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inttest/codegeneration: Update baseline post-86d6822
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@lentinj
lentinj committed Mar 26, 2024
1 parent 0c04ecd commit 545f80b
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Showing 2 changed files with 20 additions and 20 deletions.
18 changes: 9 additions & 9 deletions inttest/codegeneration/ling.R
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@ structure(function (param)
stopifnot("ling.rec.2017" %in% names(param))
stopifnot("ling.rec.2018" %in% names(param))
stopifnot("cdist_sumofsquares_ldist_lln_weight" %in% names(param))
as_integer <- as.integer
normalize_vec <- function(a) {
a/sum(a)
}
Expand Down Expand Up @@ -162,7 +163,6 @@ structure(function (param)
retro_years <- param[["retro_years"]]
start_year <- 1994L
total_steps <- length(step_lengths) * (end_year - retro_years - start_year + 0L) + length(step_lengths) - 1L
as_integer <- as.integer
nll_understocking__wgt <- array(0, dim = c(time = as_integer(total_steps + 1L)), dimnames = list(time = attributes(gen_dimnames(param))[["time"]]))
nll <- 0
cur_year <- 0L
Expand Down Expand Up @@ -249,8 +249,8 @@ structure(function (param)
{
area <- ling_imm__area
ling_imm__area_idx <- (1L)
factor <- (param[["lingimm.init.scalar"]] * exp(-1 * (param[["lingimm.M"]] + param[["ling.init.F"]]) * age) * param[["lingimm.init"]][[age - 3 + 1]])
dnorm <- ((ling_imm__midlen - (param[["ling.Linf"]] * (1 - exp(-1 * param[["ling.K"]] * ((age - cur_step_size) - (param[["recage"]] + log(1 - param[["ling.recl"]]/param[["ling.Linf"]])/param[["ling.K"]]))))))/ling_imm_stddev[[(age - cur_step_size) - 3 + 2]])
factor <- (param[["lingimm.init.scalar"]] * exp(-1 * (param[["lingimm.M"]] + param[["ling.init.F"]]) * age) * param[["lingimm.init"]][[as_integer(age) - 3 + 1]])
dnorm <- ((ling_imm__midlen - (param[["ling.Linf"]] * (1 - exp(-1 * param[["ling.K"]] * ((age - cur_step_size) - (param[["recage"]] + log(1 - param[["ling.recl"]]/param[["ling.Linf"]])/param[["ling.K"]]))))))/ling_imm_stddev[[as_integer((age - cur_step_size)) - 3 + 2]])
{
ling_imm__num[, ling_imm__area_idx, ling_imm__age_idx] <- normalize_vec(exp(-(dnorm^2) * 0.5)) * 10000 * factor
ling_imm__wgt[, ling_imm__area_idx, ling_imm__age_idx] <- param[["lingimm.walpha"]] * ling_imm__midlen^param[["lingimm.wbeta"]]
Expand All @@ -265,8 +265,8 @@ structure(function (param)
{
area <- ling_mat__area
ling_mat__area_idx <- (1L)
factor <- (param[["lingmat.init.scalar"]] * exp(-1 * (param[["lingmat.M"]] + param[["ling.init.F"]]) * age) * param[["lingmat.init"]][[age - 5 + 1]])
