Dear R-List,
I have a set of possibilities I want to sample from:
bases <- list(c('A', 'C'), c('A', 'G'), c('C', 'T'))
possibilities <- as.matrix(expand.grid(bases))
>possibilities
Var1 Var2 Var3
[1,] "A" "A" "C"
[2,] "C" "A" "C"
[3,] "A" "G" "C"
[4,] "C" "G" "C"
[5,] "A" "A" "T"
[6,]
Hi, fellow R users,
I've been asked to make a plot with two datasets each with a different x axis,
and it's been suggested one be at the top and the other at the bottom of the
graph. I normally use ggplot2, and I know how to plot multiple datasets by
simply + a new geom with a different data op
Hi R helpers,
I have a set of data best shown in this below graph.
Each coloured line represents a statistic calculated across pairs of DNA
sequences. And for each coloured line, I would like to identify breakpoints -
so identify the chunks where the values are high, for example, in the light
in so 0.05, 0.50 and
0.95, or even just 0.05 and 0.95? Then uniroot finds the root of this function
and doing so find me the small p I need?
Best,
Ben.
From: Rolf Turner [rolf.tur...@vodafone.co.nz]
Sent: 11 October 2013 02:11
To: Benjamin Ward (EN
than uniroot?
Best,
Ben.
From: Stefan Evert [stefa...@collocations.de]
Sent: 10 October 2013 09:37
To: R-help Mailing List
Cc: Benjamin Ward (ENV)
Subject: Re: [R] Small p from binomial probability function.
Sounds like you want a 95% binomial confidence interval:
Hi,
I got given some code that uses the R function pbionom:
p <- mut * t
sumprobs <- pbinom( N, B, p ) * 1000
Which gives the output of a probability as a percentage like 5, 50, 95.
What the code currently does is find me the values of t I need, by using the
above two code lines in a loop, eac
Hi,
For the past few months I've been building a simulation in R I hope to package.
It consists of two usable functions, and many internal ones which one of the
two usable functions call while looping, to perform the stages of simulation.
A simple conceptual example is:
# Abstract representati
Hi all,
I realised that my last email question and code was probably going to be a bit
of an eyesore for some people and that perhaps the best thing for me to do is
to pose the question of what it is I want to achieve, rather than what I've
written, if it helps people:
I'm writing a simulation
Hi all,
I've written a function for a simulation which will - in general operation
without being specific to the simulation scenario, duplicate or delete columns
from a matrix based on two values which determine how many as a proportion of
the matrix: the two values are always between 0.01 and
Hi, This is probably a small query but one I'm struggling with: I have a list
in which I had elements which were NA, I removed them, by doing: list2 <-
lapply(list, na.omit),
However this leaves the element there with 'character(0)' in place as well as
attributes:
e.g.
[[978]]
character(0)
at
m: arun [smartpink...@yahoo.com]
Sent: 26 January 2013 02:34
To: Benjamin Ward (ENV)
Cc: R help
Subject: Re: [R] Removal of columns from matrix where all values of the column
are identical.
Hi,
I guess this should also work:
Matrix[,apply(Matrix,2,function(x) all(c(TRUE,x[-length(x)]!=x[-1])))]
Hi all,
I'd like to write a piece of code which will remove columns from a matrix, if
the column contains only one value, say every value in the column is a "3":
Matrix <- matrix(NA, nrow=5, ncol=4)
Matrix[,1] <- c(1,2,3,4,5)
Matrix[,2] <- c(3,3,3,3,3)
Matrix[,3] <- c(5,4,3,2,1)
Matrix[,4] <- c(
Dear all,
I'm trying to write a function, that will take as an argument, some aligned
genome sequences, and using a sliding window, do pairwise comparisons of
sequence similarity. Coding the sliding window I think I can manage but what
I'm trying to get to grips with is getting it so as every p
ker.
Best Wishes,
Ben W.
UEA (ENV) and The Sainsbury Laboratory.
From: Jean V Adams [jvad...@usgs.gov]
Sent: 27 November 2012 22:01
To: Benjamin Ward (ENV)
Cc: r-help@r-project.org
Subject: Re: [R] Stuck trying to modify a function
Ben,
You can use the
Hi,
I have the following data:
Path_Number <- 5
ID.Path <- c(1:Path_Number) # Make vector of ID's.
No_of_X <- sample(50:550, length(ID.Path), replace=TRUE) #
X <- split(sample(1:1, sum(No_of_X), replace=TRUE), rep(ID.Path, No_of_X))
Y <- lapply(X,function(x) sample(x, round(runif(1, min=10, m
Hi,
I have some values in a list format generated by the following:
Path_Number <- 0010
ID.Path <- formatC(0001:Path_Number, width=4, flag=0) # Make vector of ID's.
No_of_Effectors <- sample(1:550, length(ID.Path), replace=TRUE) # Define Number
of Effectors each individual gets.
Effectors <- spli
.gov]
Sent: 08 November 2012 19:59
To: r-help@r-project.org
Cc: Benjamin Ward (ENV)
Subject: Re: [R] Extract cell of many values from dataframe cells and sample
from them.
Ben,
I think you would find lists a helpful way to arrange your data. They do not
require equal lengths of data in each ele
ividual, each slice through the array in the z direction,
would have different numbers of rows - different numbers of effectors. This may
be easier to work on, but I've not worked with multidimensional arrays, I'm
used to data in dataframes (usually from spreadsheets from experim
indexing or some such thing I can write
functions to do the interactions and immunology and such.
Best,
Ben W.
UEA (ENV) & The Sainsbury Laboratory.
From: Jean V Adams [jvad...@usgs.gov]
Sent: 07 November 2012 21:12
To: Benjamin Ward (ENV)
Cc: r-help@r-projec
Hi all,
I have a list of genes present in 500 individuals, the individuals are the
elements:
Genes <- lapply(1:nrow(inds),function(x)
sample(1:1,inds$No_of_Genes,replace=TRUE))
(This was later written to a dataframe as well as kept as the list object:
inds2 <- data.frame(inds,Genes=I(Genes
From: Benjamin Ward (ENV)
Sent: 03 November 2012 13:29
To: Jeff Newmiller; r-help@r-project.org
Subject: RE: [R] Having some Trouble Data Structures
Hi,
Thank you very much for your reply - how you prefer, is how my supervisor
implemented the layout in Minitab, however I was unsure of how to get
Hi All,
I'm trying to run a simulation of host-pathogen evolution based around
individuals.
What I need to have is a dataframe or table of some description - describing
all the individuals of a pathogen population (so far I've implemented this as a
matrix):
ID No_of_Effectors
Hello-
I am a Graduate Assistant for an instructor who has written programs for
statistics calculations such as binomial distributions and regressions.
The programs had worked with no problem in Excel 2003. Now we are trying to
use it with Excel 2007, and we are having some trouble.
I have downl
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