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Merge remote-tracking branch 'origin/master' into spectrum-art-alloc
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@jeffeaton
jeffeaton committed Dec 6, 2024
2 parents 30d4902 + 1f5b8d7 commit aa55658
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1 change: 1 addition & 0 deletions DESCRIPTION
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@@ -1,6 +1,7 @@
Package: eppasm
Title: Age-structured EPP Model for HIV Epidemic Estimates
Version: 0.8.1
Version: 0.7.7
Authors@R: person("Jeff", "Eaton", email = "[email protected]", role = c("aut", "cre"))
Description: What the package does (one paragraph).
Depends: R (>= 3.1.0),
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5 changes: 4 additions & 1 deletion NEWS.md
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Expand Up @@ -23,7 +23,10 @@
* Patch ART dropout implementation. Spectrum converts input ART dropout percent to an
annual rate using [dropout rate] = -log(1.0 - [input percent]).


## eppasm 0.7.7

* Update to use full names for R internal functions e.g. `Rf_allocVector` instead of `allocVector`. Shorthand names are no longer allowed in R v4.5.0. See Nov 10th news https://developer.r-project.org/blosxom.cgi/R-devel

## eppasm 0.7.6

* Update internal data country ISO3 list to contain St. Kitts & Nevis and Dominica
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150 changes: 75 additions & 75 deletions src/eppasm.cpp
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Expand Up @@ -232,148 +232,148 @@ extern "C" {
multi_array_ref<double, 4> paedsurv_artcd4dist(REAL(getListElement(s_fp, "paedsurv_artcd4dist")), extents[PROJ_YEARS][NG][hDS][hTS]);

// initialize output
SEXP s_pop = PROTECT(allocVector(REALSXP, pAG * NG * pDS * PROJ_YEARS));
SEXP s_pop_dim = PROTECT(allocVector(INTSXP, 4));
SEXP s_pop = PROTECT(Rf_allocVector(REALSXP, pAG * NG * pDS * PROJ_YEARS));
SEXP s_pop_dim = PROTECT(Rf_allocVector(INTSXP, 4));
INTEGER(s_pop_dim)[0] = pAG;
INTEGER(s_pop_dim)[1] = NG;
INTEGER(s_pop_dim)[2] = pDS;
INTEGER(s_pop_dim)[3] = PROJ_YEARS;
setAttrib(s_pop, R_DimSymbol, s_pop_dim);
memset(REAL(s_pop), 0, length(s_pop)*sizeof(double));
Rf_setAttrib(s_pop, R_DimSymbol, s_pop_dim);
memset(REAL(s_pop), 0, Rf_length(s_pop)*sizeof(double));

SEXP s_hivpop = PROTECT(allocVector(REALSXP, hDS * hAG * NG * PROJ_YEARS));
SEXP s_hivpop_dim = PROTECT(allocVector(INTSXP, 4));
SEXP s_hivpop = PROTECT(Rf_allocVector(REALSXP, hDS * hAG * NG * PROJ_YEARS));
SEXP s_hivpop_dim = PROTECT(Rf_allocVector(INTSXP, 4));
INTEGER(s_hivpop_dim)[0] = hDS;
INTEGER(s_hivpop_dim)[1] = hAG;
INTEGER(s_hivpop_dim)[2] = NG;
INTEGER(s_hivpop_dim)[3] = PROJ_YEARS;
setAttrib(s_hivpop, R_DimSymbol, s_hivpop_dim);
setAttrib(s_pop, install("hivpop"), s_hivpop);
memset(REAL(s_hivpop), 0, length(s_hivpop)*sizeof(double));
Rf_setAttrib(s_hivpop, R_DimSymbol, s_hivpop_dim);
Rf_setAttrib(s_pop, Rf_install("hivpop"), s_hivpop);
memset(REAL(s_hivpop), 0, Rf_length(s_hivpop)*sizeof(double));