dnorm <- ((ling_mat__midlen - (param[["ling.Linf"]] * (1 - exp(-1 * param[["ling.K"]] * ((age - cur_step_size) - (param[["recage"]] + log(1 - param[["ling.recl"]]/param[["ling.Linf"]])/param[["ling.K"]]))))))/ling_mat_stddev[[(age - cur_step_size) - 5 + 2]])
factor <- (param[["lingmat.init.scalar"]] * exp(-1 * (param[["lingmat.M"]] + param[["ling.init.F"]]) * age) * param[["lingmat.init"]][[as_integer(age) - 5 + 1]])
dnorm <- ((ling_mat__midlen - (param[["ling.Linf"]] * (1 - exp(-1 * param[["ling.K"]] * ((age - cur_step_size) - (param[["recage"]] + log(1 - param[["ling.recl"]]/param[["ling.Linf"]])/param[["ling.K"]]))))))/ling_mat_stddev[[as_integer((age - cur_step_size)) - 5 + 2]])
{
ling_mat__num[, ling_mat__area_idx, ling_mat__age_idx] <- normalize_vec(exp(-(dnorm^2) * 0.5)) * 10000 * factor
ling_mat__wgt[, ling_mat__area_idx, ling_mat__age_idx] <- param[["lingmat.walpha"]] * ling_mat__midlen^param[["lingmat.wbeta"]]
Expand Down Expand Up @@ -578,11 +578,11 @@ structure(function (param)
}))
{
comment("g3a_renewal for ling_imm")
for (age in seq(ling_imm__minage, ling_imm__maxage, by = 1)) if (cur_step == 1 && age == 5) {
for (age in seq(ling_imm__minage, ling_imm__maxage, by = 1)) if (cur_step == 1 && age == 3) {
ling_imm__age_idx <- age - ling_imm__minage + 1L
area <- ling_imm__area
ling_imm__area_idx <- (1L)
dnorm <- ((ling_imm__midlen - (param[["ling.Linf"]] * (1 - exp(-1 * param[["ling.K"]] * (age - (param[["recage"]] + log(1 - param[["ling.recl"]]/param[["ling.Linf"]])/param[["ling.K"]]))))))/ling_imm_stddev[[age - 3L + 1L]])
dnorm <- ((ling_imm__midlen - (param[["ling.Linf"]] * (1 - exp(-1 * param[["ling.K"]] * (age - (param[["recage"]] + log(1 - param[["ling.recl"]]/param[["ling.Linf"]])/param[["ling.K"]]))))))/ling_imm_stddev[[as_integer(age) - 3 + 1]])
{
ling_imm__renewalnum[, ling_imm__area_idx, ling_imm__age_idx] <- normalize_vec(exp(-(dnorm^2) * 0.5)) * 10000 * factor
ling_imm__renewalwgt[, ling_imm__area_idx, ling_imm__age_idx] <- param[["lingimm.walpha"]] * ling_imm__midlen^param[["lingimm.wbeta"]]
Expand All @@ -600,11 +600,11 @@ structure(function (param)
}))
{
comment("g3a_renewal for ling_imm")
for (age in seq(ling_imm__minage, ling_imm__maxage, by = 1)) if (cur_step == 1 && age == 3) {
for (age in seq(ling_imm__minage, ling_imm__maxage, by = 1)) if (cur_step == 1 && age == 5) {
ling_imm__age_idx <- age - ling_imm__minage + 1L
area <- ling_imm__area
ling_imm__area_idx <- (1L)
dnorm <- ((ling_imm__midlen - (param[["ling.Linf"]] * (1 - exp(-1 * param[["ling.K"]] * (age - (param[["recage"]] + log(1 - param[["ling.recl"]]/param[["ling.Linf"]])/param[["ling.K"]]))))))/ling_imm_stddev[[age - 3 + 1]])
