biogas package

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## DETAILED LOG ########################
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13 November 2019 and earlier SDH and NL
Version 1.22

calcBgVol.R, calcBgMan.R
Additional development and name changes from cumBg.

calcBgGD.R
Additional improvement of function and name change from cumBgGD.

18 August 2019 and earlier NL and SDH
Version 1.17

cumBgVol.R
New function for volumetric data only.

cumBgDataPrep.R
New function for preparing cumBg* data.

13 June 2019 SDH
Version 1.16.5

summBg.R
Pass when.min to subset call. Was omitted. 

12 June 2019 SDH
Vresion 1.16.3

cumBgGD.R
Add code for vol.hs and temp.init to be used for headspace correction.

5 June 2019 SDH
Version 1.16.2

summBg.R
Fix bugs in when = 'total', remove 'VDI2016' option and automatic 25 d minimum
(now must be set through when.min).

summBg.R
Correct when.min so it actually returns BMP from minimum time, not just
changes time.

29 May 2019 SDH
Version 1.16

gasDens.R, GDComp.R, cumBgGD.R
New functions

29 April 2019 SDH
Version 1.15

cumBg.R
Switch to new manometric calculations based on discussion with Pierre B
(INSA).

10 April 2019 SDH
Version 1.14.1

cumBg.R
Add [1] for dealing with legnth 2 logical results in && comparisons.

28 March 2019 SDH
Version 1.14.0

summBg.R
Add recursive loop for multiple-element when argument.
Add when.min argument.

28 March 2019 SDH
Version 1.13.0

cumBg.R
Add quiet argument to suppress messages.

20 March 2019 SDH
Version 1.12.0

summBg.R
Can handle vol.name with length > 1, i.e., multiple response variables in the
same call.

More flexible handling of multiple when elements, e.g., 
when = list(20, "1p3d").

New when.min argument for use in combination with relative durations.

1 March 2019 SDH
Version 1.11.5

cumBg.R
Add rh.resid argument to override the calculation of residual relative
humidity if desired (e.g., for comparison).

14 Feb 2019 SDH
Version 1.11.4

summBg.R summBg.Rd
Add option for multiple sets/experiments/methods, etc. by using a list of data
frames for vol argument.

12 Jan 2019 SDH
Version 1.11.3

cumBg.R
Fixes. Handles NAs in empty.name column now. Switch to interval data for
calculations with empty.name (mixed cum/interval) because composition is interval.


08 Jan 2019 SDH
Version 1.11.2

cumBg.R, cumBg.Rd
Add empty.name argument for mixed cumulative/interval volumetric data.

24 Nov 2018 SDH
Version 1.11.1

summBg.Rd
Add description of optional output.

summBg.R
Change name of vol.mi.rsd to rsd.inoc for output with show.obs.

cumBg.R
Fix need for comp with data.struct = longcombo even though it wasn't used. Fix
related error with use of vol instead of mass object in grav code.

21 and 22 June 2018 Sasha D. Hafner
Version 1.11.0

summBg.R
Added rate.crit argument for VDI 2016 gross 1% etc. criteria.

16 May 2018 Sasha D. Hafner
version 1.10.3

biogas-package.Rd
Deleted

startup.R
Deleted

2 May 2018 Sasha D. hafner
Version 1.10.2

summBg.R
Fixed pdwhen if statement so comparison length > 1 warning (soon error) is
gone. Response to email form Kurt Hornik.

20 April 2018 Sasha D. hafner
Version 1.10.1

summBg.R
Fixed bug that threw error after selecting latest pd time for replicates if a
single replicate didn't extend far enough. 

2 March 2018 Sasha D. Hafner
Version 1.10.1

summBg.R
When pd criteria are not met, latest times are selected and returned with no
error. Instead, warning is given and new attribute rate.not.met is set to bottle
id values that do not meet criteria.

5 Feb 2018 Sasha D. Hafner
Version 1.10.0

planBMP.R, planBMP.Rd
New function.


25 Jan 2018 Sasha D. Hafner
Version 1.9.3

summBg.R
Fixed some checks of when argument so comparison length > 1 warning is gone.
Did this in response to message from Tomas K. Built and checked by going
through biogas-Ex.Rout.

10 Jan 2018 Sasha D. Hafner
Version 1.9.2

summBg.R
Changes to error propagation so it is based on standard error and not standard
deviation now. Input VS mass variability now must be standard error. Function
now works for variable replication.

8 Jan 2018 Sasha D. Hafner
Version 1.9.1

summBg.R
Changed error propagation for sd1 and sd2 slightly--using correct approach to
calculate mean of multiple replicates now instead of simple mean. Effect in
most cases will be in perhaps 4th digit.


3 Jan 2018 Sasha D. Hafner
Version 1.9.0

Vignettes
Removed mhchem package reference and use of \ce{} (which means some ugly stuff
now) because of problem with r-release-osx-x86_64. 

summBg.R
Added when argument warning and override when show.rates = TRUE so when no 
longer matters.

31 Dec 2017 Sasha D. Hafner
Version 1.8.3

summBg.R
Now summ1 is sorted by id and time before being returned when show.rates =
TRUE.

