TODO:
* Remove the additional start() parameters once that data is transferred to inputData
* Test with rSFSW2 and rSOILWAT2 once changes have been done there (has succesfully worked with local old repos)
* Confirm placement of global variable initializations

Includes:
* Adding a structure SW_Carbon to avoid clogging up the global space
* Moved R CO2 settings to S4 class
* onGet/onSet functions to interact with S4 class and its respective object
* Removal of additional parameters to SEXP start()

SOILWAT2 remains fully functional by itself, and seems fully functional with rSOILWAT2's CO2 branch

…e_CO2_multipliers()"

This changes results massively. Linear equations were previously used for WUE and Biomass multipliers, which have been switched to power equations in this commit. Additionally, the correct source is being used for the PPMs now.

* @biomass --> @CO2EFFECTS
* Added yearly output
* Added a total biomass column
* Added a WUE multiplier column
* Removed additional column
* This slot, and this slot only, now reflects the proper future simulation years

Previously, when future scenarios were run, the original years would be used as output. For instance, a scenario in 2020-2050 would have outputs from 1980-2010. I've utilized the delta year that I pass in for carbon effects and added it to the model year ONLY IN THE OUTPUT FUNCTIONALITY. The rest of the model still needs the 'incorrect' years.

Apply biomass multiplier to tree's fraction live biomass, not total biomass. Note that the output column name still needs to be changed in rSFSW2/rSOILWAT2.

Disregard the description in the last commit, I forgot that SOILWAT2 holds the instance of the rSOILWAT2 output class

…e code

Close #29: CO2 multipliers incorrect when scenario doesn't exist
Close #34: Properly initialize the CO2 variables

# Conflicts:
#	makefile --> merged
#	makefile_n --> removed

Tabs to spaces, reducing reliance on hard-coded values, constructor, comments, change the stomatal term to water-usage efficiency, be more consistent on variable names

2280 was used to test the performance and robustness of CO2 calculations

- updated code because GET_SLOT(object, install("CO2ppm") is now a
matrix with two columns 'Year' and 'CO2ppm'
- we first need to find the correct row based on 'Year'
- then we can loop and extract CO2 concentration data

- functions 'onGetInputDataFromFiles' and '_read_inputs' are now
reading in CO2 data from the input file on disk -- in parallel to their
behavior of reading in all other data from disk files
- function 'onGetInputDataFromFiles' gained an internal 'debug'
variable which now prints debug statements (instead having comments in
the code)
- Function 'SW_CBN_read' is currently a mock

- split previous '#ifndef RSOILWAT' version of function
'calculate_CO2_multipliers' up into its two parts:
(1) read data from file --> code copied to 'SW_CBN_read'
(2) calculate CO2 multipliers --> code merged with '#ifdef RSOILWAT'
version of function 'calculate_CO2_multipliers'

- nonsensical CO2 value check "ppm < 0.1 && ppm > -0.1" replaced with
"LT(ppm, 0.)" in function 'calculate_CO2_multipliers'

Previously, the module-level variable 'MyFileName' was only created if
not RSOILWAT, but the new function 'SW_CBN_read' needs this variable
whether or not RSOILWAT

Code still not functional

- variable 'CEntries' was not initialized properly because we don't
have a .C() call in rSOILWAT2

- addressing issue #33
- defined macro for printing so that we can write `swprintf(format,
...)` whether we are compiling with RSOILWAT flag or for standalone
SOILWAT2

- function 'SW_CTL_init_model' no longer calls '_read_inputs' so that
we can call it inside the function 'onGetInputDataFromFiles' for
initialization only
- renamed '_read_inputs' to 'SW_CTL_obtain_inputs'
- defined 'SW_CTL_read_inputs_from_disk'

- GET_SLOT(object, install("CO2ppm")) is a vector of length 2 where the
first element is the vector of years and the second element are the CO2
values.
- n = length is now correctly calculated
- but finding the correct year and extracting the data still fail

- code compiles for RSOILWAT, but likely crashes during run-time
- handle S4 class object by coercing to vectors: '*years' and '*CO2ppm'
- fixed logic of loop to locate index of first year for which we need
CO2 data --> if we found the index of the year then 'break' (instead of
'continue') otherwise increment index
- fixed logic of check that we have enough data --> we need at least
index plus number of simulation years of available data (and not
'c->addtl_yr')
- fixed logic of loop to copy CO2 concentration values to SOILWAT
variable --> make sure that we don't overflow either the index nor the
maximal number of CO2 years

- added debug print statements
- aligned inputting of c->use_bio_mult, c->use_wue_mult, and
c->scenario with other code in the function

- close DrylandEcology/rSOILWAT2#77
- The function 'onGet_SW_CARBON' did not copy the values of the C
variable `SW_Carbon` into a new created R-typed (S4-classed rSOILWAT2)
variable representation.

