Add methane support to COSORE

[bpbond]

This PR does the initial work of including CH4 in COSORE. Specifically:

• A one-time add_ch4() function to convert older data
• Changed field names in all already-incorporated datasets and the metadata file ( a8cfda1 )
• Changed all existing metadata files - basically COLUMNS.txt - to use new names ( 01c5291 )
• Code changes to handle new names ( 06c3b63 )
• Updated reporting ( eca4518 ) and vignette ( e53f587 )

Not everything is "feature-parity" between CO2 and CH4, but this gets us 90% of the way there I think.

@stephpenn1 Could you look through changes? Also cc @avnimalhotra and @dschristianson

Closes #181

[codecov-io]

Codecov Report

Merging #182 into master will increase coverage by 0.01%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #182      +/-   ##
==========================================
+ Coverage   97.86%   97.87%   +0.01%     
==========================================
  Files           8        8              
  Lines         749      754       +5     
==========================================
+ Hits          733      738       +5     
  Misses         16       16              

Impacted Files	Coverage Δ
R/utils.R	100.00% <ø> (ø)
R/parser.R	100.00% <100.00%> (ø)
R/qaqc.R	100.00% <100.00%> (ø)

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[bpbond]

Here is the metadata file now (showing relevant sections only):

Table_name	Field_name	Description	Class	Units	Required
data
data	CSR_DRY_CO2	Chamber CO~2~ concentration	numeric	ppmv	FALSE
data	CSR_DRY_CH4	Chamber CH~4~ concentration	numeric	ppbv	FALSE
data	CSR_CO2_AMB	Ambient CO~2~ concentration	numeric	ppmv	FALSE
data	CSR_COMMENTS	Comments	character		FALSE
data	CSR_CRVFIT_CO2	CO2 flux computation method ("Lin" or "Exp" for linear and exponential)	character		FALSE
data	CSR_CRVFIT_CH4	CH4 flux computation method ("Lin" or "Exp" for linear and exponential)	character		FALSE
data	CSR_ERROR	Error raised by instrument or during import	logical		FALSE
data	CSR_FLUX_CO2	Soil respiration flux	numeric	µmol CO~2~/m^2^/s	TRUE
data	CSR_FLUX_CH4	Methane flux (positive = to atmosphere)	numeric	nmol CH~4~/m^2^/s	FALSE
data	CSR_FLUX_SE_CO2	Standard error of soil respiration flux	numeric	µmol CO2/m^2^/s	FALSE
data	CSR_FLUX_SE_CH4	Standard error of soil methane flux	numeric	nmol CH~4~/m^2^/s	FALSE
data	CSR_LABEL	Port/chamber label	character		FALSE
data	CSR_NEE	Tower (not chamber) net ecosystem exchange	numeric	µmol CO~2~/m^2^/s	FALSE
data	CSR_PAR	Photosynthetically active radiation	numeric	µmol photons/m^2^/s	FALSE
data	CSR_PORT	Port/chamber number	numeric		TRUE
data	CSR_PRECIP	Precipitation	numeric	mm	FALSE
data	CSR_R2_CO2	CO2 flux computation R^2^	numeric	fraction	FALSE
data	CSR_R2_CH4	CH4 flux computation R^2^	numeric	fraction	FALSE
data	CSR_RECORD	Record number within file	numeric		FALSE
data	CSR_RH	Chamber relative humidity	numeric	%	FALSE
data	CSR_SMx	Volumetric soil moisture at x cm (other CSR_SMx fields follow same format)	numeric	m^3^/m^3^	FALSE
data	CSR_Tx	Temperature at x cm (other CSR_Tx fields follow same format)	numeric	°C	FALSE
data	CSR_TAIR	Ambient air temperature	numeric	°C	FALSE
data	CSR_TCHAMBER	Chamber temperature	numeric	°C	FALSE
data	CSR_TIMESTAMP_BEGIN	Timestamp of beginning of flux observation, written YYYY-MM-DD HH:MM:SS	POSIXct		TRUE
data	CSR_TIMESTAMP_END	Timestamp of end of flux observation, written YYYY-MM-DD HH:MM:SS	POSIXct		TRUE
data	CSR_WIND	Wind speed	numeric	m/s	FALSE
data	CSR_WTD	Water table depth, positive numbers are depth	numeric	cm	FALSE
description
ports
ports	CSR_PORT	Port (chamber) number; "0" means all ports	numeric		TRUE
ports	CSR_MSMT_VAR	Measurement variable: "Rs", "Rh", "Reco", or "NEE"	character		TRUE
ports	CSR_TREATMENT	Chamber treatment; default is "None"	character		TRUE
ports	CSR_AREA	Area of measurement chamber	numeric	cm^2^	FALSE
ports	CSR_DEPTH	Depth of collar insertion	numeric	cm	FALSE
ports	CSR_SPECIES	Comma-separated species list	character		FALSE
ports	CSR_SENSOR_DEPTHS	Comma-separated sensor depths	character	cm	FALSE
diagnostics	CSR_ASSUMED_MSMT_LENGTH	If no measurement length is provided this is set to assumed value	numeric	s	FALSE
diagnostics	CSR_BAD_TEMPERATURE	Number of observations removed for bad temperature values	numeric		TRUE
diagnostics	CSR_EXAMPLE_BAD_TIMESTAMPS	Example bad timestamps	character		FALSE
diagnostics	CSR_FLUX_HIGH_LIM_CO2	CO2 flux high bound; values above this are removed	numeric		TRUE
diagnostics	CSR_FLUX_LOW_LIM_CO2	CO2 flux low bound; values above this are removed	numeric		TRUE
diagnostics	CSR_FLUX_HIGH_LIM_CH4	CH4 flux high bound; values above this are removed	numeric		TRUE
diagnostics	CSR_FLUX_LOW_LIM_CH4	CH4 flux low bound; values above this are removed	numeric		TRUE
diagnostics	CSR_RECORDS	Records in final dataset	numeric		TRUE
diagnostics	CSR_RECORDS_REMOVED_ERR	Number of observations removed for error code	numeric		TRUE
diagnostics	CSR_RECORDS_REMOVED_NA	Number of observations removed for missing flux	numeric		TRUE
diagnostics	CSR_RECORDS_REMOVED_TIMESTAMP	Number of observations removed for bad timestamp	numeric		TRUE
diagnostics	CSR_REMOVED_HIGH_CO2	Number of observations removed for CO2 flux too high	numeric		TRUE
diagnostics	CSR_REMOVED_LOW_CO2	Number of observations removed for CO2 flux too low	numeric		TRUE
diagnostics	CSR_REMOVED_HIGH_CH4	Number of observations removed for CH4 flux too high	numeric		TRUE
diagnostics	CSR_REMOVED_LOW_CH4	Number of observations removed for CH4 flux too low	numeric		TRUE
diagnostics	CSR_TIME_BEGIN	Year and month of first observation in dataset	character		FALSE
diagnostics	CSR_TIME_END	Year and month of last observation in dataset	character		FALSE