19 Dec 2017 Sasha D. Hafner
Version 1.8.3

summBg.R
Replaced when = '1p' etc. with more flexible approach, could be '1p3d' 0.5p2d'
etc.

13 Dec 2017 Sasha D. Hafner
Version 1.8.2

summBg.R
Changed error propagation for substrate VS

constants.R
Changed formula for protein to ADM1 version.

28 Nov 2017 Sasha D. Hafner
Version 1.8.2

stdVol.R and cumBg.R
Added automatic conversion of standard conditions if unspecified

unitConvert.R
Added mbar

22 Nov 2017 Sasha D. Hafner
Version 1.8.2

constants.R
Added ash = "NaCl"

checkArgClassValue
Added any() call so objects with multiple classes check correctly.
Added with data tables in mind.
Then undid this change because data tables do not work for other checks in
summBg() at least.

17 Nov 2017 Sasha D. Hafner
Version 1.8.2

summBg.R
Adding to show.more output

31 Oct 2017 Sasha D. Hafner
Version 1.8.2

summBg.R
Added show.more argument for additional information.


22 October 2017 Sasha D. Hafner
Version 1.8.2

summBg.R
Added quiet argument to suppress messages.

25 September 2017 Sasha D. Hafner
Version 1.8.2

summBg.R
Added show.rates argument to do what show.obs did when when argument was 
when = '1p',  which was to return data frame with all obs and rates.
Now it is possible to use show.obs with when = '1p'

23 August 2017 Sasha D. Hafner
Version 1.8.2

predBg.R
Finally fixed error in reactionc option that dropped substrate. Fixed by
adding drop = FALSE to indexing operation around line 166.

11 August 2017 Sasha D. Hafner
Version 1.8.1

Removed two LaTeX style files from vignettes directory (had been added in 
v1.8.0) and removed use of geometry and siunitx packages in both vignettes.

9 August 2017 Sasha D. Hafner
Version 1.8.0

startup.R
Updated email address


7 April 2017 Sasha D. Hafner
Version 1.7.2

cumBg.Rd
Added details for pres argument. Can be character as well as numeric, but must
be absolute pressure.


10 Mar 2017 Sasha D. Hafner
Version 1.7.2

calcCOD.R
Major bug in code (assumed readFormula() was vectorized when it wasn't) caused
nonsense COD' values for input with length > 1. Put all calcs in a loop. 

9 Mar 2017 Sasha D. Hafner
Version 1.7.1

cumBg.R
Added exception to error for missing dat.name for wide data. Now NAs are
dropped with warning.

Added check.names = FALSE on data.frame() calls for reshaping from wide to
long and elsewhere to avoid problems with poor OBA names

6 Mar 2017 Sasha D. Hafner
Version 1.7.1

summBg.R
Added 0.5p option. Just extension of 1p option but with cutoff of 0.5%.

28 Feb 2017 Sasha D. Hafner
Version 1.7.1

cumBg.R
Added exception for check for missing values in dat.name column when data are
cumulative. And below, drop missing values in this case. Not tested.

25 Feb 2017 Sasha D. Hafner
Version 1.7.1

summBg.R
Small change for clarity in 1p code. No expected effect on calculations.

24 Feb 2017 Sasha D. Hafner
Version 1.7.0

NEWS and DESCRIPTION
Updated for submission to CRAN.

*cumBg.R
Column name "time" was used in data frame t0 temporarily in two places.
Replaced with "tt" to try to avoid check warning (but was unrelated).

Fixed bug line 139 where time was used as a data frame name instead of dat.

23 Feb 2017 Sasha D. Hafner
Version 1.6.3

cumBg.R
Minor changes to returned value for gca method.

22 Feb 2017 Sasha D. Hafner
Version 1.6.2

cumBg.R
Continuing with gca method. Changed input units to micromoles. Added if
constructs to stop adding xCH4 column. Added sorting at end.

20 Feb 2017 Sasha D. Hafner
Version 1.6.2

summBg.R
Fixed problem that showed up with setup had a column named "time". Now only
merge inoculum mass column with summ.inoc instead of complete setup data
frame.


16 Feb 2017 Sasha D. Hafner
Version 1.6.2

predBg.R
Reduced digits in mcomp output formula (also used for calculations) from 6 to
4.

13 Feb 2017 Sasha D. Hafner
Version 1.6.2

cumBg.R
Fixed check from 9 Feb for id.name that was causing an "undefined column"
error. Now only checked if id.name is in dat (was problem for wide data where
id.name is not present in dat).

9 Feb 2017 Sasha D. Hafner
Version 1.6.2

cumBg.R
Added checks for missing observations in id.name, dat.name, and time.name
columns.

For calculation of residual relative humidity for manometric method, values >
1.0 were possible when residual pressure was > initial pressure. Set to
maximum of 1.0.

1-4 Feb 2017 Sasha D. Hafner
Version 1.6.2

cumBg.R
Finished first draft of gca method.

summBg.R
Notes on 1p (confirmed it makes sense)

27 Jan 2017 Sasha D. Hafner
Version 1.6.2

checkArgClassValue.R
Added case.sens argument, default = TRUE

cumBg.R
Added method for dat.type = 'gca'. Needs refinement.

