Skip to content

Commit

Permalink
implement excess non-AIDS mortality among PLHIV
Browse files Browse the repository at this point in the history
  • Loading branch information
@jeffeaton
jeffeaton committed Jun 25, 2024
1 parent 4fd7a52 commit 7f34ae0
Show file tree
Hide file tree
Showing 3 changed files with 96 additions and 12 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: eppasm
Title: Age-structured EPP Model for HIV Epidemic Estimates
Version: 0.7.3
Version: 0.8.0
Authors@R: person("Jeff", "Eaton", email = "[email protected]", role = c("aut", "cre"))
Description: What the package does (one paragraph).
Depends: R (>= 3.1.0),
Expand Down
4 changes: 4 additions & 0 deletions NEWS.md
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
## eppasm 0.8.0

* Add excess non-AIDS mortality among PLHIV. New model parameters `cd4_nonaids_excess_mort` and `art_nonaids_excess_mort`.

## eppasm 0.7.3

* Bug fix: account for end-year net migration in the ART population in the first year of ART start.
Expand Down
102 changes: 91 additions & 11 deletions src/eppasm.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,9 @@ extern "C" {
multi_array_ref<double, 3> cd4_initdist(REAL(getListElement(s_fp, "cd4_initdist")), extents[NG][hAG][hDS]);
multi_array_ref<double, 3> cd4_prog(REAL(getListElement(s_fp, "cd4_prog")), extents[NG][hAG][hDS-1]);
multi_array_ref<double, 3> cd4_mort(REAL(getListElement(s_fp, "cd4_mort")), extents[NG][hAG][hDS]);
multi_array_ref<double, 3> cd4_nonaids_excess_mort(REAL(getListElement(s_fp, "cd4_nonaids_excess_mort")), extents[NG][hAG][hDS]);
multi_array_ref<double, 4> art_mort(REAL(getListElement(s_fp, "art_mort")), extents[NG][hAG][hDS][hTS]);
multi_array_ref<double, 4> art_nonaids_excess_mort(REAL(getListElement(s_fp, "art_nonaids_excess_mort")), extents[NG][hAG][hDS][hTS]);
multi_array_ref<double, 2> artmx_timerr(REAL(getListElement(s_fp, "artmx_timerr")), extents[PROJ_YEARS][hTS]);

// sub-fertility
Expand Down Expand Up @@ -290,6 +292,17 @@ extern "C" {
setAttrib(s_pop, 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));

SEXP s_excessnonaidsdeaths = PROTECT(allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_excessnonaidsdeaths_dim = PROTECT(allocVector(INTSXP, 3));
INTEGER(s_excessnonaidsdeaths_dim)[0] = pAG;
INTEGER(s_excessnonaidsdeaths_dim)[1] = NG;
INTEGER(s_excessnonaidsdeaths_dim)[2] = PROJ_YEARS;
setAttrib(s_excessnonaidsdeaths, R_DimSymbol, s_excessnonaidsdeaths_dim);
setAttrib(s_pop, install("excessnonaidsdeaths"), s_excessnonaidsdeaths);
multi_array_ref<double, 3> excessnonaidsdeaths(REAL(s_excessnonaidsdeaths), extents[PROJ_YEARS][NG][pAG]);
memset(REAL(s_excessnonaidsdeaths), 0, length(s_excessnonaidsdeaths)*sizeof(double));


SEXP s_aidsdeaths_noart = PROTECT(allocVector(REALSXP, hDS * hAG * NG * PROJ_YEARS));
SEXP s_aidsdeaths_noart_dim = PROTECT(allocVector(INTSXP, 4));
Expand All @@ -302,6 +315,28 @@ extern "C" {
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));

SEXP s_natdeaths_noart = PROTECT(allocVector(REALSXP, hDS * hAG * NG * PROJ_YEARS));
SEXP s_natdeaths_noart_dim = PROTECT(allocVector(INTSXP, 4));
INTEGER(s_natdeaths_noart_dim)[0] = hDS;
INTEGER(s_natdeaths_noart_dim)[1] = hAG;
INTEGER(s_natdeaths_noart_dim)[2] = NG;
INTEGER(s_natdeaths_noart_dim)[3] = PROJ_YEARS;
setAttrib(s_natdeaths_noart, R_DimSymbol, s_natdeaths_noart_dim);
setAttrib(s_pop, install("natdeaths_noart"), s_natdeaths_noart);
multi_array_ref<double, 4> natdeaths_noart(REAL(s_natdeaths_noart), extents[PROJ_YEARS][NG][hAG][hDS]);
memset(REAL(s_natdeaths_noart), 0, length(s_natdeaths_noart)*sizeof(double));

