Re: [R] species accumulation curve with percentages

2020-06-16 Thread Jim Lemon
Hi Eddie, Upon reading your initial request more carefully, the last command should be: plot(nspec/nspec[50]*100,type="l",xlab="Sites", ylab="Species accumulation (%)",ylim=c(1,100)) Jim On Wed, Jun 17, 2020 at 8:23 AM Jim Lemon wrote: > > Hi Eddie, > I don't have the vegan package, but this

Re: [R] species accumulation curve with percentages

2020-06-16 Thread Jim Lemon
Hi Eddie, I don't have the vegan package, but this may help: accum<-function(x,y) return(x+(y-x)/7) nspec<-90 for(i in 2:50) nspec[i]<-accum(nspec[i-1],220) plot(nspec/nspec[1]*100,type="l",xlab="Sites", ylab="Species accumulation (%)") Jim On Wed, Jun 17, 2020 at 1:15 AM Eddie Tsyrlin wrote:

[R-es] De R a pyspark

2020-06-16 Thread Samura .
Hola, alguien sabr�a decirme como "traducir" este c�digo de R a c�digo Spark con Python (pyspark) para rellenar los valores nulos de una columna con los valores de otra. idx <- which(is.na(df$columna3)) df[idx, 'columna3'] <- df[idx, 'columna4'] Muchas gracias! [[alternative HTML

Re: [R] how to change manhattan plot code to get a different color per chromosome

2020-06-16 Thread Ana Marija
Hi Jim, thank you so much for this elaborate code I will definitely use some hacks from it in the future. For now, for the purpose of compactness of the code I just set manually colors which I want to be there: manhattan(results_log,chr="CHR",bp="POS",p="META_pval",snp="MARKER",suggestiveline =

Re: [R] Rstudio does not run on ubuntu 20

2020-06-16 Thread Luigi Marongiu
No it wasn't, in fact is the same I have already downloaded... On Tue, Jun 16, 2020 at 7:45 PM David Winsemius wrote: > > > On 6/16/20 10:11 AM, Luigi Marongiu wrote: > > Thank you, but isn't this the link to Rstudio server? Is there one for > > Rstudio desktop? > > > It didn't seem that

Re: [R] Rstudio does not run on ubuntu 20

2020-06-16 Thread David Winsemius
On 6/16/20 10:11 AM, Luigi Marongiu wrote: Thank you, but isn't this the link to Rstudio server? Is there one for Rstudio desktop? It didn't seem that difficult to find: https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.3.959-amd64.deb -- David. On Tue, Jun 16, 2020 at

Re: [R] Error message in meta-analysis package Metafor-weights =""

2020-06-16 Thread K Amoatwi
Thank you, very much appreciated. On Tue, Jun 16, 2020 at 12:50 PM Viechtbauer, Wolfgang (SP) < wolfgang.viechtba...@maastrichtuniversity.nl> wrote: > Dear Amoatwi, > > This way of using the escalc() function has been deprecated. It might be > added back once there is actually any benefit from

Re: [R] species accumulation curve with percentages

2020-06-16 Thread Bert Gunter
Probably: ?sum ?cumsum e.g. > x <- runif(100, 10,20) > cumsum(x)/sum(x) *100 Cheers, Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Tue, Jun 16, 2020 at

Re: [R] Rstudio does not run on ubuntu 20

2020-06-16 Thread Luigi Marongiu
Thank you, but isn't this the link to Rstudio server? Is there one for Rstudio desktop? On Tue, Jun 16, 2020 at 5:41 PM Jeroen Ooms wrote: > > On Mon, Jun 15, 2020 at 2:47 PM Luigi Marongiu > wrote: > > > > Hello, > > all of a sudden rstudio stopped working on ubuntu 20.04. I > > re-installed

Re: [R] Error message in meta-analysis package Metafor-weights =""

2020-06-16 Thread Viechtbauer, Wolfgang (SP)
Dear Amoatwi, This way of using the escalc() function has been deprecated. It might be added back once there is actually any benefit from having this functionality, but for years it just meant that I had to maintain two different ways of doing the exact same thing without any additional

Re: [R] Rstudio does not run on ubuntu 20

2020-06-16 Thread Jeroen Ooms
On Mon, Jun 15, 2020 at 2:47 PM Luigi Marongiu wrote: > > Hello, > all of a sudden rstudio stopped working on ubuntu 20.04. I > re-installed from `rstudio-1.3.959-amd64.deb` but it does not launch > even if there is an icon. On terminal I got: > ``` > $ rstudio > rstudio: error while loading

[R] species accumulation curve with percentages

2020-06-16 Thread Eddie Tsyrlin
I need to express species accumulation curve in percentage terms, i.e. the vertical axis is from 1% to 100% I have community data similar to BCI (from vegan package). I can construct the 'usual' species curve (see below) but I need to convert the species number to percentage. data("BCI")

[R] Error message in meta-analysis package Metafor-weights =""

2020-06-16 Thread K Amoatwi
Dear All, I am using the example from one of the tutorial about "Metafor" package and "escalc" function, to learn how this package can be applied to do meta-analysi; the code and the data is directly from the tutorials but "weights=freq" option in the escalc function is given me error message This

[ESS] Display color of colors()

2020-06-16 Thread John Haman via ESS-help
In an iESS buffer, is it possible to color the output of colors()? I tried rainbow-mode but it didn't work. Thanks. John [[alternative HTML version deleted]] __ ESS-help@r-project.org mailing list

Re: [R] how to change manhattan plot code to get a different color per chromosome

2020-06-16 Thread Jim Lemon
Hi Ana, Your attached image seems to have bailed out before landing in the list. Here's how to do it using a simple manhattan plot with the data from: https://reneshbedre.github.io//assets/posts/mhat/gwas_res_sim.csv gwas<-read.csv("gwas_res_sim.csv",stringsAsFactors=FALSE) # get the data into