23 Jan 2017 Sasha D. Hafner
Version 1.6.2

summBg.R
Again 1p option for when. It will now return first observation < 1% for three
days not three + (replaced i3 with i3 - 1 in index).

21 Jan 2017 Sasha D. Hafner
Version 1.6.2

summBg.R
Now drops NA values in vol.name column so when = 'end' will work when 
there are NAs at the end.

Added warning for case when inoculum-only times do not go as far as other
times. Problem for when = 'end'.

7 Jan 2017 Sasha D. Hafner
Version 1.6.2

summBg.R
Corrected bug in 1p option. Now it behaves as described below. Tested with
Konrad Koch's data.

1 Jan 2017 Sasha D. Hafner
Vesion 1.6.1

summBg.R
Changed 1p option again.
Now selected time must be at least three days from first time < 1%/d, and all
following rates must be < 1%/d.

16 Dec 2016 Sasha D. Hafner
Version 1.6.1

cumBg.R
Fixed bug in getting vol columnes for data.struct = 'wide'. I had used nrow()
instead of ncol().

15-16 Dec 2016 Sasha D. Hafner
Version 1.6.0

cumBg.R 
Removed hardcoded 'temp.init' used in pressure method.

summBg.R
Changes in when = '1p' option to fix bugs. Previously when time for
bottles with same description differed, the time was changed to the max but
the response variable was not changed. Now max time is selected first and
summ1 data frame is then made. When a bottle doesn't have a time equal to the
time selected for its description, the next later time is used. This should
show up in the resulting output.

Also added relative rates to show.obs = TRUE output and moved show.obs
return() call so it can be used to see rates without getting an error for
rates > 1%.

Changed argument order so inoc.name and inoc.m.name are next to each other.

s3*.Rda and s3*.Rd
Changed 'time' to 'time.d', 'vol' to 'vol.d'. Required changes in at least one
other help file.

12 Dec 2016 Sasha D. Hafner
Version 1.5.1

summBg.R
Now NA in inoculum-only bottle volumes will be dropped before calculation of
means. Updated warning message.

8 Dec 2016 Sasha D. Hafner
Version 1.5.1

cumBg.R
Added na.omit() to xCH4 check.

summBg.R
Changed default argument for m.inoc.name to NULL. Was previously 'minoc'. How
did this work when user didn't want to subtract inoculum contribution?

3 Dec 2016 Sasha D. Hafner
Version 1.5.1

cumBg.R
Replaced check of xCH4 values > 1 with a correction (division by 100) in this
case, along with a warning.

1 Dec 2016 Sasha D. Hafner 
Version 1.5.1

cumBg.R
Fixed bug that always used 'id' for new id.name column when starting with wide
data. Now uses id.name argument.

Added code to remove NAs present to the latest time for each bottle. Designed
for wide data where measurements end for some bottles earlier than others.

Fixed checks for missing columns in dat for long, longcombo, and wide.

summBg.R
Added check for inoc.m.name column in setup data frame.

Added check for NAs in (interpolated) inoculum-only volumes.

Now when there is only one inoculum-only bottle, sd for inoculum contribution
is set to 0, which allows calculation of BMP sd (was NA before).


28 Nov 2016 Sasha D. Hafner 
Version 1.5.1

cumBg.R
Added new 'dry' argument for so standardized (dry) volumetric data can be used
(thinking of AMPTS output).

26 Nov 2016 Sasha D. Hafner 
Version 1.5.1

summBg.R
Improved when = '1p' option. Criterion is now: rate <1% for observation and
all following observations, and observation is >= 3 days from end of
incubation.

23 Nov 2016 Sasha D. Hafner 
Version 1.5.1

cumBg.R
Added warning for case when composition data were not provided.

Fixed bug in skipping interpolation for a single comp observation for mass
data written when options were only mass and vol around line 229.

21 Nov 2016 Sasha D. Hafner 
Version 1.5.1

cumBg.Rd
Clarified pres.init gauge/absolute pressure.

cumBg.R
Fixed error in pres and temp arguments in mass2vol() call for times 1 and 2.
Row index had been omitted. 

Function now expects pres.init as gauge pressure if absolute = FALSE. 
Previously pres.init always had to be as absolute pressure.

19 Nov 2016 Sasha D. Hafner 
Version 1.5.1

cumBg.Rd
Clarified how absolute argument applies to pres.resid (applies) and pres.amb
(doesn't).

4 Nov 2016 - 16 Nov 2016 Sasha D. Hafner and Charlotte Rennuit
Version 1.5.0

summBg.R
Changed name of new when option to '1p'. Fixed bug for when = '1p' option. Now
function throws a useful error when a bottle does not have any rates that meet
the criterion.

