[R] matrix creation -- answer: data.matrix()

[Martin Maechler]

>>>>> "GS" == Gavin Simpson <gavin.simpson at ucl.ac.uk>
>>>>>     on Tue, 29 Jan 2008 00:09:05 +0000 writes:

    GS> hits=-2.6 tests=BAYES_00
    GS> X-USF-Spam-Flag: NO

    GS> On Mon, 2008-01-28 at 12:17 -0700, Michelle DePrenger-Levin wrote:
    >> I was asked for the following information and hope it might help those who
    >> could answer my question...

    GS> That looks fine to me Michelle. 

    GS> You will have problems with as.matrix on this though as a matrix in R
    GS> has to contain *all* elements of the same kind, text or numeric. As $X
    GS> is a factor, the matrix ends up as a character matrix, as this example
    GS> shows:

    GS> my.dat <- data.frame(X = gl(4,5), Vegetative = runif(20), Dormant =
    GS> runif(20))
    GS> str(my.dat)
    GS> as.matrix(my.dat)


    [...............]

    GS> You could convert the factor column to its numeric representation and
    GS> then you can produce a matrix that is numeric

    GS> my.dat$X <- as.numeric(my.dat$X)
    GS> str(my.dat)
    GS> as.matrix(my.dat)

That's exactly what the  --- seemlingy much underused ---
function
	data.matrix() 
is for !

my.dat <- data.frame(X = gl(4,5), Veg = runif(20), Dorm = runif(20))
my.mat <- data.matrix(my.dat)
str(my.mat) # all numeric

In short:  

   Use  data.matrix(d), not as.matrix(d)  
   if d potentially is a data frame  !!

Regards,
Martin 

    GS> *But* you should read the help for popbio to see what you are required
    GS> to provide as what I show is only a workaround for the matrix issue - I
    GS> have no idea what a projection matrix is in the sense of popbio or how
    GS> to use the functions in that package.

    GS> HTH

    GS> G

    >> 
    >> 
    >> 
    >> To import the table I used:
    >> 
    >> AsMi05test=read.csv("C:/AsMi_Site05_1998.csv")
    >> 
    >> 
    >> 
    >> > str(AsMi05test)
    >> 
    >> `data.frame':   12 obs. of  8 variables:
    >> 
    >> $ X                          : Factor w/ 6 levels "Dead","Dormant",..: 5 6 3
    >> 4 2 1 5 6 3 4 ...
    >> 
    >> $ Vegetative                 : num  0.25 0.50 0.17 0.08 0.00 ...
    >> 
    >> $ Vegetative.with.Herbivory  : num  0.13 0.5 0.33 0.67 0 0 0.41 0.5 0 0 ...
    >> 
    >> $ Reproductive               : num  0 0 0 0 0 0 0 0 0 0 ...
    >> 
    >> $ Reproductive.with.Herbivory: num  0 0 0 0 0 ...
    >> 
    >> $ Dormant                    : num  0.08 0 0.33 0.08 1 0 0.06 0 0 0 ...
    >> 
    >> $ Dead                       : num  0.42 0.00 0.33 0.17 0.00 ...
    >> 
    >> $ End.Date                   : int  1998 1998 1998 1998 1998 1998 1999 1999
    >> 1999 1999 ...
    >> 
    >> 
    >> 
    >> 
    >> 
    >> ________________________________
    >> 
    >> From: Michelle DePrenger-Levin 
    >> Sent: Monday, January 28, 2008 11:35 AM
    >> To: 'r-help at r-project.org'
    >> Subject: matrix creation
    >> 
    >> 
    >> 
    >> Hello,
    >> 
    >> 
    >> 
    >> I am trying to create multiple matrices (to run a PVA) but can't import all
    >> of them from a .csv without the numbers treated as labels and not factors.
    >> 
    >> 
    >> 
    >> I can enter the matrix slowly:
    >> 
    >> Site05_96 <- matrix(c(0.07,0,0.03,0.00,NA,0.00,
    >> 0.09,0.166666667,0.31,0.42,NA,0.00,  0.00,0,0.00,0.00,NA,0.00, 
    >> 
    >> 0.00,0,0.00,0.00,NA,0.00,
    >> 0.26,0.166666667,0.19,0.00,NA,0.00,  0.58,0.666666667,0.47,0.58,0,0.00),
    >> 
    >> nrow = 6, ncol = 6, 
    >> 
    >> dimnames = list(c("Vegetative", "Vegetative with herbivory",
    >> "Reproductive", 
    >> 
    >> "Reproductive with herbivory", "Dormant", "Dead"),
    >> c("Vegetative", "Vegetative with herbivory", "Reproductive", 
    >> 
    >> "Reproductive with herbivory", "Dormant", "Dead")))
    >> 
    >> 
    >> 
    >> I would like to list all matrices (for all 12 years and all 4 sites) in one
    >> Excel sheet (.csv) and then read each matrix as chucks of 6 rows. However,
    >> when I try this I either get all the values (the %) in quotes (not as
    >> factors) and if I try to force them with as.factor, it no longer seems to be
    >> a matrix. 
    >> 
    >> 
    >> 
    >> AsMi0598test2 <- as.matrix(AsMi05test[1:6,1:6])
    >> 
    >> X                             Vegetative Vegetative.with.Herbivory
    >> Reproductive Reproductive.with.Herbivory Dormant
    >> 
    >> 1 "Vegetative"                  "0.25"     "0.13"                    "0"
    >> "0"                         "0.08" 
    >> 
    >> 2 "Vegetative with Herbivory"   "0.50"     "0.50"                    "0"
    >> "0"                         "0.00" 
    >> 
    >> 3 "Reproductive"                "0.17"     "0.33"                    "0"
    >> "0"                         "0.33" 
    >> 
    >> 4 "Reproductive with Herbivory" "0.08"     "0.67"                    "0"
    >> "0"                         "0.08" 
    >> 
    >> 5 "Dormant"                     "0.00"     "0.00"                    "0"
    >> "0"                         "1.00" 
    >> 
    >> 6 "Dead"                        "0.00"     "0.00"                    "0"
    >> "0"                         "0.00"
    >> 
    >> 
    >> 
    >> When I add AsMi0598test2 <- as.factor(as.matrix(AsMi05test[1:6,1:6])) I get
    >> this:
    >> 
    >> [1] Vegetative                  Vegetative with Herbivory   Reproductive
    >> Reproductive with Herbivory
    >> 
    >> [5] Dormant                     Dead                        0.25
    >> 0.50                       
    >> 
    >> [9] 0.17                        0.08                        0.00
    >> 0.00                       
    >> 
    >> [13] 0.13                        0.50                        0.33
    >> 0.67                       
    >> 
    >> [17] 0.00                        0.00                        0
    >> 0                          
    >> 
    >> [21] 0                           0                           0
    >> 0                          
    >> 
    >> [25] 0                           0                           0
    >> 0                          
    >> 
    >> [29] 0                           0                           0.08
    >> 0.00                       
    >> 
    >> [33] 0.33                        0.08                        1.00
    >> 0.00                       
    >> 
    >> 16 Levels: 0 0.00 0.08 0.13 0.17 0.25 0.33 0.50 0.67 1.00 Dead Dormant
    >> Reproductive ... Vegetative with Herbivory
    >> 
    >> 
    >> 
    >> I want to read all matrices into stoch.projection( ) {popbio}
    >> 
    >> 
    >> 
    >> Thanks for any suggestions. I could enter them all in the .txt document if I
    >> can't read them from the Excel sheet. 
    >> 
    >> 
    >> 
    >> Michelle DePrenger-Levin