SEXP s_artpop = PROTECT(allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
SEXP s_artpop_dim = PROTECT(allocVector(INTSXP, 5));
SEXP s_artpop = PROTECT(Rf_allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
SEXP s_artpop_dim = PROTECT(Rf_allocVector(INTSXP, 5));
INTEGER(s_artpop_dim)[0] = hTS;
INTEGER(s_artpop_dim)[1] = hDS;
INTEGER(s_artpop_dim)[2] = hAG;
INTEGER(s_artpop_dim)[3] = NG;
INTEGER(s_artpop_dim)[4] = PROJ_YEARS;
setAttrib(s_artpop, R_DimSymbol, s_artpop_dim);
setAttrib(s_pop, install("artpop"), s_artpop);
memset(REAL(s_artpop), 0, length(s_artpop)*sizeof(double));
Rf_setAttrib(s_artpop, R_DimSymbol, s_artpop_dim);
Rf_setAttrib(s_pop, Rf_install("artpop"), s_artpop);
memset(REAL(s_artpop), 0, Rf_length(s_artpop)*sizeof(double));

SEXP s_infections = PROTECT(allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_infections_dim = PROTECT(allocVector(INTSXP, 3));
SEXP s_infections = PROTECT(Rf_allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_infections_dim = PROTECT(Rf_allocVector(INTSXP, 3));
INTEGER(s_infections_dim)[0] = pAG;
INTEGER(s_infections_dim)[1] = NG;
INTEGER(s_infections_dim)[2] = PROJ_YEARS;
setAttrib(s_infections, R_DimSymbol, s_infections_dim);
setAttrib(s_pop, install("infections"), s_infections);
Rf_setAttrib(s_infections, R_DimSymbol, s_infections_dim);
Rf_setAttrib(s_pop, Rf_install("infections"), s_infections);
multi_array_ref<double, 3> infections(REAL(s_infections), extents[PROJ_YEARS][NG][pAG]);
memset(REAL(s_infections), 0, length(s_infections)*sizeof(double));
memset(REAL(s_infections), 0, Rf_length(s_infections)*sizeof(double));

SEXP s_hivdeaths = PROTECT(allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_hivdeaths_dim = PROTECT(allocVector(INTSXP, 3));
SEXP s_hivdeaths = PROTECT(Rf_allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_hivdeaths_dim = PROTECT(Rf_allocVector(INTSXP, 3));
INTEGER(s_hivdeaths_dim)[0] = pAG;
INTEGER(s_hivdeaths_dim)[1] = NG;
INTEGER(s_hivdeaths_dim)[2] = PROJ_YEARS;
setAttrib(s_hivdeaths, R_DimSymbol, s_hivdeaths_dim);
setAttrib(s_pop, install("hivdeaths"), s_hivdeaths);
Rf_setAttrib(s_hivdeaths, R_DimSymbol, s_hivdeaths_dim);
Rf_setAttrib(s_pop, Rf_install("hivdeaths"), s_hivdeaths);
multi_array_ref<double, 3> hivdeaths(REAL(s_hivdeaths), extents[PROJ_YEARS][NG][pAG]);
memset(REAL(s_hivdeaths), 0, length(s_hivdeaths)*sizeof(double));
memset(REAL(s_hivdeaths), 0, Rf_length(s_hivdeaths)*sizeof(double));

SEXP s_natdeaths = PROTECT(allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_natdeaths_dim = PROTECT(allocVector(INTSXP, 3));
SEXP s_natdeaths = PROTECT(Rf_allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_natdeaths_dim = PROTECT(Rf_allocVector(INTSXP, 3));
INTEGER(s_natdeaths_dim)[0] = pAG;
INTEGER(s_natdeaths_dim)[1] = NG;
INTEGER(s_natdeaths_dim)[2] = PROJ_YEARS;
setAttrib(s_natdeaths, R_DimSymbol, s_natdeaths_dim);
setAttrib(s_pop, install("natdeaths"), s_natdeaths);
Rf_setAttrib(s_natdeaths, R_DimSymbol, s_natdeaths_dim);
Rf_setAttrib(s_pop, Rf_install("natdeaths"), s_natdeaths);
multi_array_ref<double, 3> natdeaths(REAL(s_natdeaths), extents[PROJ_YEARS][NG][pAG]);
memset(REAL(s_natdeaths), 0, length(s_natdeaths)*sizeof(double));
memset(REAL(s_natdeaths), 0, Rf_length(s_natdeaths)*sizeof(double));