3 Nov 2016 Sasha D. Hafner
Version 1.5.0

summBg.R
Added when = 'r1%c' for automatic selection of times when rate of CH4
production is <= 1% of cumulative value.

cumBg.R
Added difftime as a class for time.name column

2 Nov 2016 Sasha D. Hafner
Version 1.5.0

cumBg.R
Changed name of data.format to data.struct (because it describes data's
structure not format). For 'longcombo' structure, added code to handle missing
values in comp.name column. Previously comp interpolation section was skipped
for longcombo, but now, if there are missing comp.name values, dat is split
into dat and comp and data.struct is changed to 'long' so interpolation
section is used. Added new pres.amb argument to (correctly) calculate absolute
pressure from gauge values. Previously, residual pressure was incorrectly
added. Absolute residual pressure is now also calculated. For all data
structures missing comp values are now dropped before interpolation.

30 Oct 2016 Sasha D. Hafner
Version 1.4.2

summBg.R
Added new argument norm.sd.name and error propagation to normalization based
on uncertainty in VS mass.

25 Oct 2016 Sasha D. Hafner
Version 1.4.2

cumBg.R
Dropped first.col.dat and first.col.comp arguments, instead just using
dat.name and comp.name arguments.

24 Oct 2016 Sasha D. Hafner
Version 1.4.2

cumBg.R
Added data format flexibility. New argument for data format: data.format
(options 'long' (default), 'wide', 'longcombo'). For 'wide' option, two other
arguments are used: first.col.dat and first.col.comp to indicate where the dat
and composition data start in the dat and comp data frames. Note that checks
for input errors need to be updated.

4-10 Oct 2016 Sasha D. Hafner
Version 1.4.1

cumBg.R
Added check for missing observations in comp data frame. Now will throw useful
error message. Possibly a few other changes.

16-18 August 2016 Sasha D. Hafner
Version 1.4.1

cumBg.R
For subtraction of initial headspace gas in manometric method when interval =
FALSE, changed temp argument to temp.init. Also moved code for *.prev columns
and (separately) rh.resid into if (interval) block because they are not used
for interval = FALSE.  The pres.resid column is still added. 

watVap.R
Switched to a new equation from Alduchov and Eskridge J Applied Meteorology
35: 601-609 . Changes in standardized volume becaue of change will be very
small (<0.07%)

06 June 2016 Sasha D. Hafner
Version 1.4.1

stdVol.Rd
Added pres.std to example (had been using 1 kPa as standard--holdover from
early version of code) and deleted an example.

31 May 2016 Sasha D. Hafner
Version 1.4.1

cumBg.R
Started adding unit.mass and unit.vol. Will need to add to others and update
unitConvert.R.

24 May 2016 Sasha D. Hafner
Version 1.4.0

DESCRIPTION
Changed version number for submission to CRAN. Slightly changed description to
include manometric method. 

strawPresure.rda, strawMass.rda, strawSetup.rda, strawComp.rda
New example data files

strawPresure.Rd, strawMass.Rd, strawSetup.Rd, strawComp.Rd
New help files

22-24 May 2016 Sasha D. Hafner
Version 1.3.2

*test_HighLevelFunctions.R
Around lines 44 and 69, changed check of "cumulative sum and rates are corrrectly
calculated with default values" and  "cumulative sum, rates and methane volume
are corrrectly calculated using one value for comp". Replaced "0" for first
observation (added t0 obs) of vol in output with "NA". cumBg() now returns NA
(and should, I think, since there was no measurement). Added simple test of
cumBg() with pressure data (manometric approach).

*summBg.R 
Fixed problem with new check of 'when' argument.

*cumBg.R
Fixed error in addition of temp.prev to dat data frame for pres approach (was
repeating temp.init, fixed with rep() call). Changed merge() with headspace
data frame so it only bring two necessary columns. 

18-20 May 2016 Sasha D. Hafner
Version 1.3.1

*cumBg.R
Removed pres.resid.name argument. Now pres.resid is either length-one numeric
or a column name. pres.resid is from the dat data frame. Fixed error where
previous residual headspace pressure and previous relative humidity were added
to dat. Added temp.init to dat and then stdVol() calls for dat.type = 'pres'.
These calls now correctly use initial headspace temperature (and so temp.init)
is required for dat.type = 'pres'. Made checks for required arguments for
dat.type = 'pres'. Made changes (corrections) for cmethod = 'total', which can
be applied for dat.type = 'vol' or 'pres' (standardized headspace volume!).
Moved position of cmethod correction (addition of headspace CH4--this is all
cmethod = 'total' does). Headspace CH4 is now added to cvCH4 (was vCH4) for
cmethod = 'total, and vCH4 is calculated from cvCH4 in this case, and also
when interval = FALSE.

17 May 2016 Sasha D. Hafner
Version 1.3.1

*cumBg.R
Switch gauge argument to absolute (and changed code to reflect it). pres.resid
and pres.init are used now (pres.resid replaces pres.atm).

*summBg.R
Added check: error thrown when 'when' argument > all times in vol data frame.
Previously function returned NA for means and sd.

14 May 2016 Sasha D. Hafner
Version 1.3.1

*stdVol.R
Added warn argument so warnings can be avoided.

*cumBg.R
Significant rewrite related to dat.type = 'pres'. pres2vol() is not needed and 
no longer called. Instead stdVol() is used to go from pressure to volume (and
standardize in one call). Eliminated *.orig objects added for 'pres' option.
Atmospheric pressure is required for 'pres' (otherwise residual headspace
volume cannot be calculated). Few days before, added gauge argument. Function
works with absolute pressures internally, and will calculate if gauge = TRUE.

