Merge pull request #306 from DrylandEcology/feature_DecadalAggregations

Feature decadal aggregations

.Rbuildignore

@@ -1,5 +1,16 @@
 ^appveyor\.yml$
+^\.appveyor_clear_cache\.txt$
 ^\.travis\.yml$
 ^codecov\.yml$
-^CONDUCT\.md$
+^CODE_OF_CONDUCT\.md$
 ^data-raw$
+^.lintr$
+
+# RStudio stuff
+^.*\.Rproj$
+^\.Rproj\.user$
+
+# CRAN stuff
+^cran-comments\.md$
+^NEWS\.md$
+

.gitignore

@@ -11,3 +11,12 @@ inst/doc
 
 # Package check files
 ..Rcheck
+rSFSW2.Rcheck
+
+# Package builds
+*tar.gz
+
+# Compiled source code
+src/*.o
+src/*.so
+src/*.dll

.lintr

@@ -0,0 +1,22 @@
+linters: with_defaults(
+  #--- DEFAULT LINTERS
+  # Default line length:
+  line_length_linter(80L),
+  # Turn off default linters for now:
+  object_name_linter = NULL,
+  camel_case_linter = NULL,
+  snake_case_linter = NULL,
+  #--- NON-DEFAULT LINTERS
+  # Not activated non-default linters:
+  #extraction_operator_linter,
+  #implicit_integer_linter,
+  #todo_comment_linter,
+  #absolute_path_linter,
+  # Activated non-default linters:
+  T_and_F_symbol_linter,
+  nonportable_path_linter,
+  semicolon_terminator_linter,
+  seq_linter,
+  undesirable_function_linter,
+  undesirable_operator_linter,
+  unneeded_concatenation_linter)

.travis.yml

@@ -7,14 +7,15 @@ sudo: false
 cache: packages
 warnings_are_errors: false # turn this back on for more severe testing
 
-# next three settings (latex, r_build_args, and r_check_args -- though, the latter two
-# are not used because we use our own 'script' section: see there): because unit tests take
-# now too much time due to the extended unit test project; some travis runs fail due to
-# taking longer than the allotted 60-min maximum; for now omit PDF vignettes and manual
-# until we have proper, fast running unit tests
+# Next three settings (latex, r_build_args, and r_check_args -- though, the latter two
+# are not used because we use our own 'script' section: see there): because unit tests
+# take now too much time due to the extended unit test project; some travis runs fail
+# due to taking longer than the allotted 60-min maximum; for now omit PDF vignettes and
+# manual until we have proper, fast running unit tests
 latex: false
 r_build_args: '--no-build-vignettes --no-manual'
 r_check_args: '--ignore-vignettes --no-manual'
+#r_packages: hunspell
 
 addons:
   apt:
@@ -25,19 +26,26 @@ addons:
     - libnetcdf-dev
 
 before_install:
-  # install dependencies of rSOILWAT2 (because rSOILWAT2 is installed 'before install' and
-  #   thus dependencies are not installed and r_packages has not taken effect yet)
+  # pwd = <repo>/<repo-name>, here DrylandEcology/rSFSW2
+  # Install dependencies of rSOILWAT2 (because rSOILWAT2 is installed 'before install'
+  #   and thus dependencies are not installed and r_packages has not taken effect yet)
   - Rscript -e 'pkgs <- setdiff(c("blob", "DBI", "RSQLite"), installed.packages()); if (length(pkgs) > 0) utils::install.packages(pkgs)'
-  # obtain source code of rSOILWAT2 from github
-  - git clone -b master --single-branch --recursive https://github.com/Burke-Lauenroth-Lab/rSOILWAT2.git /tmp/rSOILWAT2
-  # install rSOILWAT2 without help pages and without vignettes
-  - R CMD INSTALL --no-docs --no-help /tmp/rSOILWAT2
+  # Obtain source code of rSOILWAT2 from github and save at DrylandEcology/rSOILWAT2
+  - git clone -b master --single-branch --recursive https://github.com/DrylandEcology/rSOILWAT2.git ../rSOILWAT2
+  # Install rSOILWAT2 without help pages and without vignettes
+  - R CMD INSTALL --no-docs --no-help ../rSOILWAT2
+  # Instead of `r_packages`, install dependencies of unit tests only if not already
+  #   available in cached packages
+  - Rscript -e 'pkgs <- setdiff(c("hunspell"), installed.packages()); if (length(pkgs) > 0) utils::install.packages(pkgs)'
+
 