SEXP s_aidsdeaths_noart = PROTECT(allocVector(REALSXP, hDS * hAG * NG * PROJ_YEARS));
SEXP s_aidsdeaths_noart_dim = PROTECT(allocVector(INTSXP, 4));
SEXP s_aidsdeaths_noart = PROTECT(Rf_allocVector(REALSXP, hDS * hAG * NG * PROJ_YEARS));
SEXP s_aidsdeaths_noart_dim = PROTECT(Rf_allocVector(INTSXP, 4));
INTEGER(s_aidsdeaths_noart_dim)[0] = hDS;
INTEGER(s_aidsdeaths_noart_dim)[1] = hAG;
INTEGER(s_aidsdeaths_noart_dim)[2] = NG;
INTEGER(s_aidsdeaths_noart_dim)[3] = PROJ_YEARS;
setAttrib(s_aidsdeaths_noart, R_DimSymbol, s_aidsdeaths_noart_dim);
setAttrib(s_pop, install("aidsdeaths_noart"), s_aidsdeaths_noart);
Rf_setAttrib(s_aidsdeaths_noart, R_DimSymbol, s_aidsdeaths_noart_dim);
Rf_setAttrib(s_pop, Rf_install("aidsdeaths_noart"), s_aidsdeaths_noart);
multi_array_ref<double, 4> aidsdeaths_noart(REAL(s_aidsdeaths_noart), extents[PROJ_YEARS][NG][hAG][hDS]);
memset(REAL(s_aidsdeaths_noart), 0, length(s_aidsdeaths_noart)*sizeof(double));
memset(REAL(s_aidsdeaths_noart), 0, Rf_length(s_aidsdeaths_noart)*sizeof(double));

SEXP s_aidsdeaths_art = PROTECT(allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
SEXP s_aidsdeaths_art_dim = PROTECT(allocVector(INTSXP, 5));
SEXP s_aidsdeaths_art = PROTECT(Rf_allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
SEXP s_aidsdeaths_art_dim = PROTECT(Rf_allocVector(INTSXP, 5));
INTEGER(s_aidsdeaths_art_dim)[0] = hTS;
INTEGER(s_aidsdeaths_art_dim)[1] = hDS;
INTEGER(s_aidsdeaths_art_dim)[2] = hAG;
INTEGER(s_aidsdeaths_art_dim)[3] = NG;
INTEGER(s_aidsdeaths_art_dim)[4] = PROJ_YEARS;
setAttrib(s_aidsdeaths_art, R_DimSymbol, s_aidsdeaths_art_dim);
setAttrib(s_pop, install("aidsdeaths_art"), s_aidsdeaths_art);
Rf_setAttrib(s_aidsdeaths_art, R_DimSymbol, s_aidsdeaths_art_dim);
Rf_setAttrib(s_pop, Rf_install("aidsdeaths_art"), s_aidsdeaths_art);
multi_array_ref<double, 5> aidsdeaths_art(REAL(s_aidsdeaths_art), extents[PROJ_YEARS][NG][hAG][hDS][hTS]);
memset(REAL(s_aidsdeaths_art), 0, length(s_aidsdeaths_art)*sizeof(double));
memset(REAL(s_aidsdeaths_art), 0, Rf_length(s_aidsdeaths_art)*sizeof(double));


SEXP s_popadjust = PROTECT(allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_popadjust_dim = PROTECT(allocVector(INTSXP, 3));
SEXP s_popadjust = PROTECT(Rf_allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_popadjust_dim = PROTECT(Rf_allocVector(INTSXP, 3));
INTEGER(s_popadjust_dim)[0] = pAG;
INTEGER(s_popadjust_dim)[1] = NG;
INTEGER(s_popadjust_dim)[2] = PROJ_YEARS;
setAttrib(s_popadjust, R_DimSymbol, s_popadjust_dim);
setAttrib(s_pop, install("popadjust"), s_popadjust);
Rf_setAttrib(s_popadjust, R_DimSymbol, s_popadjust_dim);
Rf_setAttrib(s_pop, Rf_install("popadjust"), s_popadjust);
multi_array_ref<double, 3> popadjust(REAL(s_popadjust), extents[PROJ_YEARS][NG][pAG]);
memset(REAL(s_popadjust), 0, length(s_popadjust)*sizeof(double));
memset(REAL(s_popadjust), 0, Rf_length(s_popadjust)*sizeof(double));

