update with main fork#2
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ktoddbrown merged 267 commits intoDec 7, 2018
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fix doi checks
move Treat 2016 processing to dev branch
spelling fix for He
… from SoilOrder_LEN_USDA_original, BulkDensity_original, and pct_C_original. Added USDA as pro_soil_taxon_sys. Added Yujie He as contact_name
Minor updates to read_YujieHe2016.R function
QAQC now provides a list of rows containing mismatched naming conventions between tabs
Added 3 to the row # of mismatched name code from previous commits to reflect the actual row numbers found in the excel sheet, instead of the number of the line in the R object (I think I used the nomenclature right here.)
Added pro_elevation, flx_name, ist_name, and inc_name fields to template and info files. All non-required. May want to require the name fields in the future.
Forgot to update template_version field in previous commit
Fixed pro_name error in incubation QAQC
Fixed lyr_name mismatch error in incubation QAQC
Updated incubation studies to add "inc_name" field and remove dummy layers created for reps, if present. Changed longitude to negative in Marin-Spiotta_2008 and Crow_2015. Updated lyr_soc in Binkley_1999 w/ correct units.
Commented out code running QAQC function to allow compile function to execute successfully. Biggest problem is datasets with "israd" entered for doi, I believe. Ultimately this should be handled with additional code but we need a version of this that works today. Also, I thought I had previously committed these changes but I don't see it on the page. Sorry if I double-committed...
lyr_fraction_modern upper limit removed to allow for "Inf" as proxy for "modern"
Adjusted layers to accommodate inc_name fields and deleted lyr_non_bulk
Added all the "ready for github" files, and updated the ones in the repository to pass the dev branch QAQC Need to replace ISRaD_summary.csv and ISRaD_flat.csv
Generated w/ slightly modified version of flatten.r (no need to remove header rows now)
Changed frc_frc_modern to frc_fraction_modern for consistency
changed frc_frc_modern field names to frc_fraction_modern
corrected typo causing the reports function to fail.
Additional soil order translations added based on unique values of profile$pro_soil_taxon as of 12/3/18
Cleaned up formatting
Adds new report options including "count_data" and "site_map" to report function
Edit of install_github command
… error in Clark_2002
Add `frc_data` report to summarize the number of observations of both frc_scheme and frc_property
Adding r scripts for individual report types in order to clean up and simplify the reports function.
Individual report type code is now broken out into separate files.
changed format slightly
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