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Added descriptions to rgroup_Establish, clarified comments in _add_an…
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…nuals and formatted code
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kpalmqui committed May 30, 2018
1 parent 43cf852 commit 9370619
Showing 1 changed file with 51 additions and 62 deletions.
113 changes: 51 additions & 62 deletions ST_resgroups.c
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Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,7 @@ static RealF _add_annuals(const GrpIndex rg, const SppIndex sp, const RealF last
* seeds from the seedbank.*/

IntU i, num_est; //number of individuals that will establish this year
RealF viable_seeds; //viable seed
RealF viable_seeds; //number of viable seeds in the seedbank
float var; //random number draw from beta distribution for calculation of num_est
GroupType *g;
SpeciesType *s;
Expand All @@ -204,12 +204,12 @@ static RealF _add_annuals(const GrpIndex rg, const SppIndex sp, const RealF last
/*Get viable seeds from seed bank*/
viable_seeds = (g->regen_ok) ? _get_annual_maxestab(sp) : 0;

/*Create a beta random number draw based on alpha and beta for each species (calculated based on mean (s->seedling_estab_prob
* and variance (s->var)) */
/* Create a beta random number draw based on alpha and beta for each species
* (calculated based on mean (s->seedling_estab_prob and variance (s->var)) */
var = RandBeta(Species[sp]->alpha, Species[sp]->beta);

/*Determine number of seedlings to add. If the beta random number of viable seeds
* is larger than max_seed_estab, max_seed_estab value is used instead*/
/*Determine number of seedlings to add. If the number of seeds calculated
* from the random draw is larger than max_seed_estab, max_seed_estab is used instead*/
num_est = min(viable_seeds * var, s->max_seed_estab);
//printf("Species name=%s , num_est =%u \n",s->name, num_est);

Expand All @@ -226,19 +226,18 @@ static RealF _add_annuals(const GrpIndex rg, const SppIndex sp, const RealF last

static RealF _get_annual_maxestab(SppIndex sp) {
/*======================================================*/
/* Get the maximum number of viable seeds from the seedbank that can
establish this year*/
/* Get the maximum number of viable seeds from the seedbank that can
establish this year*/
IntU i;
RealF sum = 0.; //sum of the viable seedbank
SpeciesType *s = Species[sp];

for (i = 0; i <= s->viable_yrs; i++)
{

for (i = 0; i <= s->viable_yrs; i++) {
sum += s->seedprod[i];
}
//printf("sum =%f \n",sum);
return sum;

return sum;
}

static void _add_annual_seedprod(SppIndex sp, RealF lastyear_relsize) {
Expand All @@ -250,25 +249,26 @@ static void _add_annual_seedprod(SppIndex sp, RealF lastyear_relsize) {

/*Age of seeds is increased by one year, seed mortality occurs, and seeds produced in the
previous year are added to the seedbank at relative age 0 */
for (i = s->viable_yrs - 1; i > 0; i--)
{
for (i = s->viable_yrs - 1; i > 0; i--) {
//printf("Species name=%s , seedprod before decay s->seedprod[%hu]= %d \n", s->name, i, s->seedprod[i]);
s->seedprod[i] = s->seedprod[i - 1] / pow(i, s->exp_decay);
//printf("Species name=%s , seedprod after decay s->seedprod[%hu]= %d \n", s->name, i, s->seedprod[i]);
}

// printf("Species name=%s ,old Array array 0 index i=%u, value =%hu \n", s->name, i, s->seedprod[i]);

//If the current year is year 1 of the simulation, then the number of seeds added is a random number draw between
//1 and the maximum number of seedlings that can establish. Otherwise, this year's seed production is a function of the number
//of seeds produced per unit biomass, max biomass, and last year's species relative size.
// printf("Species name=%s ,old Array array 0 index i=%u, value =%hu \n", s->name, i, s->seedprod[i]);

/* If the current year is year 1 of the simulation, then the number of seeds
* added is a random number draw between 1 and the maximum number of seedlings
* that can establish. Otherwise, this year's seed production is a function
* of the number of seeds produced per unit biomass multiplied by species biomass
* (maximum species biomass * last year's species relative size). */
if (Globals.currYear == 1) {
s->seedprod[0] = RandUniRange(1, s->max_seed_estab);
//printf("Species name=%s ,currYear =1 so new calculated value s->seedprod[%u]= %hu , s->max_seed_estab =%hu\n", s->name, i, s->seedprod[i], s->max_seed_estab);
//printf("Species name=%s ,currYear =1 so new calculated value s->seedprod[%u]= %hu , s->max_seed_estab =%hu\n", s->name, i, s->seedprod[i], s->max_seed_estab);