SEXP s_artinit = PROTECT(allocVector(REALSXP, hDS * hAG * NG * PROJ_YEARS));
SEXP s_artinit_dim = PROTECT(allocVector(INTSXP, 4));
SEXP s_artinit = PROTECT(Rf_allocVector(REALSXP, hDS * hAG * NG * PROJ_YEARS));
SEXP s_artinit_dim = PROTECT(Rf_allocVector(INTSXP, 4));
INTEGER(s_artinit_dim)[0] = hDS;
INTEGER(s_artinit_dim)[1] = hAG;
INTEGER(s_artinit_dim)[2] = NG;
INTEGER(s_artinit_dim)[3] = PROJ_YEARS;
setAttrib(s_artinit, R_DimSymbol, s_artinit_dim);
setAttrib(s_pop, install("artinit"), s_artinit);
Rf_setAttrib(s_artinit, R_DimSymbol, s_artinit_dim);
Rf_setAttrib(s_pop, Rf_install("artinit"), s_artinit);
multi_array_ref<double, 4> artinit(REAL(s_artinit), extents[PROJ_YEARS][NG][hAG][hDS]);
memset(REAL(s_artinit), 0, length(s_artinit)*sizeof(double));
memset(REAL(s_artinit), 0, Rf_length(s_artinit)*sizeof(double));


SEXP s_pregprevlag = PROTECT(allocVector(REALSXP, PROJ_YEARS));
setAttrib(s_pop, install("pregprevlag"), s_pregprevlag);
SEXP s_pregprevlag = PROTECT(Rf_allocVector(REALSXP, PROJ_YEARS));
Rf_setAttrib(s_pop, Rf_install("pregprevlag"), s_pregprevlag);

SEXP s_incrate15to49_ts = PROTECT(allocVector(REALSXP, (PROJ_YEARS-1) * HIVSTEPS_PER_YEAR));
setAttrib(s_pop, install("incrate15to49_ts"), s_incrate15to49_ts);
SEXP s_incrate15to49_ts = PROTECT(Rf_allocVector(REALSXP, (PROJ_YEARS-1) * HIVSTEPS_PER_YEAR));
Rf_setAttrib(s_pop, Rf_install("incrate15to49_ts"), s_incrate15to49_ts);
double *incrate15to49_ts_out = REAL(s_incrate15to49_ts);
memset(incrate15to49_ts_out, 0, length(s_incrate15to49_ts)*sizeof(double));
memset(incrate15to49_ts_out, 0, Rf_length(s_incrate15to49_ts)*sizeof(double));

SEXP s_prev15to49_ts = PROTECT(allocVector(REALSXP, (PROJ_YEARS-1) * HIVSTEPS_PER_YEAR));
setAttrib(s_pop, install("prev15to49_ts"), s_prev15to49_ts);
SEXP s_prev15to49_ts = PROTECT(Rf_allocVector(REALSXP, (PROJ_YEARS-1) * HIVSTEPS_PER_YEAR));
Rf_setAttrib(s_pop, Rf_install("prev15to49_ts"), s_prev15to49_ts);
double *prev15to49_ts_out = REAL(s_prev15to49_ts);
memset(prev15to49_ts_out, 0, length(s_prev15to49_ts)*sizeof(double));
memset(prev15to49_ts_out, 0, Rf_length(s_prev15to49_ts)*sizeof(double));

SEXP s_rvec_ts = PROTECT(allocVector(REALSXP, (PROJ_YEARS-1) * HIVSTEPS_PER_YEAR));
setAttrib(s_pop, install("rvec_ts"), s_rvec_ts);
SEXP s_rvec_ts = PROTECT(Rf_allocVector(REALSXP, (PROJ_YEARS-1) * HIVSTEPS_PER_YEAR));
Rf_setAttrib(s_pop, Rf_install("rvec_ts"), s_rvec_ts);
double *rvec = REAL(s_rvec_ts);

SEXP s_prev15to49 = PROTECT(allocVector(REALSXP, PROJ_YEARS));
setAttrib(s_pop, install("prev15to49"), s_prev15to49);
SEXP s_prev15to49 = PROTECT(Rf_allocVector(REALSXP, PROJ_YEARS));
Rf_setAttrib(s_pop, Rf_install("prev15to49"), s_prev15to49);
double *prev15to49 = REAL(s_prev15to49);
prev15to49[0] = 0.0;

SEXP s_pregprev = PROTECT(allocVector(REALSXP, PROJ_YEARS));
setAttrib(s_pop, install("pregprev"), s_pregprev);
SEXP s_pregprev = PROTECT(Rf_allocVector(REALSXP, PROJ_YEARS));
Rf_setAttrib(s_pop, Rf_install("pregprev"), s_pregprev);
double *pregprev = REAL(s_pregprev);
pregprev[0] = 0.0;

