# derived data log
2020-04-10
  - created a summary file "OakRidge_CO2_fluxes_summary_2020-04-09.xlsx" for Oak Ridge CO2 flux data
  - copied each set of CO2 concentrations from 'CO2_FLUXES' sheet of "Incubations_August_2004_samples.xlsx" onto sheet 'timeSeries' of new file
  - calculated mass of CO2 from LiCor data in raw file using PV=nRT
  - dry soil mass data on sheet 'finalData' of new file came from "Incubations_August_2004_samples.xlsx" cell refs 'SUMMARY_ALL_DATA!H30:H31'

2020-04-13
  - renamed summary file "OakRidge_CO2_fluxes_summary_2020-04-09.xlsx" to "co2Flux_ornl_sum_2020-04-13.xlsx" using new convention: dataType_source_category_YYYY-MM-DD
  - updated 'meta' sheet with dry soil mass source
  - may want to change absolute values to links to preserve sources of copied data, but then again, I really dislike Excel files with links to external files, so maybe not...

2020-04-20
  - creating single excel files from previous "master" data file (arc_inc_IDs.xlsx)
  - new .xlsx files will consist of a metadata sheet, the original data, and the transformed data in a .csv-friendly format

2020-04-21
  - major updates in readmes and .csv files
  - details noted in readmes
  - completed Rmd section for plotting CO2 curves, using new data structure and moving some of the data wrangling to R

2020-04-22
  - goal for the day is to recreate as many of the key manuscript figures as possible with the new code and new file system
  - first task is to create folders/transparent csv files for iso data
  - only made READMEs for 14C files, as not doing much with 13C data at this point
  - created script for bulk ingest of Jena AMS results
  - progress on cleaned Rmd file for data analysis

2020-04-24
  - goal for the day is to recreate as many of the key manuscript figures as possible with the new code and new file system!
  - first need to set up a data frame in a "tidy" format, e.g. each obsv in a unique row
  - still need to make READMEs for the 13C data
  - would be nice to eventually add some tests...
  - updated error in "Period" col in rewetting raw data summary and corresponding .csv files
  - updated error in cmtv time cols in all raw flux data summary sheets and corresponding .csv files
  - added more 14C data that I had missed initially

2020-04-26
  - made a lot of progress on Rmd script
  - still need to wrangle round 1 14C data (basically just create a template for merging with raw data)
  - plots to make:
    - 1:1 of treatment/control for all data, bracketed by per mille "confidence lines"
    - multiple time point constraint conceptual figure
    - mean difference +/- 95%CI by time archived
  - general issues:
    - how to make figure captions work in pdf output? include special characters?
    - figure formatting in pdf output

2020-04-28
  - working on ingesting data from external samples, i.e. experiment 3 on storage duration effects (very time consuming)
  - not sure how best to include it in the data analysis work flow, as the data are in very different "shape"
  - current approach is to make a summary sheet with all possible info in the "derived" data directory, while copying source files to the "external" data directory
  - seem to be missing some data, e.g. fluxes for Sue's data
