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SCBI-ForestGEO / McGregor_climate-sensitivity-variation

repository for linking the climate sensitity of tree growth (derived from cores) to functional traits
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symbols in Tables #75

Closed teixeirak closed 4 years ago

teixeirak commented 4 years ago

@mcgregorian1, Becky managed to get symbols in tables, with what appears to be fairly simple code. I just granted you access to read the repository so that you can see what she did. See Table 1 in appendix.Rmd.

I tried to repeat that in your tables & figures doc, but kept getting errors. You may have better luck.

mcgregorian1 commented 4 years ago

I checked with Becky and sent her a subset of the full code that only included Table 2 (along with the table2 csv) and asked if she could replicate the symbols when knitting to pdf. She was able to without a problem, so I think this should be fine and good to go!

That being said, it still won't render on my computer, so I think the problem is an underlying wrong assortment of packages installed on my machine or I don't have the right package installed, or something else. I otherwise have no idea why it works with Becky's and not mine (and this would make sense considering I've had the correct symbol format all along).

That being said, I have added the knitr options from Becky's code into the tables&figures.Rmd, so that as it is technically renders fine. Can you try and let me know? Upon success we can update the symbol equations in markdown.

teixeirak commented 4 years ago

I just tried it on both my laptop and desktop (both Mac), and neither worked. Here's the error I get:

Screen Shot 2020-02-20 at 9 43 34 AM

Are you on a Mac or PC?

@ValentineHerr, could you please try running this script to see if it knits correctly for you?

mcgregorian1 commented 4 years ago

I've been trying to run it on a pc. I'm not sure what computer Becky was using.

On Thu, Feb 20, 2020 at 9:45 AM Kristina Anderson-Teixeira < notifications@github.com> wrote:

I just tried it on both my laptop and desktop (both Mac), and neither worked. Here's the error I get:

[image: Screen Shot 2020-02-20 at 9 43 34 AM] https://user-images.githubusercontent.com/6355854/74945341-8ef05800-53c5-11ea-9c90-8cb81f1b75ed.png

Are you on a Mac or PC?

@ValentineHerr https://github.com/ValentineHerr, could you please try running this script https://github.com/SCBI-ForestGEO/McGregor_climate-sensitivity-variation/blob/master/manuscript/tables%26figures.Rmd to see if it knits correctly for you?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/SCBI-ForestGEO/McGregor_climate-sensitivity-variation/issues/75?email_source=notifications&email_token=AJNRBEIYV3DN4XTFO7BVIOLRD2JSDA5CNFSM4KWQLK6KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMOL45I#issuecomment-589086325, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJNRBEI4T3TPAMRXGAAML33RD2JSDANCNFSM4KWQLK6A .

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Ian McGregor

Ph.D. Student | Center for Geospatial Analytics

College of Natural Resources

Jordan Hall 4120 | Campus Box 7106

North Carolina State University

2800 Faucette Dr.

Raleigh, NC 27695 USA imcgreg@ncsu.edu | 714-864-1005 | geospatial.ncsu.edu

ValentineHerr commented 4 years ago

@ValentineHerr, could you please try running this script to see if it knits correctly for you?

It looks like if you remove 

, 
        escape=FALSE

on line 63 and 64 it works.

Let me know if that works for you too.

mcgregorian1 commented 4 years ago

When you remove that, though, did the symbol for TLP appear correctly in the table? I was under the impression escape=FALSE is necessary for that.

On Thu, Feb 20, 2020 at 11:12 AM Valentine Herrmann < notifications@github.com> wrote:

@ValentineHerr https://github.com/ValentineHerr, could you please try running this script https://github.com/SCBI-ForestGEO/McGregor_climate-sensitivity-variation/blob/master/manuscript/tables%26figures.Rmd to see if it knits correctly for you?

It looks like if you remove

, escape=FALSE

on line 63 and 64 it works.

Let me know if that works for you too.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/SCBI-ForestGEO/McGregor_climate-sensitivity-variation/issues/75?email_source=notifications&email_token=AJNRBEL4QEIB7YI25DAI3D3RD2TXZA5CNFSM4KWQLK6KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMO54HA#issuecomment-589159964, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJNRBEL3R3P3IXGQYVWM46TRD2TXZANCNFSM4KWQLK6A .

--

Ian McGregor

Ph.D. Student | Center for Geospatial Analytics

College of Natural Resources

Jordan Hall 4120 | Campus Box 7106

North Carolina State University

2800 Faucette Dr.

Raleigh, NC 27695 USA imcgreg@ncsu.edu | 714-864-1005 | geospatial.ncsu.edu

teixeirak commented 4 years ago

I just tried and it knit but the symbol in the table didn't have latex styling.

ValentineHerr commented 4 years ago

I'll look into this

mcgregorian1 commented 4 years ago

Becky is also confirming that when she tries to knit the whole script then table 2 is now giving the error, even tho when I made a separate Rmd only containing the table 2 code it knit and made the symbols perfectly.

On Thu, Feb 20, 2020 at 11:49 AM Valentine Herrmann < notifications@github.com> wrote:

I'll look into this

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Ian McGregor

Ph.D. Student | Center for Geospatial Analytics

College of Natural Resources

Jordan Hall 4120 | Campus Box 7106

North Carolina State University

2800 Faucette Dr.

Raleigh, NC 27695 USA imcgreg@ncsu.edu | 714-864-1005 | geospatial.ncsu.edu

teixeirak commented 4 years ago

Why not just make a separate pdf for this table? They'll all have to be appended to the main document anyway.

ValentineHerr commented 4 years ago

@mcgregorian1 add a backslash \ in fromt of "%" in the csv file of table2 and that will work.

mcgregorian1 commented 4 years ago

Yes Becky came to the same conclusion and I have confirmed that works. I can't believe it was as simple as that.

Thank you Valentine!

On Thu, Feb 20, 2020 at 12:08 PM Valentine Herrmann < notifications@github.com> wrote:

@mcgregorian1 https://github.com/mcgregorian1 add a backslash \ in fromt of "%" in the csv file of table2 and that will work.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/SCBI-ForestGEO/McGregor_climate-sensitivity-variation/issues/75?email_source=notifications&email_token=AJNRBEJONVTPASX7EHR7VXDRD22HBA5CNFSM4KWQLK6KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMPGRSA#issuecomment-589195464, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJNRBEO32IJVZJFFPOCIDNLRD22HBANCNFSM4KWQLK6A .

--

Ian McGregor

Ph.D. Student | Center for Geospatial Analytics

College of Natural Resources

Jordan Hall 4120 | Campus Box 7106

North Carolina State University

2800 Faucette Dr.

Raleigh, NC 27695 USA imcgreg@ncsu.edu | 714-864-1005 | geospatial.ncsu.edu

teixeirak commented 4 years ago

Yes, I also just tried it and pushed the changed file. HOORAY!!!! And thanks so much @ValentineHerr (and Becky)!

teixeirak commented 4 years ago

I tried and failed to repeat this success on Table 1. There are also symbols in the other tables that should be changed, also.

This doesn't need to be done before coauthor review. I"ll check the SI and then send it around.

mcgregorian1 commented 4 years ago

I tried and failed to repeat this success on Table 1. There are also symbols in the other tables that should be changed, also.

I'm not sure I understand what you're trying to do with Table 1. I was able to render the document fine as is (I added "\" before the "-" but it wasn't necessary)

teixeirak commented 4 years ago

It's not a big deal. I was just thinking of putting in variable symbols with latex, but its not needed. I just added variable symbols to all the other tables with no problem; not sure what's going on with Table 1.