SEXP s_incid15to49 = PROTECT(allocVector(REALSXP, PROJ_YEARS));
setAttrib(s_pop, install("incid15to49"), s_incid15to49);
SEXP s_incid15to49 = PROTECT(Rf_allocVector(REALSXP, PROJ_YEARS));
Rf_setAttrib(s_pop, Rf_install("incid15to49"), s_incid15to49);
double *incid15to49 = REAL(s_incid15to49);
memset(incid15to49, 0, length(s_incid15to49)*sizeof(double));
memset(incid15to49, 0, Rf_length(s_incid15to49)*sizeof(double));

SEXP s_entrantprev_out = PROTECT(allocVector(REALSXP, PROJ_YEARS));
setAttrib(s_pop, install("entrantprev"), s_entrantprev_out);
SEXP s_entrantprev_out = PROTECT(Rf_allocVector(REALSXP, PROJ_YEARS));
Rf_setAttrib(s_pop, Rf_install("entrantprev"), s_entrantprev_out);
double *entrantprev_out = REAL(s_entrantprev_out);
memset(entrantprev_out, 0, length(s_entrantprev_out)*sizeof(double));
memset(entrantprev_out, 0, Rf_length(s_entrantprev_out)*sizeof(double));

double *hivn15to49 = (double*) R_alloc(PROJ_YEARS, sizeof(double));
double *hivp15to49 = (double*) R_alloc(PROJ_YEARS, sizeof(double));
Expand Down Expand Up @@ -405,7 +405,7 @@ extern "C" {
// ART population with stage stratification
// double artpop[PROJ_YEARS][NG][hAG][hDS][hTS];
multi_array_ref<double, 5> artpop(REAL(s_artpop), extents[PROJ_YEARS][NG][hAG][hDS][hTS]);
// memset(REAL(s_artpop), 0, length(s_artpop) * sizeof(double)); // initialize artpop to 0
// memset(REAL(s_artpop), 0, Rf_length(s_artpop) * sizeof(double)); // initialize artpop to 0
if(t_ART_start < PROJ_YEARS)
for(int g = 0; g < NG; g++)
for(int ha = 0; ha < hAG; ha++)
Expand Down Expand Up @@ -1136,24 +1136,24 @@ extern "C" {

SEXP getListElement(SEXP list, const char *str)
{
SEXP elmt = R_NilValue, names = getAttrib(list, R_NamesSymbol);
SEXP elmt = R_NilValue, names = Rf_getAttrib(list, R_NamesSymbol);
int i;
for ( i = 0; i < length(list); i++ )
for ( i = 0; i < Rf_length(list); i++ )
if ( strcmp(CHAR(STRING_ELT(names, i)), str) == 0 ) {
elmt = VECTOR_ELT(list, i);
break;
}

if ( elmt == R_NilValue )
error("%s missing from list", str);
Rf_error("%s missing from list", str);

return elmt;
}

int checkListElement(SEXP list, const char *str)
{
SEXP names = getAttrib(list, R_NamesSymbol);
for (int i = 0; i < length(list); i++ )
SEXP names = Rf_getAttrib(list, R_NamesSymbol);
for (int i = 0; i < Rf_length(list); i++ )
if (strcmp(CHAR(STRING_ELT(names, i)), str) == 0 )
return 1;

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6 changes: 3 additions & 3 deletions src/functions.c
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Expand Up @@ -4,14 +4,14 @@
SEXP ageprevC(SEXP s_mod, SEXP s_aidx, SEXP s_sidx, SEXP s_yidx, SEXP s_agspan) {

double *mod = REAL(s_mod);
int *dim = INTEGER(getAttrib(s_mod, R_DimSymbol));
int *dim = INTEGER(Rf_getAttrib(s_mod, R_DimSymbol));
int *aidx = INTEGER(s_aidx);
int *sidx = INTEGER(s_sidx);
int *yidx = INTEGER(s_yidx);
int *agspan = INTEGER(s_agspan);

int n = length(s_aidx);
SEXP s_out = PROTECT(allocVector(REALSXP, n));
int n = Rf_length(s_aidx);
SEXP s_out = PROTECT(Rf_allocVector(REALSXP, n));
double *out = REAL(s_out);

for(int i = 0; i < n; i++){
Expand Down

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