 script:
   - R CMD build --no-build-vignettes --no-manual .
-  # the extended unit test project (commit db3948e6aa746d012dbc4f25b0e9bb2a4186305f)
-  # takes too long for the default settings (> 10 min without output)
-  - travis_wait 30 R CMD check *tar.gz --as-cran --ignore-vignettes --no-manual
+  # The extended unit test project (commit db3948e6aa746d012dbc4f25b0e9bb2a4186305f)
+  # takes about 16 min which is too long for the default settings of 10-min and times out
+  # On failure, display file 'testthat.Rout.fail' for more information and fail
+#  - travis_wait 30 R CMD check *tar.gz --as-cran --ignore-vignettes --no-manual || { cat rSFSW2.Rcheck/tests/testthat.Rout* && 1; }
+  - travis_wait 30 R CMD check *tar.gz --as-cran --ignore-vignettes --no-manual && cat rSFSW2.Rcheck/tests/testthat.Rout*
 
 after_success:
   - travis_wait 30 Rscript -e 'covr::codecov()'

DESCRIPTION

@@ -1,19 +1,22 @@
 Package: rSFSW2
 Title: Simulation Framework for SOILWAT2
-Version: 2.7.4
-Date: 2018-05-02
-Authors@R: c(person("Daniel", "Schlaepfer", email = "daniel.schlaepfer@yale.edu", role = c("aut", "cre")),
-      person("Caitlin", "Andrews", role = "ctb"),
-      person("Zach", "Kramer", role = "ctb"),
-      person("Ryan", "Murphy", role = "ctb"))
+Version: 3.0.0
+Date: 2018-08-04
+Authors@R: c(
+  person("Daniel", "Schlaepfer", email = "daniel.schlaepfer@yale.edu",
+    comment = c(ORCID = "0000-0001-9973-2065"), role = c("aut", "cre")),
+  person("Caitlin", "Andrews", role = "ctb"),
+  person("Zach", "Kramer", role = "ctb"),
+  person("Charlie", "Duso", role = "ctb"),
+  person("Ryan", "Murphy", role = "ctb"))
 Description: Setting up, carrying out, and analyzing ecosystem water balance
     simulation experiments with SOILWAT2.
 Depends:
     R (>= 3.3.0)
 Imports:
-    rSOILWAT2 (>= 2.3.0),
-    RSQLite (>= 2.0),
-    DBI (>= 0.7),
+    rSOILWAT2 (>= 2.3.2),
+    RSQLite (>= 2.1.1),
+    DBI (>= 1.0),
     Rcpp (>= 0.12.12),
     raster (>= 2.5.8),
     sp (>= 1.2.3),
@@ -38,7 +41,7 @@ Suggests:
       dplyr,
     knitr,
     rmarkdown,
-    testthat,
+    testthat (>= 2.0.0),
     covr,
     lintr
 Remotes:
@@ -49,7 +52,7 @@ LazyData: true
 ByteCompile: true
 NeedsCompilation: yes
 License: GPL-3 + file LICENSE
-URL: https://github.com/Burke-Lauenroth-Lab/rSFSW2
-BugReports: https://github.com/Burke-Lauenroth-Lab/rSFSW2/issues
+URL: https://github.com/DrylandEcology/rSFSW2
+BugReports: https://github.com/DrylandEcology/rSFSW2/issues
 RoxygenNote: 6.0.1
 VignetteBuilder: knitr

