similar to using the aov() function. In doing a two-group comparison, you concatenate the two data vectors and make a data frame with an index. What do you do for ANOVA? Thanks, Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes "In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation." --John Janovy, Jr., "On Becoming a Biologist" ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Using rq() for least absolute deviation regression
I've seen several websites say that the function rq() from the package quantreg can be used to do least absolute deviation regression. How do you go about doing this and what's the connection between quantile regression and LAD? (I'm very new to the former topic.) Thanks, Jane -- ----- Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes "In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation." --John Janovy, Jr., "On Becoming a Biologist" ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] Linear Model of Data in Matrix Form
Thank you; that works! Best, Jane On Sun, Apr 3, 2011 at 8:22 PM, Christian Roy wrote: > On Sun, Apr 3, 2011 at 11:05 PM, Jane Shevtsov wrote: >> >> Thanks, but that doesn't quite work. Using your toy example gives an >> error about variable lengths. >> >> > z <- matrix(1:9,nrow=3,dimnames=list(1:3,4:6)) >> > z.melt <- melt(z) >> > z.melt >> X1 X2 value >> 1 1 4 1 >> 2 2 4 2 >> 3 3 4 3 >> 4 1 5 4 >> 5 2 5 5 >> 6 3 5 6 >> 7 1 6 7 >> 8 2 6 8 >> 9 3 6 9 >> > lm(z ~ z.melt$X1 + z.melt$X2) > > In this example the syntax for your model is: >> lm(z.melt$value ~ z.melt$X1 + z.melt$X2) > Call: > lm(formula = z.melt$value ~ z.melt$X1 + z.melt$X2) > Coefficients: > (Intercept) z.melt$X1 z.melt$X2 > -12 1 3 > Best, > Chris > --- >> >> Error in model.frame.default(formula = z ~ z.melt$X1 + z.melt$X2, >> drop.unused.levels = TRUE) : >> variable lengths differ (found for 'z.melt$X1') >> I'm using R 2.12.0 on Windows and just installed the reshape package. >> >> Jane >> >> On Sun, Apr 3, 2011 at 3:40 PM, Ben Bolker wrote: >> > -BEGIN PGP SIGNED MESSAGE- >> > Hash: SHA1 >> > >> > On 11-04-02 10:39 PM, Jane Shevtsov wrote: >> >> I have data in matrix form from a parameter scan of a food web >> >> simulation. (The matrix entry M[i,j] gives the variable of interest >> >> for a web size i and connectance j.) How would I find an equation >> >> expressing the variable of interest to web size and connectance? Can >> >> lm() do it? >> >> >> >> Thanks, >> >> Jane Shevtsov >> >> >> > >> > suppose your size and connectance vectors were sizevec and connvec. >> > Then something like >> > >> > dimnames(M) <- list(sizevec,connvec) >> > library(reshape) >> > X <- melt(M) >> > lm(value~X1+X2) >> > >> > will do it. >> > >> > Mini example: >> > >> >> z <- matrix(1:9,nrow=3,dimnames=list(1:3,4:6)) >> >> library(reshape) >> > Loading required package: plyr >> > >> > Attaching package: 'reshape' >> > >> > The following object(s) are masked from 'package:plyr': >> > >> > round_any >> > >> >> str(melt(z)) >> > 'data.frame': 9 obs. of 3 variables: >> > $ X1 : int 1 2 3 1 2 3 1 2 3 >> > $ X2 : int 4 4 4 5 5 5 6 6 6 >> > $ value: int 1 2 3 4 5 6 7 8 9 >> > -BEGIN PGP SIGNATURE- >> > Version: GnuPG v1.4.10 (GNU/Linux) >> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> > >> > iEYEARECAAYFAk2Y90MACgkQc5UpGjwzenOmPQCdFAOGcxnzADXZNv9ikgDzJcPQ >> > 3/IAn1ayn1HVOQOdlqFDPoq+Et6rR5nt >> > =cfIQ >> > -END PGP SIGNATURE- >> > >> > ___ >> > R-sig-ecology mailing list >> > R-sig-ecology@r-project.org >> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> > >> >> >> >> -- >> - >> Jane Shevtsov >> Ecology Ph.D. candidate, University of Georgia >> co-founder, >> Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes >> >> "In the long run, education intended to produce a molecular >> geneticist, a systems ecologist, or an immunologist is inferior, both >> for the individual and for society, than that intended to produce a >> broadly educated person who has also written a dissertation." --John >> Janovy, Jr., "On Becoming a Biologist" >> >> ___ >> R-sig-ecology mailing list >> R-sig-ecology@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > -- > Christian Roy, Biol. Msc. > Étudiant au Doctorat / Phd Student > courriel: christian.roy...@ulaval.ca > Université Laval, Faculté de foresterie, de géographie et de géomatique > -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes "In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation." --John Janovy, Jr., "On Becoming a Biologist" ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] Linear Model of Data in Matrix Form
