[R] missing NEWS.pdf
I usually compile my own version of R on Ubuntu, now 18.04 and it works fine. I recently tried to compile v 3.6.1 and it all worked until the end of the "make install" which did not complete because it said it was missing "NEWS.pdf". Is this a bug or oversight, or have I done something wrong? Thanks J -- Jim Maas jimmaasuk at gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem installing Rmpi
Can anyone tell me to start looking to fix this, when attempting to install
Rmpi on Ubuntu 16.04, just updated R version to 3.3.2
** building package indices
** testing if installed package can be loaded
Error in system2(file.path(R.home("bin"), "R"), c(if (nzchar(arch))
paste0("--arch=", :
error in running command
* removing ‘/usr/local/lib/R/site-library/Rmpi’
Thanks, J
--
Jim Maas
[[alternative HTML version deleted]]
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[R] age old problem with rJava
I've installed oracle java 8, at least think I have and tried many things but still getting this error. For some reason if I run R as sudo, then the library rJava loads just fine, but not as user. Any suggestions most welcome. Ubuntu 16.04 linux, R 3.3.1 64-bit Thanks J > library(rJava) Error : .onLoad failed in loadNamespace() for 'rJava', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/usr/local/lib/R/site-library/rJava/libs/rJava.so': libjvm.so: cannot open shared object file: No such file or directory Error: package or namespace load failed for ‘rJava’ -- Jim Maas [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] apply a function containing a reduce statement to all rows of a 2d array?
If possible I would like to apply a function, that contains a reduce
statement, across the rows of 2d array. This code works for me right up
until the last. Can it be done or is there a better way? My next challenge
is to pass it a vector of starting values, i.e. each row will have a
different initial value.
func1 - function (x,y) {x * 0.6}
Reduce(func1, x = seq_len(10), accumulate = TRUE, init = 3)
totalfunc - function (x) {Reduce(func1, x = seq_len(10),
accumulate = TRUE, init = 3)
}
totalfunc(0)
startarray - t(array(1:100, c(10,10)))
newarray - apply(x = startarray, margin = 1, fun = totalfunc)
Thanks
J
--
Jim Maas
[[alternative HTML version deleted]]
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[R] fill an array by rows
I've dug around but not been able to find anything, am probably missing something obvious. How can I fill a three-dimensional (or higher dimension) array by rows instead of columns. eg new1 - array(c(1:125), c(5,5,5)) works fine for me but fills it by columns and new2 - array(c(1:125), c(5,5,5), byrow=TRUE) throws an error. Am I missing something obvious? I also tried transposing the 3-d array but that didn't work either. TIA Jim -- Dr. Jim Maas University of East Anglia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] constrain min and max of output
Hello, Is there a simple way/function to constrain the minimum and maximum value of an output from an assignment? if I have z - x +y but I want z to always be between 1 and 5, such that z=5 if (x+y = 5) and z=1 if (x+y = 1). I know it sounds simple, I can do it with if statements but just wondered if there is a simpler way? Thanks a bunch, J -- Jim Maas University of East Anglia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] procedure Power in module Math
Hi All, I'm attempting to compile and run a BUGS model using OpenBUGS from R and getting this message. I've googled around not found much, it may well be a problem with OpenBUGS and not R. Any suggestions or clues as to how to find the problem would be welcome. ** Sorry something went wrong in procedure Power in module Math ** Thanks a bunch, Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] cannot correct step size, geweke.diag of coda
Intermittently I'm getting this error from the geweke.diag function of
the coda package. Would anyone be kind enough to enlighten me as to the
possible source of such an error, or how to debug/locate it?
Error in { : task 22 failed - inner loop 1; cannot correct step size
Thanks a bunch.
J
--
Dr. Jim Maas
University of East Anglia
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[R] deSolve, extracting variable values from inside ode function
I'm just getting to grips with using ode function and have used the
examples and vignettes to produce a small model of a one-pool,
michaelis-menten, enzyme kinetic reaction. The rate of flux of substrate
into pool A is constant (fluxoa) however the rate of flux out of pool A
is controlled by the HMM equation (v = Vmax/ ( 1 + (Km / Concentration A
)) ). This function works fine and gives correct answers for the
size of the pool of quantity of substrate in pool A at all times,
however if possible I'd like to also extract the values of interim
variables at each time t. Could anyone give me a clue of how to include
the value of CA at each time t, along with QA in the results?
Thanks
Jim
R code
==
parameters - c(vola = 17.3629, vmax = 4.7, mmk = 0.5435, fluxoa =
2.389)
state - c(QA=9.437)
MM - function(t, state, parameters) {
with(as.list(c(state, parameters)),{
## concentration of substrate in pool A, quantity
## divided by the volume of the solvent pool
CA - QA/vola
## output of substrate from pool A
fluxao - vmax / (1 + (mmk/CA))
## rate of change of quantity of substrate
## in pool A
dA - fluxoa - fluxao
## return the rate of change
list(dA)
})
}
times - seq(0, 100, by = 5)
library(deSolve)
out1 - ode(y = state, times = times, func = MM, parms = parameters)
head(out1)
--
Dr. Jim Maas
University of East Anglia
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[R] elegant way of removing NA's and selecting specific values from a data.frame
I have a data.frame e and would like to extract the 23rd column, remove any NA's and then remove any values = 30. I can do it in steps such as this but have failed to figure out how to do it in a single line any suggestions? first - e[,23] second - first[!is.na(first)] third - second[second=30] thanks a bunch J -- Dr. Jim Maas University of East Anglia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] calculating mean of list components
I get a list object from an iterative function. I'm trying to figure out the most efficient way to calculate the mean of one element, across all components of the overall list. I've tried output - mean (listobject[[1:5]]$element) to get the mean of element in the first five components? It doesn't like the $. I'm suspect one of the apply functions will work, but again I've not had success Thanks a bunch. J Jim Maas University of East Anglia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] simplify if statement in R ?
I found a form of the if statement that works but it is very long. I'm
attempting to check the value of of two different variables to see if
they evaluate to either of two different values, which will result in a
division by 0 in the final equation. This first if statement works for me
___
if ((x0.trial01 == 0.0)||(x0.trial01 == npt01)||(x1.trial01 ==
0.0)||(x1.trial01 == npt01))
{
x0.trial01.in - x0.trial01 + 0.5
x1.trial01.in - x1.trial01 + 0.5
npt01.in - npt01 + 1.0
}
else
{
x0.trial01.in - x0.trial01
x1.trial01.in - x1.trial01
npt01.in - npt01
}
__
I've tried
if ( ( x0.trial01 || x1.trial01) == ( 0.0 || npt01) )
..
but it doesn't seem to work correctly. Is there a simpler way to check
two variables for two different valuables?
Thanks
J
Jim Maas
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