Addition of two functions

[lhenneman]

combine_inmap_output uses spatial linkages of an inMAP outputs to combine output multiple runs. Employs the sf package. The goal here to is make it easier to plot/analyze many InMAP run output files simultaneously. User provides a directory that contains InMAP output and an optional pattern that matches specific files in the directory

plot_inmap takes output from combine_inmap_output and saves spatial plots to a directory

[cchoirat]

Thanks @lhenneman!

Have you tried a call such as makeCluster(detectCores() - 1) with condor? Is it compatible with condor's request_cpus tag?

[cchoirat]

@lhenneman : Also, we need to add the packages that your functions are using to the DESCRIPTION file.

Apart from ggplot2, what else do you use?

[lhenneman]

Cool...I was wondering which other parts of the process I was missing. I'll address these and get back in a bit.

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On Mon, Oct 23, 2017 at 12:40 PM, Christine Choirat < ***@***.***> wrote: @lhenneman <https://github.com/lhenneman> : Also, we need to add the packages that your functions are using to the DESCRIPTION file. Apart from ggplot2, what else do you use? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#7 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AdmcW_AtYN6VFFszjGmkKot4sCElmRK6ks5svMGEgaJpZM4QDIJH> .

-- Lucas R.F. Henneman (404) 788-2161 lhenneman@gmail.com

[lhenneman]

A potential issue - the 'sf' packages isn't available on RCE, and the install is bugging out...it looks like it's something to do with installing the dependancies (u2units2 in particular). Do you have any insight here?

[cchoirat]

Have you tried installing from source? install.packages(pkg, type = "source")?

[lhenneman]

Okay, all should be functional now on RCE. combine_inmap_output combines all the output in the inmap output directory that match the pattern, and adds the simple features data only if the sf package is installed. plot_inmap currently only works if the suggested packages are installed.

[cchoirat]

I merged your patch-3 branch into new dev branch.

[lhenneman]

Great. About to add some to `combine_inmap_output`. Should I work in the dev branch or branch off that?

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On Wed, Oct 25, 2017 at 9:06 PM, Christine Choirat ***@***.*** > wrote: I merged you patch-3 branch into new dev branch. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#7 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AdmcW0oEG_-jJ7Dmfqkhtrq2jqzs3uyNks5sv9sUgaJpZM4QDIJH> .

-- Lucas R.F. Henneman (404) 788-2161 lhenneman@gmail.com

[cchoirat]

up to you, but fine with me in the dev branch just created a vignette template btw On Wed, Oct 25, 2017 at 9:12 PM, Lucas Henneman <notifications@github.com> wrote:

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Great. About to add some to `combine_inmap_output`. Should I work in the dev branch or branch off that? On Wed, Oct 25, 2017 at 9:06 PM, Christine Choirat < ***@***.*** > wrote: > I merged you patch-3 branch into new dev branch. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#7 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AdmcW0oEG_- jJ7Dmfqkhtrq2jqzs3uyNks5sv9sUgaJpZM4QDIJH> > . > -- Lucas R.F. Henneman (404) 788-2161 ***@***.*** — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD-wZbL20jjBwrtTUn-4VhcbeKyHdKR-ks5sv9x2gaJpZM4QDIJH> .

[lhenneman]

Alright, `combine_inmap_output` and `plot_inmap` are now on the dev branch. They work just fine for me on my computer, and `plot_inmap` doesn't work on RCE because of the issue with `sf`. I put an example here: /nfs/bigdata_nobackup_ci3/n/ci3_nsaph/LucasH/inmap/run_inmap_dev.R On Wed, Oct 25, 2017 at 9:14 PM, Christine Choirat <notifications@github.com

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wrote: up to you, but fine with me in the dev branch just created a vignette template btw On Wed, Oct 25, 2017 at 9:12 PM, Lucas Henneman ***@***.***> wrote: > Great. About to add some to `combine_inmap_output`. Should I work in the > dev branch or branch off that? > > On Wed, Oct 25, 2017 at 9:06 PM, Christine Choirat < > ***@***.*** > > wrote: > > > I merged you patch-3 branch into new dev branch. > > > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub > > <#7 (comment)>, or > mute > > the thread > > <https://github.com/notifications/unsubscribe-auth/AdmcW0oEG_- > jJ7Dmfqkhtrq2jqzs3uyNks5sv9sUgaJpZM4QDIJH> > > . > > > > > > -- > Lucas R.F. Henneman > (404) 788-2161 > ***@***.*** > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#7 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AD-wZbL20jjBwrtTUn- 4VhcbeKyHdKR-ks5sv9x2gaJpZM4QDIJH> > . > — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#7 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AdmcW-k2b1-EoawcneRbDxFAP76YEnIuks5sv90FgaJpZM4QDIJH> .

-- Lucas R.F. Henneman (404) 788-2161 lhenneman@gmail.com