Thanks, but that doesn't quite work. Using your toy example gives an error about variable lengths. > z <- matrix(1:9,nrow=3,dimnames=list(1:3,4:6)) > z.melt <- melt(z) > z.melt X1 X2 value 1 1 4 1 2 2 4 2 3 3 4 3 4 1 5 4 5 2 5 5 6 3 5 6 7 1 6 7 8 2 6 8 9 3 6 9 > lm(z ~ z.melt$X1 + z.melt$X2) Error in model.frame.default(formula = z ~ z.melt$X1 + z.melt$X2, drop.unused.levels = TRUE) : variable lengths differ (found for 'z.melt$X1') I'm using R 2.12.0 on Windows and just installed the reshape package. Jane On Sun, Apr 3, 2011 at 3:40 PM, Ben Bolker wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > On 11-04-02 10:39 PM, Jane Shevtsov wrote: >> I have data in matrix form from a parameter scan of a food web >> simulation. (The matrix entry M[i,j] gives the variable of interest >> for a web size i and connectance j.) How would I find an equation >> expressing the variable of interest to web size and connectance? Can >> lm() do it? >> >> Thanks, >> Jane Shevtsov >> > > suppose your size and connectance vectors were sizevec and connvec. > Then something like > > dimnames(M) <- list(sizevec,connvec) > library(reshape) > X <- melt(M) > lm(value~X1+X2) > > will do it. > > Mini example: > >> z <- matrix(1:9,nrow=3,dimnames=list(1:3,4:6)) >> library(reshape) > Loading required package: plyr > > Attaching package: 'reshape' > > The following object(s) are masked from 'package:plyr': > > round_any > >> str(melt(z)) > 'data.frame': 9 obs. of 3 variables: > $ X1 : int 1 2 3 1 2 3 1 2 3 > $ X2 : int 4 4 4 5 5 5 6 6 6 > $ value: int 1 2 3 4 5 6 7 8 9 > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iEYEARECAAYFAk2Y90MACgkQc5UpGjwzenOmPQCdFAOGcxnzADXZNv9ikgDzJcPQ > 3/IAn1ayn1HVOQOdlqFDPoq+Et6rR5nt > =cfIQ > -END PGP SIGNATURE- > > ___ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes "In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation." --John Janovy, Jr., "On Becoming a Biologist" ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Linear Model of Data in Matrix Form
I have data in matrix form from a parameter scan of a food web simulation. (The matrix entry M[i,j] gives the variable of interest for a web size i and connectance j.) How would I find an equation expressing the variable of interest to web size and connectance? Can lm() do it? Thanks, Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes "In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation." --John Janovy, Jr., "On Becoming a Biologist" ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Positioning color key in heatmap
This is probably really basic, but I'm drawing a heatmap using the heatmap.2() function from gplots and want to place the color key along the left side of the plot. How do I do that? Thanks, Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes "In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation." --John Janovy, Jr., "On Becoming a Biologist" ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] lines() adds extra line
Thanks; that works! Best, Jane On Mon, Jan 24, 2011 at 10:15 AM, Sarah Goslee wrote: > R is doing just as you asked. If you look at the middle of c(x, x) the > x values jump from 10 to -10 and R draws the line segment connecting > them, as it's been told. > >> c(x,x)[195:205] > [1] 9.4 9.5 9.6 9.7 9.8 9.9 10.0 -10.0 -9.9 -9.8 -9.7 > > You might rather have: >> x2.rev <- c(x, rev(x)) >> x.rev.pred <- predict(lm(dataBoth.poly ~ x2.rev + >> I(x2.rev^2)+I(x2.rev^3)+I(x2.rev^4)+I(x2.rev^5)+I(x2.rev^6))) >> plot(x2.rev, x.rev.pred, type="l") > > Sarah > > > On Mon, Jan 24, 2011 at 1:04 PM, Jane Shevtsov wrote: >> I'm trying a bit of an experiment with polynomial curve fitting (don't >> worry, I wouldn't do this to actual data -- it's just a toy model for >> a specific question). When I generate a linear model of the data and >> plot it using plot(), everything works fine. But when I use plot(..., >> type="l") or lines(), I get an extra line connecting two points. How >> do I stop this from happening? >> >> Here's the code: >> x = seq(-10, 10, by=0.1) >> data1poly <- 0.1*x + 0.2*x^2 + 0.3*x^3 + 0.4*x^4 + 0.5*x^5 + 0.6*x^6 + >> 0.7 + rnorm(length(x),1E-3, 1E-4) >> data2poly <- 0.1*x + 0.2*x^2 + 0.3*x^3 + 0.4*x^4 + 0.5*x^5 + 0.6*x^6 - >> 1 + rnorm(length(x), 1E-3, 1E-4) >> dataBoth.poly <- c(data1poly, data2poly) >> #Works well >> plot(c(x,x), predict(lm(dataBoth.poly ~ c(x,x) + >> I(c(x,x)^2)+I(c(x,x)^3)+I(c(x,x)^4)+I(c(x,x)^5)+I(c(x,x)^6 >> #Adds extra line >> plot(c(x,x), predict(lm(dataBoth.poly ~ c(x,x) + >> I(c(x,x)^2)+I(c(x,x)^3)+I(c(x,x)^4)+I(c(x,x)^5)+I(c(x,x)^6))), >> type="l") #or >> lines(c(x,x), predict(lm(dataBoth.poly ~ c(x,x) + >> I(c(x,x)^2)+I(c(x,x)^3)+I(c(x,x)^4)+I(c(x,x)^5)+I(c(x,x)^6 >> >> Thanks, >> Jane >> >> -- > > -- > Sarah Goslee > http://www.functionaldiversity.org > -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes "The whole person must have both the humility to nurture the Earth and the pride to go to Mars." --Wyn Wachhorst, The Dream of Spaceflight ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] lines() adds extra line
I'm trying a bit of an experiment with polynomial curve fitting (don't worry, I wouldn't do this to actual data -- it's just a toy model for a specific question). When I generate a linear model of the data and plot it using plot(), everything works fine. But when I use plot(..., type="l") or lines(), I get an extra line connecting two points. How do I stop this from happening? Here's the code: x = seq(-10, 10, by=0.1) data1poly <- 0.1*x + 0.2*x^2 + 0.3*x^3 + 0.4*x^4 + 0.5*x^5 + 0.6*x^6 + 0.7 + rnorm(length(x),1E-3, 1E-4) data2poly <- 0.1*x + 0.2*x^2 + 0.3*x^3 + 0.4*x^4 + 0.5*x^5 + 0.6*x^6 - 1 + rnorm(length(x), 1E-3, 1E-4) dataBoth.poly <- c(data1poly, data2poly) #Works well plot(c(x,x), predict(lm(dataBoth.poly ~ c(x,x) + I(c(x,x)^2)+I(c(x,x)^3)+I(c(x,x)^4)+I(c(x,x)^5)+I(c(x,x)^6 #Adds extra line plot(c(x,x), predict(lm(dataBoth.poly ~ c(x,x) + I(c(x,x)^2)+I(c(x,x)^3)+I(c(x,x)^4)+I(c(x,x)^5)+I(c(x,x)^6))), type="l") #or lines(c(x,x), predict(lm(dataBoth.poly ~ c(x,x) + I(c(x,x)^2)+I(c(x,x)^3)+I(c(x,x)^4)+I(c(x,x)^5)+I(c(x,x)^6 Thanks, Jane -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes "The whole person must have both the humility to nurture the Earth and the pride to go to Mars." --Wyn Wachhorst, The Dream of Spaceflight ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Stochastic Model Gives Deterministic Output
I'm using R 2.10.1 (running on Ubuntu) to implement a simple null
model. The model (code below) assigns species to plots by shuffling
the numbers 1-# of plots and assigning the species to the first N
plots in the resulting vector, where N is the number of plots at which
the species was found in real life. The code works fine, except for
one problem -- different runs give exactly the same results! (Each
matrix is different, but matrix 1 of run 1 is identical to matrix 1 of
run 2.) How do I fix this? Is it possible to get R to use the time as
the seed for random number generation?
Thanks,
Jane Shevtsov
#input: vector of species occurences, # of iterations, #plots at site
nullModel.spsite <- function(occ, iter, plots) {
spp <- length(occ)
#Allocate array for co-occurrence frequencies of each species pair.
sitespArr <- array(0, c(spp, plots, iter))
#Pre-allocate other stuff
sitesp <- array(0, c(plots, spp)) #Preserve matrix orientation to
minimize recoding; transpose later
order <- array(0, plots)
for (i in 1:iter) {
#Zero out site-sp matrix
sitesp <- array(0, c(plots, spp))
for (j in 1:spp) {
#Randomly shuffle plots
order <- sample(1:plots, plots, replace=FALSE)
#Put sp i in first k (# plots where species i occurs)
plots
according to order vector
sitesp[order[1:occ[j]], j] = 1
}
sitespArr[,,i] = t(sitesp)
}
return(sitespArr)
}
--
-
Jane Shevtsov
Ecology Ph.D. candidate, University of Georgia
co-founder,
Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes
"The whole person must have both the humility to nurture the
Earth and the pride to go to Mars." --Wyn Wachhorst, The Dream
of Spaceflight
___
R-sig-ecology mailing list
R-sig-ecology@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] p-Function for Empirical Distributions
Does R have a p-function for empirical distributions? In other words, how can I find out what fraction of the values in my data set are smaller than a given value? -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes "The whole person must have both the humility to nurture the Earth and the pride to go to Mars." --Wyn Wachhorst, The Dream of Spaceflight ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
