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FoRTExperiment / fortedata

FoRTE project data
https://fortexperiment.github.io/fortedata/
Creative Commons Attribution 4.0 International
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Aboveground data update with a few other fixes #81

Closed mgrigri1 closed 3 years ago

mgrigri1 commented 3 years ago

I've added all the aboveground data. It's all tidy and ready to go, and I made functions that pull each data set. They look good, but don't work yet. Error occurs when trying to find the data file with read_csv_file(). Note sure what's going on there. I've added all the data (from google drive) into the inst/extdata/ folder, but the function can't find them...In other news, this is my first pull request so apologies if I'm doing something wrong here!

codecov-io commented 3 years ago

Codecov Report

Merging #81 (f652de5) into master (319ca2c) will increase coverage by 2.32%. The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #81      +/-   ##
==========================================
+ Coverage   75.42%   77.74%   +2.32%     
==========================================
  Files          11       14       +3     
  Lines         350      382      +32     
==========================================
+ Hits          264      297      +33     
+ Misses         86       85       -1
Impacted Files Coverage Δ
R/fd_belowground.R 100.00% <ø> (ø)
R/fd_litter.R 100.00% <ø> (ø)
R/fd_remote_sensing.R 59.52% <ø> (ø)
R/fd_inventory.R 58.82% <100.00%> (-1.18%) :arrow_down:
R/fd_leaf_physiology.R 100.00% <100.00%> (ø)
R/fd_seedling_sapling.R 100.00% <100.00%> (ø)
R/fd_subcanopy_density.R 100.00% <100.00%> (ø)
R/fd_subcanopy_diameter.R 100.00% <100.00%> (ø)
R/utils.R 46.15% <100.00%> (ø)
... and 3 more

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bpbond commented 3 years ago

👏 @mgrigri1 !

If it's OK I'm going to push some fixes here.

bpbond commented 3 years ago

I have cleaned up the documentation a bit, renamed a subplot column to subplot_id for consistency, and added some basic tests.

Two large problems remain:

  1. @mgrigri1 Can you open up inst/extdata/forte_table_metadata.csv and add field descriptions, including units, for your new tables? If you have questions about how to do this lmk.
  2. @atkinsjeff The package tests are generating huge numbers of warnings, it looks like on some file read. Do you know about this? It needs to be fixed; lmk if you have time, otherwise I will.
mgrigri1 commented 3 years ago

Alright @bpbond, I edited the 'inst/extdata/forte_table_metadata.csv' , lmk what else I can/should do

bpbond commented 3 years ago

@mgrigri1 The fd_seedling_sapling_xxxx.csv files have the word "new" in some entries of the height_total_cm field. Why? Does it need to be there? It's causing what should be a numeric column to become character, which isn't great.

mgrigri1 commented 3 years ago

@bpbond Alrighty, I made the fix to the data files and uploaded the new files. Should be good on that issue.

bpbond commented 3 years ago

Thanks Max. I'm going to tackle the crazy number of warnings in the test suite; makes it impossible to see real problems.

bpbond commented 3 years ago

@atkinsjeff @mgrigri1 fortedata now passes all tests, as well as R CMD CHECK, cleanly on my machine.

atkinsjeff commented 3 years ago

merging in Max's changes