NAMESPACE

@@ -11,8 +11,6 @@ export(ExtractGriddedDailyWeatherFromMaurer2002_NorthAmerica)
 export(ExtractGriddedDailyWeatherFromNRCan_10km_Canada)
 export(Grass_ANPP)
 export(GriddedDailyWeatherFromNCEPCFSR_Global)
-export(PotNatVeg_Composition_Estimate_ShrubsC3C4_Fraction)
-export(PotNatVeg_MonthlyBiomassPhenology_from_Climate)
 export(PrepareClimateScenarios)
 export(SMR_logic)
 export(SMR_names)
@@ -25,8 +23,8 @@ export(TranspCoeffByVegType)
 export(VWCtoSWP)
 export(align_with_target_grid)
 export(align_with_target_res)
-export(calc_BareSoilEvaporationCoefficientsFromSoilTexture)
-export(calc_ExtendSoilDatafileToRequestedSoilLayers)
+export(calc_BareSoilEvapCoefs)
+export(calc_RequestedSoilLayers)
 export(calc_SiteClimate)
 export(check_aggregated_output)
 export(check_cltool)
@@ -37,27 +35,33 @@ export(check_rSFSW2_project_input_data)
 export(check_weatherDB)
 export(climscen_metadata)
 export(compare_test_output)
+export(compare_two_dbOutput)
 export(compile_overall_timer)
 export(convert_precipitation)
 export(convert_temperature)
-export(create_dbWork)
 export(crs_units)
+export(dbConnect2)
+export(dbExecute2)
 export(dbOutput_ListDesignTables)
+export(dbOutput_ListInternalTables)
 export(dbOutput_ListOutputTables)
 export(dbOutput_Tables_have_SoilLayers)
 export(dbOutput_update_OverallAggregationTable)
-export(dbW_sites_with_missingClimScens)
-export(dbWork_check)
+export(dbWork_Ntodo)
+export(dbWork_agg_timing)
+export(dbWork_check_design)
+export(dbWork_check_granular)
+export(dbWork_check_run)
+export(dbWork_check_status)
 export(dbWork_clean)
 export(dbWork_redo)
+export(dbWork_report_completion)
 export(dbWork_timing)
 export(dbWork_todos)
-export(dbWork_update_job)
 export(delete_test_output)
 export(determine_simulation_size)
 export(dir_safe_create)
 export(doQmapQUANT_drs)
-export(do_ExtractSkyDataFromNCEPCFSR_Global)
 export(do_OneSite)
 export(do_compare)
 export(do_prior_TableLookups)
@@ -66,15 +70,19 @@ export(downscale.deltahybrid)
 export(downscale.deltahybrid3mod)
 export(downscale.raw)
 export(enable_debug_dump)
+export(estimate_PotNatVeg_biomass)
+export(estimate_PotNatVeg_composition)
 export(exit_SFSW2_cluster)
 export(export_objects_to_workers)
 export(extract_SFSW2_cells_from_raster)
 export(extract_SFSW2_cells_from_shp)
 export(extract_SFSW2_points_from_shp)
 export(extract_blocks)
+export(extract_climate_NCEPCFSR)
 export(extract_daily_weather_from_livneh)
 export(extract_from_external_raster_old)
 export(extract_rSFSW2)
+export(find_sites_with_bad_weather)
 export(gather_objects_for_export)
 export(generate_OverallAggregation_fields)
 export(generate_RNG_streams)
@@ -100,9 +108,11 @@ export(it_sim0)
 export(it_sim2)
 export(it_site)
 export(it_site2)
+export(kill_seedling)
 export(list.dbTables)
 export(list.dbVariables)
 export(list.dbVariablesOfAllTables)
+export(load_preprocessed_inputs)
 export(local_weatherDirName)
 export(lock_access)
 export(lock_attempt)
@@ -114,9 +124,9 @@ export(missing_Pids_outputDB)
 export(move_output_to_dbOutput)
 export(mpi_work)
 export(populate_rSFSW2_project_with_data)
-export(prepare_climatedata_netCDF_files)
+export(prepare_climatedata_netCDFs)
 export(quickprepare_dbOutput_dbWork)
-export(read_SOILWAT2_FileDefaults)
+export(read_SOILWAT2_DefaultInputs)
 export(read_time_netCDF)
 export(reaggregate_raster)
 export(reaggregate_shapefile)
@@ -126,7 +136,6 @@ export(remove_lock)
 export(run_simulation_experiment)
 export(run_test_projects)
 export(save_to_rds_with_backup)
-export(setFALSE_SeedlingSurvival_1stSeason)
 export(set_RNG_stream)
 export(set_full_RNG)
 export(set_options_warn_error)
@@ -137,22 +146,17 @@ export(setup_rSFSW2_project_infrastructure)
 export(setup_spatial_simulation)
 export(simulate_SOILWAT2_experiment)
 export(unlock_access)
+export(update_actions)
 export(update_intracker)
 export(upgrade_datafile)
 export(upgrade_prodin_v10_to_v11)
 export(upgrade_soilsin_v11_to_v12)
 export(weighted.agg)
+import(RSQLite)
+import(methods)
 importClassesFrom(raster,Raster)
 importClassesFrom(sp,SpatialPoints)
 importClassesFrom(sp,SpatialPolygons)
 importFrom(Rcpp,evalCpp)
 importFrom(Rcpp,sourceCpp)
-importFrom(methods,"slot<-")
-importFrom(methods,as)
-importFrom(methods,isGeneric)
-importFrom(methods,new)
-importFrom(methods,setGeneric)
-importFrom(methods,setMethod)
-importFrom(methods,signature)
-importFrom(methods,slot)
 useDynLib(rSFSW2, .registration = TRUE)