ESSD 4 - Leaf phys vignette

[atkinsjeff]

Leaf physiology vignette needs to be ship-shaped

[lisahaber]

@atkinsjeff Let me know if I'm missing anything from the To Do list below for this vignette.

**NOTE: It looks like the fd_photosynthesis() data set includes ONLY subcanopy measurements from 2018, whereas fd_leaf_spectrometry() includes ONLY canopy measurements from 2018. Not necessarily an issue but requires two distinct methodology sections, for sure.

TO DO: --fleshed out/distinct methods sections for fd_photosynthesis() and fd_leaf_spectrometry() --revised boxplot figures for each data set --data availability figures for each data set --references

[lisahaber]

@atkinsjeff Also noting that the fd_leaf_spectrometry() dataframe still returns as just the first 8 rows

[atkinsjeff]

reinstall the package from github

On Wed, Dec 9, 2020 at 11:36 AM Lisa T. Haber notifications@github.com wrote:

@atkinsjeff https://github.com/atkinsjeff Also noting that the fd_leaf_spectrometry() dataframe still returns as just the first 8 rows

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/FoRTExperiment/fortedata/issues/64#issuecomment-741892129, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB7XVVKPJ4L76IKVZ6LJ5HLST6RSJANCNFSM4USKNV7Q .

-- Jeff Atkins, PhD Post-Doctoral Fellow Department of Biology Virginia Commonwealth University atkinsjeff.github.io he/his/him

[lisahaber]

Duh. Geez.

[atkinsjeff]

😊

Jeff Atkins, Ph.D Department of Biology Virginia Commonwealth University

On Wed, Dec 9, 2020, 12:00 Lisa T. Haber notifications@github.com wrote:

Duh. Geez.

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[lisahaber]

@atkinsjeff Ok a couple of (annoying) issues to work out in fd_leaf_spectrometry():

1. Looks like the subplot_id column has "O" rather than "0" (letter rather than number zero) in the id name. Probably originally my fault.

2. The current "tree_id" column is still not right and I think we want to correct it with the later-appended (2019) tree ID's so that subsequent years' data can be easily compared to 2018's. Here's what to do:

--Use the attached look up table (ignore previously sent ones, use this one). --final column ("actual_tree_id") is the value we want to replace with. --To match these, you're going to need to concatenate the (corrected, with zeros) subplot_id + species + tree_id values in the current fd_leaf_spectrometry() data set. Example: subplot_id: D01E species: ACRU tree_id: CAN01 string: D01E_ACRU_CAN01 -- > use look up table --> actual tree id = 1EA1

Again, I apologize for the clusterf@#$ and let me know if any of this needs clarification. Hopefully it's not too big a pain in the butt to fix. fdleafspec_treeID_lookup_table.xlsx

[atkinsjeff]

No this is good. I had no idea the workflow or the objective that was being alluded to with the tree is jam.

Jeff Atkins, Ph.D Department of Biology Virginia Commonwealth University

On Wed, Dec 9, 2020, 12:19 Lisa T. Haber notifications@github.com wrote:

@atkinsjeff https://github.com/atkinsjeff Ok a couple of (annoying) issues to work out in fd_leaf_spectrometry():

1.

Looks like the subplot_id column has "O" rather than "0" (letter rather than number zero) in the id name. Probably originally my fault. 2.

The current "tree_id" column is still not right and I think we want to correct it with the later-appended (2019) tree ID's so that subsequent years' data can be easily compared to 2018's. Here's what to do:

--Use the attached look up table (ignore previously sent ones, use this one). --final column ("actual_tree_id") is the value we want to replace with. --To match these, you're going to need to concatenate the (corrected, with zeros) subplot_id + species + tree_id values in the current fd_leaf_spectrometry() data set. Example: subplot_id: D01E species: ACRU tree_id: CAN01 string: D01E_ACRU_CAN01 -- > use look up table --> actual tree id = 1EA1

Again, I apologize for the clusterf@#$ and let me know if any of this needs clarification. Hopefully it's not too big a pain in the butt to fix. fdleafspec_treeID_lookup_table.xlsx https://github.com/FoRTExperiment/fortedata/files/5667542/fdleafspec_treeID_lookup_table.xlsx

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/FoRTExperiment/fortedata/issues/64#issuecomment-741918215, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB7XVVJFWXYQAJCDRGB6NVDST6WSPANCNFSM4USKNV7Q .

[lisahaber]

@atkinsjeff fd_leaf_spectrometry() missing disturbance severity and treatment. BUTTTT, because these measurements were taken from the Girdling 2.0 group, the treatment for ALL "subplots" here should be Top-down. So maybe we should leave that off, since it's a different sub-experiment?

[lisahaber]

Two more questions @atkinsjeff whenever you get to them, not urgent:

(1) How do we add images to vignettes using paths that won't break when we push changes? Looks like the pictures in other vignettes are sourced from github but I only have mine on my local

(2) Did you cut and paste your references from a manuscript, or format them another way?

[atkinsjeff]

1) @kdorheim taught me this trick, but post the image into a comment on here and then copy the URL

2) I copied refs via Google Scholar using APA style as it is the one most similar to what a lot of journals in science do.

[lisahaber]

[lisahaber]

[lisahaber]

[atkinsjeff]

@lisahaber looks good. I am just updating w/ lower res photos