dnorm <- ((ling_imm__midlen - (param[["ling.Linf"]] * (1 - exp(-1 * param[["ling.K"]] * (age - (param[["recage"]] + log(1 - param[["ling.recl"]]/param[["ling.Linf"]])/param[["ling.K"]]))))))/ling_imm_stddev[[as_integer(age) - 3L + 1L]])
{
ling_imm__renewalnum[, ling_imm__area_idx, ling_imm__age_idx] <- normalize_vec(exp(-(dnorm^2) * 0.5)) * 10000 * factor
ling_imm__renewalwgt[, ling_imm__area_idx, ling_imm__age_idx] <- param[["lingimm.walpha"]] * ling_imm__midlen^param[["lingimm.wbeta"]]
Expand Down
22 changes: 11 additions & 11 deletions inttest/codegeneration/ling.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,9 @@ Type objective_function<Type>::operator() () {
PARAMETER(ling__rec__2018);
std::map<std::tuple<int>, Type*> ling__rec = {{std::make_tuple(1994), &ling__rec__1994}, {std::make_tuple(1995), &ling__rec__1995}, {std::make_tuple(1996), &ling__rec__1996}, {std::make_tuple(1997), &ling__rec__1997}, {std::make_tuple(1998), &ling__rec__1998}, {std::make_tuple(1999), &ling__rec__1999}, {std::make_tuple(2000), &ling__rec__2000}, {std::make_tuple(2001), &ling__rec__2001}, {std::make_tuple(2002), &ling__rec__2002}, {std::make_tuple(2003), &ling__rec__2003}, {std::make_tuple(2004), &ling__rec__2004}, {std::make_tuple(2005), &ling__rec__2005}, {std::make_tuple(2006), &ling__rec__2006}, {std::make_tuple(2007), &ling__rec__2007}, {std::make_tuple(2008), &ling__rec__2008}, {std::make_tuple(2009), &ling__rec__2009}, {std::make_tuple(2010), &ling__rec__2010}, {std::make_tuple(2011), &ling__rec__2011}, {std::make_tuple(2012), &ling__rec__2012}, {std::make_tuple(2013), &ling__rec__2013}, {std::make_tuple(2014), &ling__rec__2014}, {std::make_tuple(2015), &ling__rec__2015}, {std::make_tuple(2016), &ling__rec__2016}, {std::make_tuple(2017), &ling__rec__2017}, {std::make_tuple(2018), &ling__rec__2018}};
PARAMETER(cdist_sumofsquares_ldist_lln_weight);
auto as_integer = [](Type v) -> int {
return std::floor(asDouble(v));
};
auto normalize_vec = [](vector<Type> a) -> vector<Type> {
return a / a.sum();
};
Expand Down Expand Up @@ -229,9 +232,6 @@ Type objective_function<Type>::operator() () {
int end_year = 2018;
int start_year = 1994;
auto total_steps = (step_lengths).size()*(end_year - retro_years - start_year + 0) + (step_lengths).size() - 1;
auto as_integer = [](Type v) -> int {
return std::floor(asDouble(v));
};
array<Type> nll_understocking__wgt(as_integer(total_steps + 1)); nll_understocking__wgt.setZero();
Type nll = (double)(0);
int cur_year = 0;
Expand Down Expand Up @@ -297,9 +297,9 @@ Type objective_function<Type>::operator() () {