12 May 2016 Sasha D. Hafner
Version 1.3.1

*checkArgClassValue.R
Fixed formatting of messages on length > 1 classes using paste(..., collapse).

*interp.R
Added 'difftime' as class option for times argument.

25 April 2016 Sasha D. Hafner
Version 1.3.1

*cumBg.R
Added dat.type = "pres" option. Required changes in location of merge with headspace
data (moved up), conversion of pressures to volume (new function pres2vol()), and 
different code for stdVol() (because RH != 1). 

14 April 2016 Sasha D. Hafner
Version 1.3.0

*test_HighLevelFunctions.R
Added sort = FALSE to summBg() call at end of "summBg correctly calculates
means" test so order of two data frames matches.

*summBg.R
Fixed problem with attempt at sorting summ2 when show.obs = TRUE and mean etc.
columns are not present. Fixed reference to id.name in internal summ.inoc data
frame, which has hard-wired column name 'id'. Added as.character to correct
sorting by original description order. Added correct rownames to result.

10 April 2016 Sasha D. Hafner
Version 1.3.0

*cumBg.R
Added NULL to possible argument class for comp.name.

4 April 2016 Sasha D. Hafner
Version 1.3.0

*DESCRIPTION
Updated

*biogas_quick_start.Rnw
Removed a problematic \Sexpr{}.

#readFormula.R
Fixed problems with decimal n (and probably more general problems as well).
Included fix of scipen option.

2 & 3 April 2016 Sasha D. Hafner
Version 1.2.3

*readFormula.R
Fixed handling of formulas with ()n syntax.

*constants.R
Updated standard atomic weights. Now all elements with values from CIAAW are
included.

*predBg.R
Added value = "reactiont" option. Function returns a text reaction.

*predBg.Rd
Added documentation of value = "reactionn" and "reactionc".


19 February 2016 Sasha D. Hafner
Verion 1.2.3

*summBg.Rd
Updated file based on recent changes to R code.

*summBg.R
Removed nonsensical error check on dropping norm.name. Removed conditional
assignment of when to 'end' when it was NULL. Added a sort argument and
associated code to use descrip.name order from setup when sort = FALSE.
Removed code for one.obs option for when. With 'meas' option it makes no
sense (and was never documented).

21 March 2016 Sasha D. Hafner
Version 1.2.2

*preBg.R
Fixed argument check for mcomp.

10 February 2016 Sasha D. Hafner
Version 1.2.2

*interp.R
Added argument check for y.out

*summBg.R
Changed code significantly to allow for new when argument value 'meas', and to
remove loop that used when argument as index variable. Values in time.name 
column have now replaced when argument value in most cases.

16 December 2015 Sasha D. Hafner
Version 1.2.2
*oldcomp.rda
Removed file. Should not have been present.

14 November 2015 Sasha D. Hafner
Version 1.2.1
*biogas_quick_start.Rnw, predBg_function.Rnw
Corrected some mistakes, including identical %\VignetteIndexEntry values

*Many Rd files
Wrapped examples and usage to 69 characters

*DESCRIPTION
Updated

*calcCOD.R
Check for lowercase elements changed so it is applied to each element of form
separately

*calcCOD.Rd, molMass.Rd
Updated to reflect vectorized quality of functions

13 November 2015 Sasha D. Hafner
Version 1.2.0
*Updated DESCRIPTION to prepare for submision to CRAN

11 November 2015 Sasha D. Hafner
Version 1.1.1
*cumBg.R
Removed use of signif() in calculation of means and sd. Added checks for
duplicated rows in setup and vol.

*test_HighLevelFunctions.R test_LowLevelFunctions.R
Few updates and corrections + addition of test if mass gain is calculated in cumBg

*cumBg.R
Added detailed error message for when mass gain is observed.

09 November 2015 Sasha D. Hafner
Version 1.1.1
*Rd files
More details for stdVol.Rd, new file vol2mol.Rd, and updating reference here
and in others.

05 November 2015 Sasha D. Hafner
Version 1.1.1
*constants.R 
New file defining constants stored in three vectors: std.forms, atom.weights,
and vol.mol.

*cumBg.R, mass2vol.R, molMass.R, predBg.R, vol2mass.R
Updated code dealing with constants. In some cases, constants had been
hard-coded (molar volumes). Now they use values set in constants.R.

03 November 2015 Sasha D. Hafner
Version 1.1.1
*molMass.R
Removed name from output

*readFormula.R
Corrected bug that resulted in NA in formulas with decimal coefficients within
parentheses. Problem was missing . in '[0-9.]+' on line 34.

*predBg.R
Added HCO3- production to CO2 production for returning as total CO2
production. Previous version only used cCO2 and ignored cHCO3.

03 November 2015 Sasha D. Hafner
Version 1.1.1
*predBg.R
Changed how mass and mcomp are handled when sum(mcomp) != 1. Previously mcomp was
divided by its sum with a warning only. Now mass is set to the sum(mcomp)
first if it was not already specified.

01 November 2015 Sasha D. Hafner
Version 1.1.1
*predBg.R
Previously form argument was always capitalized before calculating molar mass,
etc. Now it is only capitalized if first letter of is lowercase. Applied
separately to each element.

