Feature veg estimation #321
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dschlaep
commented
Jul 29, 2022
dschlaep
commented
- close Estimate vegetation cover from climate before simulation run #318
- Added `allHist` double pointer to SW_WEATHER - Adjusted `_read_weather_hist` to store weather in year it is called with
- Created function `SW_WTH_read` that allocates allHist and calls `readAllWeather` - Created function `readAllWeather` which: * Reads in all weather history at once * Handles the case of missing weather (moved from and deleted _todays_weth) * Scales data depending on month (moved from `SW_WTH_new_day`) - Deleted `SW_WTH_new_year` as it is no longer needed
- Created function that is called by `SW_WTH_deconstruct` to deallocated allHist
- Deleted static version of weth_found and is now in `readAllWeather`
- Added most of documentation from old `SW_WTH_new_year()` * Describing how SOILWAT handles missing weather data
- Instead of calculating number of years multiple times, it is calculated once - n_years is initialized to 0
- Fixed how the months days are incremented - Fixed "temp_avg" calculations
- Removed numYears from `deallocateAllHistory` header - Added `isnull` to prevent empty lists from attempting to free itself
- Swapped SW_Weather.scale_temp_max/min for allHist[yearIndex]->temp_max/min
- When running STEPWAT, n_years in `SW_Weather` will be the correct value
- Swapped `ST_defines.h` for `SW_globals.h` - Removed extern `SuperGlobals` to prevent duplicates
- Updated header of `readAllWeather()` to accept `n_years` - Replaced instance of using `SW_Weather.n_years` with `n_years` from header - Updated unit test to include `SW_Weather.n_years` in call to `readAllWeather()`
- Added call to `deallocateAllHistory()` to fix memory leak
- Swapped `endYear` for `n_years` in documentation for `readAllWeather` - Deleted previously removed `numYears` parameter documentation - Added `yearWeather` documentation to `_read_weather_hist()` - Added descriptions to `_read_weather_hist()` parameters in documentation
- weather-related "WaterBalance" tests use non-default weather inputs * "WithWeatherGeneratorOnly" utilizes the weather generator for all values * "WithWeatherGeneratorForSomeMissingValues" utilizes available inputs from non-default source "Input/data_weather_missing" and uses the weather generator for missing values - updates related to `readAllWeather()` require that these tests prepare their weather data before running the simulation loop -- otherwise, they are using the "default" weather values previously obtained by `Reset_SOILWAT2_after_UnitTest()` and they would actually no longer perform the intended checks
- Added deallocation call before allocation process occurs * NOTE: In SOILWAT2 runs alone, this does not change anything * Eliminates the chance of forgetting to call `deallocateAllWeather()` in tests
- Created unit tests for the following conditions of `readAllWeather()`: * Use of weather generator to fill in missing days * Use of weather generator to fill in missing years * Only use weather generator to fill weather data
- `_clear_hist_weather()` now fills `allHist` instead of `SW_Weather.hist` - Now takes in `yearWeather` (current year's weather data) to fill with `MISSING`
- Eliminates chance of false "is not null" result when running tests
- Added new test to check for missing yearly input - "SomeMissingValuesYears" test no longer directly calls `readAllWeather()`
- Added two functions from `feature_weather_before_sim` branch
- Added input in file `veg.in` to specify method of vegetation estimation - Changed file reading to accommodate new user input
- `SW_WEATHER_2DAYS` no longer has - Accommodated code for no longer needing a "Yesterday" index - Deleted `SW_WTH_end_day()` and `_update_yesterday()`
- Moved `estimateVegetationFromClimate()` from `feature_weather_before_sim` branch - Added check to call `estimateVegetationFromClimate()`
added 2 commits
November 15, 2022 22:20
- The parameter "latitude" for `estimateVegetationFromClimate()` has existed for awhile and hasn't gotten documentation, so it has now been added
- Renamed parameter from "value" to "testValue" to be a little more descriptive - Added documentation for `cutZeroInf()` parameter, which wasn't existent previously - Replaced "value = 0." with use of macro `LT()` to account for floating-point arithmetic
dschlaep
commented
Nov 16, 2022
