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Hello,

I've just recently started running Mark on Linux (and I know very little about Linux) and was hoping to get some info on getting the VC matrix out. I'm setting everything up in Windows and running the *z.tmp files in Linux using:

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mark i=mrkXXXXz.tmp o=mrkXXXXy.tmp


I've used Mark on CSU's supercomputer using some commands Gary put together, but those automatically output the *y.tmp (results) and *v.tmp (VC matrix) files. Any ideas on how to get both out using the standard Mark for Linux?

Thanks,
Adam

AdamGreen wrote:Hello,

I've just recently started running Mark on Linux (and I know very little about Linux) and was hoping to get some info on getting the VC matrix out. I'm setting everything up in Windows and running the *z.tmp files in Linux using:

Code: Select all

mark i=mrkXXXXz.tmp o=mrkXXXXy.tmp


I've used Mark on CSU's supercomputer using some commands Gary put together, but those automatically output the *y.tmp (results) and *v.tmp (VC matrix) files. Any ideas on how to get both out using the standard Mark for Linux?

Thanks,
Adam

Not exactly sure what you're up to, but you can output the VCV from the CL in Linux

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./mark64 i=dipper.inp o=dipper.lst v=dipper.vcv


(I called it .vcv to make it clear what the file is). Note, though, that the VCV is output as a binary file. There are any number of ways to go from binary -> text. But, you'll need to know what is in the .vcv file, and where, to interpret what you get.

You may want to look at the file read.mark.binary.linux in RMark so you can work out the structure or use it to convert from binary.

--jeff

jlaake wrote:You may want to look at the file read.mark.binary.linux in RMark so you can work out the structure or use it to convert from binary.

--jeff

Great suggestion -- forgot about that.

cooch wrote:

jlaake wrote:You may want to look at the file read.mark.binary.linux in RMark so you can work out the structure or use it to convert from binary.

--jeff

Great suggestion -- forgot about that.

You can find read.mark.binary.linux at Jeff's git site: https://raw.githubusercontent.com/jlaak ... ry.linux.R

If you have (say) dipper.vcv, with no derived parms, then something like the following in an R session will work

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source("read.mark.binary.R")
binary.output <- read.mark.binary.linux("//home//user//Desktop//dipper.vcv",NULL)

binary.output$real.vcv


That function is not exported but you can force use of any non-exported function from a package by using package:::function. In this case, it would be

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library(RMark)
binary.output <- RMark:::read.mark.binary.linux("//home//user//Desktop//dipper.vcv",NULL)