29 October 2015 Sasha D. Hafner
Version 1.1.1

*readFormula.R
Added value and cdigits arguments for returning simplified character formulas
only (when value = "shortform").

*predBg.R
Added shortform argument. Set to TRUE to simplify formula (if possible).

21 October 2015 Sasha D. Hafner
Version 1.1.1

*molMass.R
Made vectorized using a loop. Added names to output vector.

*predBg.R
Changed reaction coefficients for reaction output (value = 'reaction') so
reactants are negative, products positive. 

*predBg.R
Rewrote all code for handling mcomp. Now mcomp is converted to a formula
(form) and this is carried through. Now possible to use chemical formulas in
names for mcomp argument. Also if mass is not specified it will be set to
mcomp sum.

*predBg.R
If both COD and form arguments are given, mass is calculated and function
behaves as if mass was given.

21 October 2015 Sasha D. Hafner
Version 1.1.1

*cumBg.R
Added unit.temp and unit.pres to stdVol() call.

*vol2mol.R
New function for converting volume of pure gas to molar quantity.


18 October 2015 Sasha D. Hafner
Version 1.1.1

*molMass.R Fixed typo in error message.

*predBg.R
Changed calculation of chemical formula from mcomp argument. Values in
argument were interpreted as mole fraction originally, now are mass fraction.
Also added digits to rounded formula.


12 September 2015 Sasha D. Hafner
Version 1.1.1

*checkArgClassValue.R
Fixed message for multi-value classes with paste(..., collapse = )

19 August 2015 Sasha D. Hafner
Version 1.1.1

*predBg.R
Added new option for value argument = 'reaction' for returning the overall
chemical reaction only.

29 July 2015 Charlotte Rennuit
Version 1.1.0

*setup.Rd
Number of reactors to twelve
Added factor levels from 2_7 to 2_9
Added points at end of sentences

*setup2.Rd
Added points at end of sentences

*vol2mass.Rd 
Corrected typo error

*vol.Rd
Changed number fo observations to 288
Number of reactors to twelve
Added factor levels from 2_7 to 2_9

*summBg
Changed quotes for Examples to \sQuotes{Examples}

*biogas_quick_start.Rnw
Removed example in table 1 and corrected some spelling mistakes.


29 July 2015 Sasha D. Hafner
Version 1.1.0

*predBg.Rd
Added default of NULL to several arguments to match code

*comp.rda 
Replaced with new version from that has only measured values (previous version
had interpolated xCH4)

*All help files
Switched to British spelling of normalize/standardize and related words
Minor changes in wording

28 July 2015 Charlotte Rennuit
Version 1.1.0

*cumBG.Rd
Deleted sentences on column identification by order.

*summBg.Rd
Deleted sentences on column identification by order.
Modified examples so extrap = FALSE when using comp. 
Modified column name msub to mvs.sub in examples with normalisation using setup.

*predBg.Rd, stdVol.Rd, summBg.Rd
Adjusted length of examples in help files so it is not cut in the pdf manual. 

28 July 2015 Sasha D. Hafner
Version 1.1.0

*cumBg.R
Few changes to examples, including added pres = 1 

*mass2vol.R
Changed expected values in check of 'value' argument near top.

*checkArgClassValue.R
Added paste( ,collapse = ", ") to message returned for problem with expected values.

*DESCRIPTION
Updated version number in preparation for CRAN update

*setup.Rd
Added missing } at end of \usage

*summBg.R
Corrected spelling of length() line 89.

*mass.Rd
Added description of 'when' column.

*checkArgClassValue.R
Now remove NAs from object when checking range.

*biogas-package.Rd
Updated examples, now using vol, comp, and setup

*cumBg.R
Changed "normalized" to "standardized" in message returned when pres or temp
is not given.

*mass2vol.R
Fixed error in call to stdVol() that used temp instead of temp.k.

*cumBg.R
This change was made earlier and not documented: changed default value for showt0 to
TRUE

27 July 2015 Charlotte Rennuit
Version 1.0.4

*stdVol.Rd
New values of Antoine equation to be in accordance with the change of units in the calculations.
Addition of the function options() in links, and of a sentence specifying its possible use.

*test_HighLevelFunctions.R, test_LowLevelFunctions.R
Files updated and finalised for the release of version 1.0.4

*setup.Rd
Modified description so it corresponds to setup data frame modified earlier.

*testLowLevelFuntions.R
Changed test of molMass.R: removed signif(, 5) from the expected values so it matches changes in molMass. 

*molMass.R
Removed signif(, 5) from output value.

2015 July 26 Sasha D. Hafner
Version 1.0.4

*DESCRIPTION 
Added these two lines:
VignetteBuilder: knitr
Suggests: knitr, ggplot2
All for the vignette

*cumBg.R
Changed error message for missing norm.name column.

2015 July 24 Sasha D. Hafner
Version 1.0.4

*parCO2.R 
Changed pressure units to Pa (was atm before). This required addition of a
constant for the calculation of Henry's law constant, and a change in default
value for pres argument to 101325 (was 1 before).