auto ling_imm__area_idx = 0;

auto factor = (lingimm__init__scalar*exp(-(double)(1)*(lingimm__M + ling__init__F)*age)*lingimm__init ( age - 3 + 1 - 1 ));
auto factor = (lingimm__init__scalar*exp(-(double)(1)*(lingimm__M + ling__init__F)*age)*lingimm__init ( as_integer(age) - 3 + 1 - 1 ));

auto dnorm = ((ling_imm__midlen - (ling__Linf*((double)(1) - exp(-(double)(1)*ling__K*((age - cur_step_size) - (recage + log((double)(1) - ling__recl / ling__Linf) / ling__K)))))) / ling_imm_stddev ( (age - cur_step_size) - 3 + 2 - 1 ));
auto dnorm = ((ling_imm__midlen - (ling__Linf*((double)(1) - exp(-(double)(1)*ling__K*((age - cur_step_size) - (recage + log((double)(1) - ling__recl / ling__Linf) / ling__K)))))) / ling_imm_stddev ( as_integer((age - cur_step_size)) - 3 + 2 - 1 ));

{
ling_imm__num.col(ling_imm__age_idx).col(ling_imm__area_idx) = normalize_vec(exp(-(pow(dnorm, (Type)(double)(2)))*(double)(0.5)))*(double)(10000)*factor;
Expand All @@ -318,9 +318,9 @@ Type objective_function<Type>::operator() () {

auto ling_mat__area_idx = 0;

auto factor = (lingmat__init__scalar*exp(-(double)(1)*(lingmat__M + ling__init__F)*age)*lingmat__init ( age - 5 + 1 - 1 ));
auto factor = (lingmat__init__scalar*exp(-(double)(1)*(lingmat__M + ling__init__F)*age)*lingmat__init ( as_integer(age) - 5 + 1 - 1 ));

auto dnorm = ((ling_mat__midlen - (ling__Linf*((double)(1) - exp(-(double)(1)*ling__K*((age - cur_step_size) - (recage + log((double)(1) - ling__recl / ling__Linf) / ling__K)))))) / ling_mat_stddev ( (age - cur_step_size) - 5 + 2 - 1 ));
auto dnorm = ((ling_mat__midlen - (ling__Linf*((double)(1) - exp(-(double)(1)*ling__K*((age - cur_step_size) - (recage + log((double)(1) - ling__recl / ling__Linf) / ling__K)))))) / ling_mat_stddev ( as_integer((age - cur_step_size)) - 5 + 2 - 1 ));

{
ling_mat__num.col(ling_mat__age_idx).col(ling_mat__area_idx) = normalize_vec(exp(-(pow(dnorm, (Type)(double)(2)))*(double)(0.5)))*(double)(10000)*factor;
Expand Down Expand Up @@ -691,14 +691,14 @@ Type objective_function<Type>::operator() () {

{
// g3a_renewal for ling_imm;
for (auto age = ling_imm__minage; age <= ling_imm__maxage; age++) if ( cur_step == 1 && age == 5 ) {
for (auto age = ling_imm__minage; age <= ling_imm__maxage; age++) if ( cur_step == 1 && age == 3 ) {
auto ling_imm__age_idx = age - ling_imm__minage + 1 - 1;

auto area = ling_imm__area;

auto ling_imm__area_idx = 0;

auto dnorm = ((ling_imm__midlen - (ling__Linf*((double)(1) - exp(-(double)(1)*ling__K*(age - (recage + log((double)(1) - ling__recl / ling__Linf) / ling__K)))))) / ling_imm_stddev ( age - 3 + 1 - 1 ));
auto dnorm = ((ling_imm__midlen - (ling__Linf*((double)(1) - exp(-(double)(1)*ling__K*(age - (recage + log((double)(1) - ling__recl / ling__Linf) / ling__K)))))) / ling_imm_stddev ( as_integer(age) - 3 + 1 - 1 ));

{
ling_imm__renewalnum.col(ling_imm__age_idx).col(ling_imm__area_idx) = normalize_vec(exp(-(pow(dnorm, (Type)(double)(2)))*(double)(0.5)))*(double)(10000)*factor;
Expand All @@ -715,14 +715,14 @@ Type objective_function<Type>::operator() () {

{
// g3a_renewal for ling_imm;
for (auto age = ling_imm__minage; age <= ling_imm__maxage; age++) if ( cur_step == 1 && age == 3 ) {
for (auto age = ling_imm__minage; age <= ling_imm__maxage; age++) if ( cur_step == 1 && age == 5 ) {
auto ling_imm__age_idx = age - ling_imm__minage + 1 - 1;

auto area = ling_imm__area;

auto ling_imm__area_idx = 0;

auto dnorm = ((ling_imm__midlen - (ling__Linf*((double)(1) - exp(-(double)(1)*ling__K*(age - (recage + log((double)(1) - ling__recl / ling__Linf) / ling__K)))))) / ling_imm_stddev ( age - 3 + 1 - 1 ));
auto dnorm = ((ling_imm__midlen - (ling__Linf*((double)(1) - exp(-(double)(1)*ling__K*(age - (recage + log((double)(1) - ling__recl / ling__Linf) / ling__K)))))) / ling_imm_stddev ( as_integer(age) - 3 + 1 - 1 ));

{
ling_imm__renewalnum.col(ling_imm__age_idx).col(ling_imm__area_idx) = normalize_vec(exp(-(pow(dnorm, (Type)(double)(2)))*(double)(0.5)))*(double)(10000)*factor;
Expand Down

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