} else {
s->seedprod[0] = (IntU)(s->pseed * s->mature_biomass * lastyear_relsize);
//printf("Species name=%s ,currYear=%hu so new calculated value s->seedprod[%u]= %hu , s->max_seed_estab =%hu, lastyear_relsize=%.5f\n", s->name, Globals.currYear, i, s->seedprod[i], s->max_seed_estab, lastyear_relsize);
s->seedprod[0] = (IntU) (s->pseed * s->mature_biomass * lastyear_relsize);
//printf("Species name=%s ,currYear=%hu so new calculated value s->seedprod[%u]= %hu , s->max_seed_estab =%hu, lastyear_relsize=%.5f\n", s->name, Globals.currYear, i, s->seedprod[i], s->max_seed_estab, lastyear_relsize);
}
}

Expand Down Expand Up @@ -619,47 +619,30 @@ static void _extra_growth(GrpIndex rg)
}

}

/***********************************************************/
void rgroup_Establish(void) {
/*======================================================*/
/* PURPOSE */
/* Determines which and how many species can establish
in a given year.
For each species in each group, check that a uniform
random number between 0 and 1 is less than the species'
establishment probability.
a) If so, return a random number of individuals,
up to the maximum allowed to establish for the
species. This is the number of individuals in
this species that will establish this year.
b) If not, continue with the next species.
*/
/* Determines which and how many species can establish in a given year. For
* each species in each perennial functional group, check that a uniform
* random number between 0 and 1 is less than the species' establishment
* probability. a) If so, return a random number of individuals up to the
* maximum allowed to establish for the species. This is the number of individuals
* in this species that will establish this year. b) If not, continue with
* the next species. Establishment for species of annual functional groups
* occurs differently. See notes at the top of _add_annuals */

/* HISTORY */
/* Chris Bennett @ LTER-CSU 6/15/2000 */
/* cwb (3/7/01) - Complete rewrite that simplifies the
process and attempts to make the total number of
seedlings established match the probability of
establishment.
cwb (3/30) - Actually the probability of establishment
emulates the occurrance of microsite conditions that
allow establishment. There may be more seedlings
established than indicated by the probability.
* 7-Nov-03 (cwb) Adding the new algorithm to handle annuals.
* It's more complicated than before (which didn't really
* work) so annuals are now added in the PartResources()
* function. Only perennials are added here.
*
* Also, there's now a parameter to define the start year
* of establishment for perennials.
*
* KAP: Annual establishment now occurs here instead of in PartResources
*/
/* Chris Bennett @ LTER-CSU 6/15/2000 */
/* The probability of establishment emulates the occurrence of microsite
* conditions that allow for establishment.
* 7-Nov-03 (cwb) Adding the new algorithm to handle annuals. It's more
* complicated than before (which didn't really work) so annuals are now added
* in the PartResources()function. Only perennials are added here. Also, there's
* now a parameter to define the start year of establishment for perennials.
* KAP: Annual establishment now occurs here instead of in PartResources*/
/*------------------------------------------------------*/

IntS i, num_est; /* number of individuals of sp. that establish*/
GrpIndex rg;
SppIndex sp;
Expand All @@ -672,6 +655,7 @@ void rgroup_Establish(void) {
return; /* skip regen for all */
}

/* If the functional group is turned off, continue */
ForEachGroup(rg) {
g = RGroup[rg];
if (!g->use_me)
Expand All @@ -695,19 +679,24 @@ void rgroup_Establish(void) {
///} else
//above removed allow annuals to establish with other species (TEM 10-27-2015)
{

ForEachGroupSpp(sp, rg, i) {

/* If the species is turned off, continue */
if (!Species[sp]->use_me)
continue;
if (!Species[sp]->allow_growth)
continue;

/* Establishment for species that belong to annual functional groups*/
if (Species[sp]->max_age == 1) {
//printf("Globals.currYear = %hu, call to _add_annuals sp=%d Species[sp]->lastyear_relsize : %.5f \n", Globals.currYear, sp, Species[sp]->lastyear_relsize);
num_est = _add_annuals(rg, sp, Species[sp]->lastyear_relsize);
// printf("g->seedbank annuals=%d \n",g->seedbank);
}
else {
// printf("g->seedbank annuals=%d \n",g->seedbank);
}

/* Establishment for species that belong to perennial functional groups*/
else {
num_est = Species_NumEstablish(sp);
}

Expand All @@ -719,9 +708,9 @@ void rgroup_Establish(void) {
species_Update_Estabs(sp, num_est);
}

}
} /* end ForEachGroupSpp() */
}
}
} /* end ForEachGroup() */
}
/***********************************************************/
void rgroup_IncrAges(void)
Expand Down

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