*predBg.R
In call to partCO2, changed pres to 101325 (was 1 before).

2015 July 24 Charlotte Rennuit
Version 1.0.4

*sumBg.R
Change check for norm.name in two places: should be in names(setup) not in
setup[, descrip.name] column.

*predBg.R
Change form default to NULL, and checkArgClassValue arguments for form to
c('character', 'NULL') so there is no message error if only COD is called.
Changed checkArgClassValue arguments for mcomp to 'numeric'.

2015 July 23 Charlotte Rennuit
Version 1.0.4

*cumBg.R 
Changed calculation of vCH4 in volumetric method so it includes the difference
on molar volume of CH4 and CO2. It become consistent with mass2vol.R
calculations.

2015 July 22 Charlotte Rennuit
Version 1.0.4

*cumBg.R Add check for missing comp argument with gravimetric method

*cumBg.R modify code : names(vol) changed for names(dat) line 72 : "any(missing.col <- !c(id.name, time.name, dat.name) %in% names(dat))"

*create file testHighLevelFunctions.R: test for cumBg.R

*create file testLowerLevelFunctions.R: test for calcCOD.R, molMass.R, stdVol.R, vol2mass.R, mass2vol.R, unitConvert.R, watVap.R, readFormula.R, interp.R 

*Add test folder : run devtools::use_testthat(pkg = 'biogas')

*calcCOD.R change hard value of molar mass of oxygen to molMass('O') value. 

2015 July 22 Sasha D. Hafner
Version 1.0.4

*stdVol.R, cumBg.R, summBg.R, mass2vol.R, vol2mass.R, interp.R, molMass.R,
calcCOD.R, predBg.R 
Added checks for class (and values in some cases) of arguments at top using
checkArgClassValue().

*checkArgClassValue.R Changed name of file and function (was checkClass
previously).

*predBg.R Added default argument values of NULL to optional arguments (had no
values previously).

*stdVol.R, mass2vol.R, vol2mass.R
Replaced temp and pres variables in function with temp.k and pres.pa
where values are in K and Pa. This allowed removal of temp.orig and pres.orig
in stdVol. In mass2vol, also added conversion of temp.std and pres.std to K
and Pa near the top, and updated stdVol() call accordingly.

2015 July 21 Charlotte Rennuit
Version 1.0.4
*stdVol.Rd Added example with options()

2015 July 21 Sasha D. Hafner
Version 1.0.4

*checkClass.R New hidden function used to be used to check arguments to all
other functions.

*summBg.R and cumBg.R Removed all code for inferring column based on position in
data frame. Instead, an error is thrown if any column cannot be found. Users
now must use ___.name arguments.

*cumBg.R 
Added checks to make sure inoc.name and norm.name can be found in
descrip column of setup data frame. Otherwise an error is thrown. 

Added checks for all arguments based on class and for 'when' based on value.

Added NULL option for 'when' argument. If NULL, only a single observation is
expected for each reactor. Column with time.name is not returned in output.

2015 July 21 Sasha D. Hafner and Charlotte Rennuit
Vesion 1.0.4
*molMass.Rd Changed description of capitalization requirements.

2015 July 14 Sasha D. Hafner
Vesion 1.0.4
*mass2vol.Rd Removed rh argument. When was it added? Added pres argument to
examples and set all temp to 35.

*cumBg.R 
Added check argument and check for biogas composition (between 0 and
1).

Added temp.init argument, and added this to mass2vol call for times 1 and 2
when headspace argument is provided.

*cumBg.Rd 
Changes to match argument order and default arguments in code. Added
pres argument to mass examples and changed temp to 35.

*watVap.R 
New (hidden) function for calculating vapor pressure of water.

*stdVol.R, vol2mass.R, and mass2vol.R 
Replaced code for calculation of water vapor pressure
with call to watVap().

*vol2mass.Rd 
Fixed default arguments to match code.

*cumBg.R, vol2mass.R, stdVol.R, mass2vol.R and Rd files 
Switch order of arguments to ... unit.temp, unit.pres.

*mass2vol.R 
Added default value of NULL for temp.init, added error check is
headcomp is given but temp.init is not, and added if() before unit conversion
for temp.init. 

Moved position of temp.init in argument list (was between
unit.pres and value).

*stdVol.Rd 
Added pres argument to examples where it was missing. Cut second
example with only change from first pres = 1.03 atm instead of 1.

*vol2mass.R 
Replaced pres argument with pres.hs and pres.vol. Fixed error in
standard conditions for measured volume standardization. Now values are always
0C and 101325 Pa, but converted to unit.temp and unit.pres before stdVol call.

*vol2mass.Rd 
Updated examples. Clarified issue about mass loss not always
equaling biogas mass at time of measurement.

*predBg.Rd 
Removed degree sign, changed standarised to standardized.

2015 July 10 Sasha D. Hafner
Version 1.0.4
*molMass.R Changed grepl call to use metacharacter ^ in first argument instead 
of substr in second argument.

2015 June 30 and earlier Sasha D. Hafner
Version 1.0.4
*readFormula.R Can now handle spaces in form argument (uses gsub() to remove
them). Can now handle () within form, using coefficient at the end of ")". Can
now handle real numbers for coefficients.