SEXP s_excessnonaidsdeaths_noart = PROTECT(allocVector(REALSXP, hDS * hAG * NG * PROJ_YEARS));
SEXP s_excessnonaidsdeaths_noart_dim = PROTECT(allocVector(INTSXP, 4));
INTEGER(s_excessnonaidsdeaths_noart_dim)[0] = hDS;
INTEGER(s_excessnonaidsdeaths_noart_dim)[1] = hAG;
INTEGER(s_excessnonaidsdeaths_noart_dim)[2] = NG;
INTEGER(s_excessnonaidsdeaths_noart_dim)[3] = PROJ_YEARS;
setAttrib(s_excessnonaidsdeaths_noart, R_DimSymbol, s_excessnonaidsdeaths_noart_dim);
setAttrib(s_pop, install("excessnonaidsdeaths_noart"), s_excessnonaidsdeaths_noart);
multi_array_ref<double, 4> excessnonaidsdeaths_noart(REAL(s_excessnonaidsdeaths_noart), extents[PROJ_YEARS][NG][hAG][hDS]);
memset(REAL(s_excessnonaidsdeaths_noart), 0, length(s_excessnonaidsdeaths_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));
INTEGER(s_aidsdeaths_art_dim)[0] = hTS;
Expand All @@ -314,6 +349,29 @@ extern "C" {
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));

SEXP s_natdeaths_art = PROTECT(allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
SEXP s_natdeaths_art_dim = PROTECT(allocVector(INTSXP, 5));
INTEGER(s_natdeaths_art_dim)[0] = hTS;
INTEGER(s_natdeaths_art_dim)[1] = hDS;
INTEGER(s_natdeaths_art_dim)[2] = hAG;
INTEGER(s_natdeaths_art_dim)[3] = NG;
INTEGER(s_natdeaths_art_dim)[4] = PROJ_YEARS;
setAttrib(s_natdeaths_art, R_DimSymbol, s_natdeaths_art_dim);
setAttrib(s_pop, install("natdeaths_art"), s_natdeaths_art);
multi_array_ref<double, 5> natdeaths_art(REAL(s_natdeaths_art), extents[PROJ_YEARS][NG][hAG][hDS][hTS]);
memset(REAL(s_natdeaths_art), 0, length(s_natdeaths_art)*sizeof(double));

SEXP s_excessnonaidsdeaths_art = PROTECT(allocVector(REALSXP, hTS * hDS * hAG * NG * PROJ_YEARS));
SEXP s_excessnonaidsdeaths_art_dim = PROTECT(allocVector(INTSXP, 5));
INTEGER(s_excessnonaidsdeaths_art_dim)[0] = hTS;
INTEGER(s_excessnonaidsdeaths_art_dim)[1] = hDS;
INTEGER(s_excessnonaidsdeaths_art_dim)[2] = hAG;
INTEGER(s_excessnonaidsdeaths_art_dim)[3] = NG;
INTEGER(s_excessnonaidsdeaths_art_dim)[4] = PROJ_YEARS;
setAttrib(s_excessnonaidsdeaths_art, R_DimSymbol, s_excessnonaidsdeaths_art_dim);
setAttrib(s_pop, install("excessnonaidsdeaths_art"), s_excessnonaidsdeaths_art);
multi_array_ref<double, 5> excessnonaidsdeaths_art(REAL(s_excessnonaidsdeaths_art), extents[PROJ_YEARS][NG][hAG][hDS][hTS]);
memset(REAL(s_excessnonaidsdeaths_art), 0, length(s_excessnonaidsdeaths_art)*sizeof(double));

SEXP s_popadjust = PROTECT(allocVector(REALSXP, pAG * NG * PROJ_YEARS));
SEXP s_popadjust_dim = PROTECT(allocVector(INTSXP, 3));
Expand Down Expand Up @@ -498,6 +556,7 @@ extern "C" {
int a = 0;
for(int ha = 0; ha < hAG; ha++){
double deathsmig_ha = 0, hivpop_ha = 0;
double deaths_ha = 0.0;
for(int i = 0; i < hAG_SPAN[ha]; i++){

hivpop_ha += pop[t][HIVP][g][a];
Expand All @@ -507,6 +566,7 @@ extern "C" {
double ndeaths_a = pop[t][HIVN][g][a] * qx;
pop[t][HIVN][g][a] -= ndeaths_a; // survival HIV- population
double hdeaths_a = pop[t][HIVP][g][a] * qx;
deaths_ha += hdeaths_a;
deathsmig_ha -= hdeaths_a;
pop[t][HIVP][g][a] -= hdeaths_a; // survival HIV+ population
natdeaths[t][g][a] = ndeaths_a + hdeaths_a;
Expand All @@ -523,12 +583,16 @@ extern "C" {
}