- fix condition of loop to copy CO2 values in function 'onSet_swCarbon'

explain how calendar years are represented

- fix column names of CO2ppm matrix
- also copy 'Scenario' name to C representation
- use a dedicated SEXP variable 'CO2ppm' to copy the content of the S4
class slot of same name and convert to a real vector 'values' (which
can now easily be accessed)
- cleaner implementation of 'Locate index of first year'
- fix logic of 'Check that we have enough data' (i is base1 here)
-

- contributing to issue #59

…fects

- The global variable 'SW_Carbon' is defined in 'SW_Carbon.c'.
- Instead of being externed, it was re-defined in 'SW_Flow_lib.c',
'SW_Flow.c', 'SW_Site.c', and 'SW_VegProd.c'.
- Similar bug fix for variables 'SW_VegProd' and 'SW_Model' in file
'SW_Carbon.c'

- until we resolve issue #85, we need the functions from 'SW_Output.c'
defined alternatively
- SW_Output_mock.c provides mock definitions for these functions
- compiling unit tests with 'SW_Output_mock.c' allows us to include
'SW_Output.h' in our unit test files

- note: I attempted to eliminate compile warnings (hence some weird
code snippets), but one warning remains
> SW_Output_mock.c:204:13: warning: unused function '_echo_outputs'
[-Wunused-function]
static void _echo_outputs(void)

- We need to initialize and take down SOILWAT2 variables by imitating
'SW_Main.c/main()' because SOILWAT2 uses (global) states.

- To initialize the global SOILWAT2 variables, I set up the unit test
code to read from the SOILWAT2-standalone input files contained in the
folder 'testing/'.

- new file with unit tests 'test_SW_Carbon.cc'
- more unit tests to come

> make test test_run
c++ -Wall -Wextra -std=gnu++11		 -L. -isystem
googletest/googletest/include -pthread \
				test/*.cc -o sw_test -lgtest -lSOILWAT2++ -lm
./sw_test
[==========] Running 3 tests from 3 test cases.
[----------] Global test environment set-up.
[----------] 1 test from BetaGeneratorDeathTest
[ RUN      ] BetaGeneratorDeathTest.Errors
[       OK ] BetaGeneratorDeathTest.Errors (8 ms)
[----------] 1 test from BetaGeneratorDeathTest (8 ms total)

[----------] 1 test from CarbonTest
[ RUN      ] CarbonTest.Constructor
[       OK ] CarbonTest.Constructor (0 ms)
[----------] 1 test from CarbonTest (0 ms total)

[----------] 1 test from BetaGeneratorTest
[ RUN      ] BetaGeneratorTest.ZeroToOneOutput
[       OK ] BetaGeneratorTest.ZeroToOneOutput (0 ms)
[----------] 1 test from BetaGeneratorTest (0 ms total)

[----------] Global test environment tear-down
[==========] 3 tests from 3 test cases ran. (8 ms total)
[  PASSED  ] 3 tests.

- commit 71258d2 introduced new make
targets

- The file was not closed after it was opened.
- added 'debug' variable
- use 'EQ' instead of testing a floating-point number against exact
equality to 1
- declare and initialize variables only after code has exited if no
multiplier is turned on

- close #63

[----------] 4 tests from CarbonTest
[ RUN      ] CarbonTest.Constructor
[       OK ] CarbonTest.Constructor (0 ms)
[ RUN      ] CarbonTest.ReadInputFile
[       OK ] CarbonTest.ReadInputFile (0 ms)
[ RUN      ] CarbonTest.CO2multipliers
[       OK ] CarbonTest.CO2multipliers (1 ms)
[ RUN      ] CarbonTest.BiomassCO2effect
[       OK ] CarbonTest.BiomassCO2effect (0 ms)
[----------] 4 tests from CarbonTest (1 ms total)

- close #20

- makefile gained targets to estimate code coverage
* 'make cov' = same as 'make test' but with code coverage support
* 'make cov_run' = run unit tests and gcov on each source file (which
were in a previous step compiled with 'make cov')

- new bash script 'run_gcov.sh' which executes 'gcov' for each source
file; used by 'make cov_run'

- updated travis-ci yml to run code coverage unit tests and connect to
'codecov' server

- don't execute 'gcov' for unit test code or 'googletest' submodule
- 'codecov' will run 'gcov' so that we can use 'make test_run' instead
of 'make cov_run'

- remove 'test' dependency of target 'test_run' so that we can call on
travis-ci 'make cov test_run' where 'test_run' calls the binary
produced by 'cov' and doesn't first compile and overwrite a
non-coverage version of the binary

- moved old/outdated code change file to 'doc/'
- moved bibtex library to 'doc/' and updated 'Doxyfile'

- Remove content of `doc/html/` and only generate documentation locally
- Added content of `doc/html/` to .gitignore
- close #88

…lready exist

- variable 'key2obj' in 'SW_Output.c' contained one entry too many:
removed one 'eVES'

- moved variable 'addtl_yr' from 'SW_CARBON' to 'SW_MODEL' because it
has nothing to do with atmospheric CO2 concentration but with
simulation time