- new test helper functions * `copyL0()`: copies L0-cover inputs to expected L0-output array * `calcVegCoverL1FromL0()`: calculates L1-cover from L0-cover array * `calcGrassCoverFromL0()`: calculates grass cover components relative to total grass cover - organize tests: (i) comment; (ii) set inputs; (iii) set or calculate expected output; (iv) calculate cover; (v) test expectations - calculate expected output from (fixed) inputs or from more detailed expected output where possible -- instead of repeating hard-coded values in several places (up to three copies per value) - loop over expected grass cover array -> all but one test are passing -> the one failing test is because L1-cover output for bare ground is incorrect if bare ground input is `SW_MISSING` (see https://github.com/DrylandEcology/SOILWAT2/pull/321/files/cdbfa8b929a1c6b34e9a1c94d9b3c5e0a483c326#r1024294338)
- Appended to "inputValues" documentation to explain how SW_MISSING is handled, and that a value of 0-1 means the value is fixed - Appended to "SumGrassesFraction" documentation to elaborate on how a value that isn't SW_MISSING is handled including that grasses are estimated relative to that value
- Created a new death test handling when SumGrassesFraction is added to the initial input sum and is greater than 1 - Added documentation specifying what the two different death cases are doing
- Fixed "SumGrassFraction" to "SumGrassesFraction" where needed - Changed SW_MISSING with 0.0 when needed (within lines 283-289), fixing a failing test
…ted equations - documented behavior: "Some of the land cover/vegetation types, i.e., trees, annual grasses, and bare-ground are not estimated from climate relationships; they are either set to 0, or alternatively fixed at the value of the input argument(s)." -> explicitly set cover of trees, annual grasses, or bare ground to 0 if their input is `SW_MISSING` (user request to estimate) -> this addresses failed unit test identified by commit 3e01bb6 (2022-Nov-16) and by comment https://github.com/DrylandEcology/SOILWAT2/pull/321/files/cdbfa8b929a1c6b34e9a1c94d9b3c5e0a483c326#r1024294338
- "WaterBalanceTest" that turns on estimation of vegetation from climate (currently vegetation cover)
- Appended to the documentation of variables with names with "7thMon" or "2ndMon" to mention the targeted months in the two hemispheres - Removed all but one mention of units of a variable within the documentation * For the most part, SW_CLIMATE_YEARLY contained units in documentation and SW_CLIMATE_CLIM did not * Variables already have their unit at the end of their name * Kept unit specification in the documentation for "ddAbove65F_degday" for a bit more explanation on unit * Added a note for the structs pointing out the unit of data are within the variables' name
- Created `allocateClimateStructs()` and `deallocateClimateStructs()` to specifically allocate or deallocate climate structs - Allows the removal of "allocate = 1;" and "deallocate = 0;" lines of code in current and future uses
- The program tries to read a line of text that is not commented out, so it is interpreting it as values for vegetation type values, causing an error
- Previously, the units within the two climate structs, SW_CLIMATE_YEARLY and SW_CLIMATE_CLIM, were deleted, which was found not to be preferable - Documentation was backtracked to the most recent version that contained units within SW_CLIMATE_YEARLY - Units within SW_CLIMATE_CLIM were added to add consistency as the deletion of units was meant to do - Units within SW_CLIMATE_CLIM documentation mirror the units in the variable name, even for averages. * For example, the unit for "meanTemp_C" in the documentation is [C] and not [C / year]
…ature_veg_estimation # Conflicts: # NEWS.md
…into feature_veg_estimation
"Node.js 12 actions are deprecated. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/. Please update the following actions to use Node.js 16: actions/checkout@v2, codecov/codecov-action@v2" -> https://github.com/actions/checkout/releases/tag/v3.0.0 -> https://github.com/codecov/codecov-action/releases/tag/v3.0.0
- `driestQtrSouthAdjMonYears()`: reads, sets, and returns parameters depending on time of year; some calls do not read some parameters * we can either dissolve this function as it is used only once or silence the compile warnings `-Wunused-but-set-parameter` -> silence warnings with coercion to void
N1ckP3rsl3y
approved these changes
Dec 4, 2022
dschlaep
added a commit
to DrylandEcology/rSOILWAT2
that referenced
this pull request
Dec 7, 2022
Feature veg estimation, climate predictors, and read all weather This merge combines - feature_read_weather (close #204): read and process daily weather before main simulation loop - feature_climate_predictors (close #205): calculate long-term climate summaries - feature_veg_estimation (close #206): estimate fractional land cover representing a potential natural vegetation based on climate relationships This PR matches the underlying PR in SOILWAT2 DrylandEcology/SOILWAT2#321
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