Having some Trouble Data Structures

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                   Effectors (Sequences)
 [1,] 0001              3                   ##   3 Random Numbers ##

There will be many such rows for many individuals. They have something
called effectors, the number of which is randomly generated, so say you
get 3 in the No_of_Effectors column. Then I make R generate 3 numbers
from between 1 and 10,000, this gives me three numerical
representations of genes. These numbers will be compared to a similar
data structure of the host individuals who have their immune genes with
similar numbers.

My problem is that obviously I can't stick 3 numbers in one "cell" of
the matrix (I've tried) :

Pathogen_Individuals[1,3] <- c(2,3,4)
Error in Pathogen_Individuals[1, 3] <- c(345, 567, 678) :
 number of items to replace is not a multiple of replacement length

In future I'm also going to have more variables such as whether a gene
is expressed. Such information may require a matrix in itself -
something like:


       Effector ID             Sequence                  Expressed?
[1,]     0001              345,567,678                       1 (or 0).

Is there a way then I can put more than one value in the cell like a
list of values, or a way to put objects in a cell of a data frame,
matrix or table etc. Almost an inception deal - data structures nested
in a data structure? If I search for things like "insert list into
matrix" I get results like how to turn one into another, which is not
what I think I need to be doing.

I have been considering having several data structures not nested in
each other, something like for every individual create a new matrix
object with the name Effectors_[Individual_ID] and some how get my
simulation loops operating on those objects but I find it hard to see
how to tell R all of those matrices are to be included in an operation,
as you can all lines of a data frame for example with for loops.
This is strange for me because this model was written in a macro-code
for another program which handles data in a different format and layout
to R.

My problem is I think, each individual in the model has many variables
- in this case representations of genes. So I'm having trouble getting
my head about this.

Hopefully someone more experienced will be able to offer advice or a
solution, it will be very appreciated.

Many Thanks,
Ben Ward (ENV, UEA & The Sainsbury Lab, JIC).

P.S. I have searched previous queries to the list, and I'm not sure but
this may be useful for relevant:


Have you thought of using a list?

a <- matrix(1:10, nrow=2)
b <- 1:5
x <- list(a=a, b=b)
x

$a
    [,1] [,2] [,3] [,4] [,5]
[1,]    1    3    5    7    9
[2,]    2    4    6    8   10

$b
[1] 1 2 3 4 5

x$a

    [,1] [,2] [,3] [,4] [,5]
[1,]    1    3    5    7    9
[2,]    2    4    6    8   10

x$b

[1] 1 2 3 4 5

oliveoil and yarn datasets have been mentioned.





[[alternative HTML version deleted]]