Merge pull request #226 from DrylandEcology/feature_vegestab

Resurrect "vegetation establishment"

* `SOILWAT2` is updated to v6.7.0 which fixed vegetation establishment.

* Functionality to calculate and output establishment/recruitment of species now works and is covered by tests (issue #225, @dschlaep). Note that this functionality assesses yearly the chances of species to recruit/establish based on simulated daily conditions; however, establishment/recruitment outcomes are not utilized to inform the simulation.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rSOILWAT2
-Version: 5.3.3
+Version: 5.4.0
 Title: An Ecohydrological Ecosystem-Scale Water Balance Simulation Model
-Description: Access to the C-based SOILWAT2 v6.6.0 and functionality for
+Description: Access to the C-based SOILWAT2 v6.7.0 and functionality for
   SQLite-database of weather data.
 Authors@R: c(
   person(

NEWS.md

@@ -1,3 +1,21 @@
+# rSOILWAT2 v5.4.0
+* `SOILWAT2` is updated to v6.7.0 which fixed vegetation establishment.
+* This version produces identical simulation output
+  as the previous release under default values
+  (i.e., vegetation establishment is turned off).
+
+* Functionality to calculate and output establishment/recruitment of species
+  now works and is covered by tests (issue #225, @dschlaep).
+  Note that this functionality assesses yearly the chances of
+  species to recruit/establish based on simulated daily conditions;
+  however, establishment/recruitment outcomes are not utilized to inform the
+  simulation.
+
+## Changes to interface
+* Class `swEstabSpecies` gains new slot `"vegType"` to specify vegetation type
+  of a species establishment parameters (issue #225, @dschlaep).
+
+
 # rSOILWAT2 v5.3.3
 * This version produces identical simulation output as the previous release.
 * `get_soiltemp()` now correctly locates soil temperature output for all

R/I_swEstab.R

@@ -46,6 +46,7 @@
 #' @name swEstabSpecies-class
 #' @export
 setClass("swEstabSpecies", slot = c(fileName = "character", Name = "character",
+  vegType = "integer",
   estab_lyrs = "integer", barsGERM = "numeric", barsESTAB = "numeric",
   min_pregerm_days = "integer", max_pregerm_days = "integer",
   min_wetdays_for_germ = "integer", max_drydays_postgerm = "integer",

data-raw/prepare_testInput_objects.R

@@ -21,7 +21,7 @@ dir_in <- file.path("inst", "extdata")
 dir_backup <- sub("extdata", "extdata_copy", dir_in, fixed = TRUE)
 dir_out <- file.path("tests", "test_data")
 
-tests <- 1:5
+tests <- 1:6
 examples <- paste0("example", tests)
 
 
@@ -119,6 +119,20 @@ for (it in seq_along(tests)) {
   substr(fin[line], 1, 3) <- "-45"
   writeLines(fin, con = ftemp)
 
+# example6: vegetation establishment
+  ftemp <- file.path(dir_in, examples[6], "Input", "estab.in")
+  fin <- readLines(ftemp)
+  line <- grep("calculate and output establishment", fin, fixed = TRUE)
+  stopifnot(length(line) == 1, line > 0, line < length(fin))
+  substr(fin[line], 1, 1) <- "1"
+  writeLines(fin, con = ftemp)
+
+  ftemp <- file.path(dir_in, examples[6], "Input", "outsetup.in")
+  fin <- readLines(ftemp)
+  line <- grep("establishment results", fin, fixed = TRUE)
+  stopifnot(length(line) == 1, line > 0, line < length(fin))
+  fin[line] <- sub("OFF", "AVG", fin[line], fixed = TRUE)
+  writeLines(fin, con = ftemp)
 
 
 

inst/extdata/example1/Input/estab.in

@@ -11,6 +11,7 @@
 # soil moisture and timing parameters required for the
 # species to establish in a given year.
 # There is no limit to the number of files in the list.
+# File names with paths relative to the SOILWAT2 working directory (-d flag)
 
-Input/bouteloua.estab
-Input/bromus.estab
+Input/estab/bouteloua.estab
+Input/estab/bromus.estab

inst/extdata/example1/Input/bouteloua.estab → inst/extdata/example1/Input/estab/bouteloua.estab