2015 June 27
Version 1.0.4
*predBg.R Added condition to if statement before part.CO2 call so if there is
no CO2 (if nCO2 is <= 1E-8 mol), it is not called. In this same statement,
added [1] to missing() calls to avoid warnings.

Fixed a bug in calculation of mass from mol argument (replaced / with *).

*partCO2.R Added timer in while loop so an error is returned after 5 s.

2015 June 25-26 Sasha D. Hafner and Charlotte Rennuit
Version 1.0.4
*cumBg.R Changed code around line 55+ where composition data is sorted out
so that now a single value for each individual reactor is OK. Also added
messages to this section so user knows whether interpolation has occured, or a
single value has been used, etc.

*mass2vol.R, vol2mass.R, predBg.R Replaced numeric values for molar masses
with calls to molMass function. Corrected an error in the last stdVol call
where unit.temp and unit.pres were hard-coded. Now they are set to unit.temp
and unit.pres.

2015 June 23-25 Sasha D. Hafner
Version 1.0.3
*cumBg.R Corrected code for adding headspace volume column to dat data frame
and moved it up so it happens any time the headspace argument is provided. 

For gravimetric method, added code to use headspace argument and a new headcomp
argument to correct for initial headspace composition. If headspace argument
is provided, the initial headspace correction will be applied to the first
gravimetric result from each reactor only. 

Added checks for temp and pres at top of gravimetric section. When time column
is not recognized, now rate columns are not returned (previously they were
returned as NA).

Added cumulative mass loss column to the output for gravimetric data (name
cmassloss). 

*mass2vol.R Corrected section around line 42+ on N2 headspace correction.
stdVol call had an error with units now. Added argument temp.init for use in
this correction only.


2015 June 15 Sasha D. Hafner and Charlotte Rennuit
Version 1.0.3
*setup.rda added mcod.tot to setup data. Help file modifed accordingly

*cumBg.R added condition if rvCH4 for data screening: avoids an error if no
comp is provided.

Added default=NULL for temp and pres arguments (pres was previously 1 (atm)),
so if not provided no standardization is done. Changed code around line 150
where standardization occurs so it is skipped if either argument is NULL.

*predBG.Rd, changed nomalized in Details into standardized.

2015 June Sasha D. Hafner
Version 1.0.3
*stdVol.R, cumBg.R, mass2vol.R, vol2mass.R Changed units used in calculations
to Pa and K (originally was atm and degrees C). This required a change in the
Antoine equation parameters.

*screenRates.R New file, new function.

2015 June 9 Sasha D. Hafner
Version 1.0.2
*stdVol.R, cumBg.R, mass2vol.R Changed default values of temp.std, pres.std,
unit.pres, unit.temp so getOption() is checked. Removed code that converted 0C
and 1 atm to unit.temp and unit.pres if temp.std was the earlier default of
NULL and pres.std was the earlier default of NULL. Added message for standard
conditions and std.message argument. Removed default value of pres and temp.

*stdVol.R Added warning if temp < 0 C or >100 C and a similar one for
pressure.

*cumBg.R Added unit.temp=unit.temp and unit.pres=unit.pres arguments to stdVol
call. Probably was a bug to omit them earlier.

*vol2mass.R Changed default values of unit.pres, unit.temp so getOption() is
checked. Removed default value of pres (was 1).

2015 June 4 Sasha D. Hafner
Version 1.0.2
*stdVol.R Added message to print standard pressure and temperature

*vol2mass.R Added standardization of vol (was assumed to be at 0C and 1 atm
before), replaced temp argument with temp.hs (for headspace), added
temp.vol (for volume measurement), added rh.hs and rh.vol.

*cumBg.R Added message to print standard temperature and pressure

*summBg.R Changed messages about which columns are used by adding
deparse(substitute()) so now printed data frame name matches name 
used for actual argument

2015 May 28 Sasha D. Hafner
Version 1.0.1
*several Rd files Small corrections and addition of more details, addition
of spaces in examples

*biogas-package.Rd Extended examples and changed variable names in examples.
Also corrected error in interpretation of BMP results for cellulose
(difference of 15% not 7%).

*biogas-internal.R Deleted

2015 May 01 Sasha D. Hafner
Version 1.0.1

*summBg.R Added columns with separate response contribution of substrate and
inoculum to the data frame returned when show.obs=TRUE. Also grouped message()
statements together above the when loop to avoid duplicate messages.

*stdVol.Rd Added details on how standardization is done.

*stdVol.R Changed all occurrences of 'norm' to 'std'

2015 April 28 Sasha D. Hafner
Version 1.0.1

*summBg.Rda Changed description of when argument, which can now accept
multiple times or 'end'

2015 April 23 Sasha D. Hafner
Version 1.0.1

*summBg.R Added loop and other changes so that when argument can now be a
vector, and results will be returned for multiple times.

*summBg.R Added code to allow for a vol dataset with a single value for a
particular reactor. Value is returned if when matches time exactly, otherwise
NA is returned.

*summBg.R Added value of when argument as a column in the output data frame, 
with column name equal to time.name argument.


2015 March 06
Version 1.0