- moved 'MAX_CO2_YEAR' from 'SW_Carbon.h' to 'SW_Defines.h' and renamed
to 'MAX_NYEAR'

- defined new variable 'simyear' in 'SW_MODEL' to avoid repeated
calculation of 'year + addlt_yr' (e.g., all SW_Output.c/get_* functions
use 'simyear')

- 'SW_Carbon.h' define many vegetation variables even though this is
about vegetation and not about [CO2] and despite that 'SW_VegProd.h'
already deals with the functional types --> 'SW_VegProd.h' no longer
needs to include 'SW_Carbon.h'
* removed struct 'PTFs' (plant functional types) from 'SW_Carbon.h'
* variable 'co2_multipliers' moved from 'SW_CARBON' to 'VegType'
* function 'apply_CO2' moved from 'SW_Carbon.c' to 'SW_VegProd.c' and
renamed to 'apply_biomassCO2effect'

- cleaned up struct 'SW_VEGPROD'
* defined struct 'VegTypeOut' and 'CoverType'

- adjusted unit tests and moved vegetation-related tests to new file
'test_SW_VegProd.cc'

- passes all unit tests:
[==========] Running 7 tests from 4 test cases.
[----------] Global test environment set-up.
....
[----------] Global test environment tear-down
[==========] 7 tests from 4 test cases ran. (8 ms total)
[  PASSED  ] 7 tests.

- function 'SW_CBN_read' gained check that 'year' inputs are not
negative (values are used as index, hence negative values are not
allowed).

- eliminate compile warnings
* warning: 'XXX' may be used uninitialized in this function
[-Wmaybe-uninitialized]
* warning: format ‘%d’ expects argument of type ‘int *’, but argument 3
has type ‘TimeInt *’ [-Wformat=]

- attempt to eliminate compile warnings

- function 'SW_CTL_obtain_inputs' was supposed to call
`calculate_CO2_multipliers()` which it did in the past

- commit 6db701f removed the call to
`calculate_CO2_multipliers()` at the end of the function
`SW_CTL_obtain_inputs` previously named `_read_inputs` without
replacing it -- for some reason (that I don't understand) git blame and
diffs don't show this line being deleted by this commit

- the order in which tests are executed is not fixed
- each TEST() must carefully reset global states -- this is a pain
because our old SOILWAT2 c code is rich in functions that manipulate
global states

- `REvprintf()` returns void unlike `vfprintf()`; thus we cannot check
for EOF

- function `LogError` should only be called with argument `logfp` and
no longer with `stderr` or `stdout` directly (see commit
4e0cc0e)

- close DrylandEcology/rSOILWAT2#78
- close DrylandEcology/rSOILWAT2#73

- file 'testing/Input/outsetup_v31.in'
* fully explain what output columns are
* rename output file to 'vegetation' from 'co2_effects'

- function '_collect_values()' did not call `SW_OUT_sum_today(eVPD)`

- return value of function 'get_co2effects' was 'void' instead of
'static void' as every other 'get_*' function

- function 'SW_OUT_flush' did not call `SW_OUT_sum_today(eVPD)`

- function 'sumof_vpd' only ever added biomass values into output slots
from 'Today' which is 1 -- the correct index is 'SW_Model.doy'

- function 'average_for' precluded 'ObjType's other than 'eSWC' and
'eWTH' to perform averaging

- turn on all cover types

- replace 'nullptr' with 'NULL'

- addressing issue
DrylandEcology/rSOILWAT2#81
- define 'OBJECTS' and 'SOURCES' for rSOILWAT2 compilation

Coefficients assume that monthly biomass inputs reflect values for
conditions at 360 ppm CO2, i.e., Coeff1 * x^Coeff2 = 1 for x = 360 CO2
ppm

- addressing DrylandEcology/rSOILWAT2#81
and DrylandEcology/rSOILWAT2#66

- Makevars, SW_R_init.c, SW_R_lib.c, and SW_R_lib.h are not used by
SOILWAT2 -- they are rSOILWAT2 files
- remove rSOILWAT2 shared object target from makefile
--> this commit requires that the removed files are added to
rSOILWAT2/src/ and that the source code of SOILWAT2 is now a submodule
in rSOILWAT2/src/SOILWAT2/ -- instead of rSOILWAT2/src/

…sage

Also, i was a high number because the simstart year was 1979 and only data for 1980-2010 was provided, so the loop iterated i many times.

If the 'values' object doesn't contain the value of 'year', then the
loop was not behaving properly and didn't stop until 'i' was extremely
large.

Fix: add condition that i remains less than maximum number of years.

This and commit 48f3588 close
DrylandEcology/rSOILWAT2#80

# Conflicts:
#	SW_Output.c
#	SW_Site.c
#	generic.c
#	makefile
#	testing/Input/siteparam.in
#	testing/Input/veg.in
#	testing/Input/years.in
#	testing/files_v31.in

# Conflicts:
#	SW_Output.c

siteparam.in still uses RCP85 by default