@@ -1,18 +1,19 @@
-bogr	# 4-char name of species
+bogr # 4-char name of species
+3    # Vegetation type of species (0, trees; 1, shrubs; 2, forbs; 3 grasses)
 # soil layer parameters
 2    # number of layers affecting establishment
 10.  # SWP (bars) requirement for germination (top layer)
 15.  # SWP (bars) requirement for establishment (average of top layers)
 # timing parameters in days
 60   # first possible day of germination
-180  # last possible day of germination 
+180  # last possible day of germination
 2    # min number of consecutive "wet" days for germination to occur
-40    # max number of consecutive "dry" days after germination allowing estab 
+40    # max number of consecutive "dry" days after germination allowing estab
 5    # min number of consecutive "wet" days after germination before establishment
-15   # min number of days between germination and establishment 
-75   # max number of days between germination and establishment 
+15   # min number of days between germination and establishment
+75   # max number of days between germination and establishment
 # temperature parameters in C
-5.  # min temp threshold for germination 
-20.  # max temp threshold for germination  
-0.  # min temp threshold for establishment 
-20.  # max temp threshold for establishment  
+5.  # min temp threshold for germination
+20.  # max temp threshold for germination
+0.  # min temp threshold for establishment
+20.  # max temp threshold for establishment

inst/extdata/example1/Input/bromus.estab → inst/extdata/example1/Input/estab/bromus.estab

@@ -1,4 +1,5 @@
 brte # 4-char name of species
+3    # Vegetation type of species (0, trees; 1, shrubs; 2, forbs; 3 grasses)
 # soil layer parameters
 3    # number of layers affecting establishment - 45 cm Harris and Hulbert
 10.  # SWP (bars) requirement for germination (top layer) - Harris
@@ -7,12 +8,12 @@ brte # 4-char name of species
 200   # first possible day of germination - Hulbert and Harris
 365  # last possible day of germination  - Hulbert
 6    # min number of consecutive "wet" days for germination to occur  - Hurlbert and Harris
-45    # max number of consecutive "dry" days after germination allowing estab - Harris (longtime) 
+45    # max number of consecutive "dry" days after germination allowing estab - Harris (longtime)
 6    # min number of consecutive "wet" days after germination before establishment - Harris
 15   # min number of days between germination and establishment  - Hulbert
 90   # max number of days between germination and establishment - Harris and Hulbert
 # temperature parameters in C
 10.  # min temp threshold for germination - Hulbert and Harris
 30.  # max temp threshold for germination - Hulbert and Harris
 3.  # min temp threshold for establishment - Harris
-30.  # max temp threshold for establishment - Harris and Hulbert  
+30.  # max temp threshold for establishment - Harris and Hulbert

src/rSW_Output.c

@@ -59,9 +59,7 @@ void onSet_SW_OUT(SEXP OUT) {
 	int *use, *timePeriods, *sumtype, *first_orig, *last_orig;
 	// mykey and myobj are currently unused:
 	// int *mykey, *myobj;
-	char
-		stub[10],
-		msg[200]; // message to print
+	char msg[200]; // message to print
 	#ifdef RSWDEBUG
 	int debug = 0;
 	#endif
@@ -89,19 +87,14 @@ void onSet_SW_OUT(SEXP OUT) {
 	last_orig = INTEGER(GET_SLOT(OUT, install("last_orig")));
 	PROTECT(outfile = GET_SLOT(OUT, install("outfile")));
 
-	if (use[eSW_Estab]) {
-		sumtype[eSW_Estab] = eSW_Sum;
-		first_orig[eSW_Estab] = 1;
-		timePeriods[eSW_Estab + 0 * SW_OUTNKEYS] = eSW_Year;
-		ForEachOutPeriod(i) {
-			timePeriods[eSW_Estab + i * SW_OUTNKEYS] = eSW_NoTime;
-		}
-		last_orig[eSW_Estab] = 366;
-	}
-
 	ForEachOutKey(k) {
-		msg_type = SW_OUT_read_onekey(k, sumtype[k], stub, first_orig[k],
-			last_orig[k], msg);
+		msg_type = SW_OUT_read_onekey(
+			k,
+			sumtype[k],
+			first_orig[k],
+			last_orig[k],
+			msg
+		);
 
 		if (msg_type > 0) {
 			LogError(logfp, msg_type, "%s", msg);

src/rSW_VegEstab.c

@@ -49,15 +49,23 @@ SEXP onGet_SW_VES(void) {
 	SEXP VES;
 	SEXP use;
 	SEXP count;
+
 	PROTECT(swEstab = MAKE_CLASS("swEstab"));
 	PROTECT(VES = NEW_OBJECT(swEstab));
-	PROTECT(use = NEW_LOGICAL(1));
+
 	PROTECT(count = NEW_INTEGER(1));
 	INTEGER(count)[0] = SW_VegEstab.count;
+
+	PROTECT(use = NEW_LOGICAL(1));
 	LOGICAL(use)[0] = SW_VegEstab.use;
+
+	SET_SLOT(VES, install("count"), count);
 	SET_SLOT(VES, install("useEstab"), use);
-	if (SW_VegEstab.use)
+
+	if (SW_VegEstab.use) {
 		onGet_SW_VES_spps(VES);
+	}
+
 	UNPROTECT(4);
 	return VES;
 }
@@ -71,6 +79,7 @@ void onSet_SW_VES(SEXP VES) {
 
 	PROTECT(use = GET_SLOT(VES,install("useEstab")));
 	PROTECT(count = GET_SLOT(VES,install("count")));
+
 	if (LOGICAL(use)[0] == FALSE) {
 		//LogError(logfp, LOGNOTE, "Establishment not used.\n");
 		SW_VegEstab.use = FALSE;
@@ -82,7 +91,7 @@ void onSet_SW_VES(SEXP VES) {
 		} else {
 			SW_VegEstab.use = TRUE;
 			for (i = 0; i < nSPPS; i++)
-				onSet_SW_VES_spp(VES, i);
+				onSet_SW_VES_spp(VES, i); // sets `SW_VegEstab.count` incrementally
 		}
 	}
 
@@ -100,11 +109,12 @@ void onSet_SW_VES(SEXP VES) {
 void onGet_SW_VES_spps(SEXP SPP) {
 	int i;
 	SW_VEGESTAB_INFO *v;
-	SEXP fileName, name, estab_lyrs, barsGERM, barsESTAB, min_pregerm_days, max_pregerm_days, min_wetdays_for_germ, max_drydays_postgerm, min_wetdays_for_estab, min_days_germ2estab,
+	SEXP fileName, name, vegType, estab_lyrs, barsGERM, barsESTAB, min_pregerm_days, max_pregerm_days, min_wetdays_for_germ, max_drydays_postgerm, min_wetdays_for_estab, min_days_germ2estab,
 			max_days_germ2estab, min_temp_germ, max_temp_germ, min_temp_estab, max_temp_estab;
 
 	PROTECT(fileName = allocVector(STRSXP,SW_VegEstab.count));
 	PROTECT(name = allocVector(STRSXP,SW_VegEstab.count));
+	PROTECT(vegType = NEW_INTEGER(SW_VegEstab.count));
 	PROTECT(estab_lyrs = NEW_INTEGER(SW_VegEstab.count));
 	PROTECT(barsGERM = allocVector(REALSXP,SW_VegEstab.count));
 	PROTECT(barsESTAB = allocVector(REALSXP,SW_VegEstab.count));
@@ -124,6 +134,7 @@ void onGet_SW_VES_spps(SEXP SPP) {
 		v = SW_VegEstab.parms[i];
 		SET_STRING_ELT(fileName, i, mkChar(v->sppFileName));
 		SET_STRING_ELT(name, i, mkChar(v->sppname));
+		INTEGER(vegType)[i] = v->vegType;
 		INTEGER(estab_lyrs)[i] = v->estab_lyrs;
 		REAL(barsGERM)[i] = v->bars[0];
 		REAL(barsESTAB)[i] = v->bars[1];
@@ -141,6 +152,7 @@ void onGet_SW_VES_spps(SEXP SPP) {
 	}
 	SET_SLOT(SPP, install("fileName"), fileName);
 	SET_SLOT(SPP, install("Name"), name);
+	SET_SLOT(SPP, install("vegType"), vegType);
 	SET_SLOT(SPP, install("estab_lyrs"), estab_lyrs);
 	SET_SLOT(SPP, install("barsGERM"), barsGERM);
 	SET_SLOT(SPP, install("barsESTAB"), barsESTAB);
@@ -156,7 +168,7 @@ void onGet_SW_VES_spps(SEXP SPP) {
 	SET_SLOT(SPP, install("min_temp_estab"), min_temp_estab);
 	SET_SLOT(SPP, install("max_temp_estab"), max_temp_estab);
 
-	UNPROTECT(16);
+	UNPROTECT(17);
 }
 
 void onSet_SW_VES_spp(SEXP SPP, IntU i) {
@@ -167,6 +179,7 @@ void onSet_SW_VES_spp(SEXP SPP, IntU i) {
 	count = _new_species();
 	v = SW_VegEstab.parms[count];
 
+	v->vegType = INTEGER(GET_SLOT(SPP, install("vegType")))[i];
 	v->estab_lyrs = INTEGER(GET_SLOT(SPP, install("estab_lyrs")))[i];
 	v->bars[SW_GERM_BARS] = REAL(GET_SLOT(SPP, install("barsGERM")))[i];
 	v->bars[SW_ESTAB_BARS] = REAL(GET_SLOT(SPP, install("barsESTAB")))[i];