// migration and deaths for hivpop
double deathrate_ha = hivpop_ha > 0 ? deaths_ha / hivpop_ha : 0.0;
double deathmigrate_ha = hivpop_ha > 0 ? deathsmig_ha / hivpop_ha : 0.0;
for(int hm = 0; hm < hDS; hm++){
natdeaths_noart[t][g][ha][hm] += hivpop[t][g][ha][hm] * deathrate_ha;
hivpop[t][g][ha][hm] *= 1+deathmigrate_ha;
if(t > t_ART_start)
for(int hu = 0; hu < hTS; hu++)
for(int hu = 0; hu < hTS; hu++) {
natdeaths_art[t][g][ha][hm][hu] += artpop[t][g][ha][hm][hu] * deathrate_ha;
artpop[t][g][ha][hm][hu] *= 1+deathmigrate_ha;
}
} // loop over hm
} // loop over ha
} // loop over g
Expand Down Expand Up @@ -592,6 +656,9 @@ extern "C" {
double hivdeaths_ha[NG][hAG];
memset(hivdeaths_ha, 0, sizeof(double)*NG*hAG);

double nonaids_excess_ha[NG][hAG];
memset(nonaids_excess_ha, 0, sizeof(double)*NG*hAG);

// untreated population

// disease progression and mortality
Expand All @@ -608,10 +675,16 @@ extern "C" {
cd4mx_scale = hivpop[t][g][ha][hm] / (hivpop[t][g][ha][hm] + artpop_hahm);
}

double deaths = cd4mx_scale * cd4_mort[g][ha][hm] * hivpop[t][g][ha][hm];
hivdeaths_ha[g][ha] += DT*deaths;
aidsdeaths_noart[t][g][ha][hm] += DT*deaths;
grad[g][ha][hm] = -deaths;
double aids_deaths = cd4mx_scale * cd4_mort[g][ha][hm] * hivpop[t][g][ha][hm];
hivdeaths_ha[g][ha] += DT * aids_deaths;
aidsdeaths_noart[t][g][ha][hm] += DT * aids_deaths;

double excess_nonaids_deaths = cd4_nonaids_excess_mort[g][ha][hm] * hivpop[t][g][ha][hm];
nonaids_excess_ha[g][ha] += DT * excess_nonaids_deaths;
excessnonaidsdeaths_noart[t][g][ha][hm] += DT * excess_nonaids_deaths;


grad[g][ha][hm] = -(aids_deaths + excess_nonaids_deaths);
}
for(int hm = 1; hm < hDS; hm++){
grad[g][ha][hm-1] -= cd4_prog[g][ha][hm-1] * hivpop[t][g][ha][hm-1];
Expand Down Expand Up @@ -694,10 +767,15 @@ extern "C" {
for(int hm = everARTelig_idx; hm < hDS; hm++){

for(int hu = 0; hu < hTS; hu++){
double deaths = art_mort[g][ha][hm][hu] * artmx_timerr[t][hu] * artpop[t][g][ha][hm][hu];
hivdeaths_ha[g][ha] += DT*deaths;
aidsdeaths_art[t][g][ha][hm][hu] += DT*deaths;
gradART[g][ha][hm][hu] = -deaths;
double aids_deaths = art_mort[g][ha][hm][hu] * artmx_timerr[t][hu] * artpop[t][g][ha][hm][hu];
double nonaids_deaths = art_nonaids_excess_mort[g][ha][hm][hu] * artpop[t][g][ha][hm][hu];
hivdeaths_ha[g][ha] += DT * aids_deaths;
aidsdeaths_art[t][g][ha][hm][hu] += DT * aids_deaths;

nonaids_excess_ha[g][ha] += DT * nonaids_deaths;
excessnonaidsdeaths_art[t][g][ha][hm][hu] += DT * nonaids_deaths;

gradART[g][ha][hm][hu] = -(aids_deaths + nonaids_deaths);
}

for(int hu = 0; hu < (hTS - 1); hu++) {
Expand Down Expand Up @@ -903,9 +981,11 @@ extern "C" {
for(int ha = 0; ha < hAG; ha++){
if(hivpop_ha[ha] > 0){
double hivqx_ha = hivdeaths_ha[g][ha] / hivpop_ha[ha];
double nonaids_excess_qx_ha = nonaids_excess_ha[g][ha] / hivpop_ha[ha];
for(int i = 0; i < hAG_SPAN[ha]; i++){
hivdeaths[t][g][a] += pop[t][HIVP][g][a] * hivqx_ha;
pop[t][HIVP][g][a] *= (1.0-hivqx_ha);
excessnonaidsdeaths[t][g][a] += pop[t][HIVP][g][a] * nonaids_excess_qx_ha;
pop[t][HIVP][g][a] *= (1.0 - hivqx_ha - nonaids_excess_qx_ha);
a++;
}
} else {
Expand Down Expand Up @@ -1061,7 +1141,7 @@ extern "C" {
incid15to49[t] /= incid15to49_denom;
}

UNPROTECT(28);
UNPROTECT(38);
return s_pop;
}
}
Expand Down

0 comments on commit 7f34ae0

Please sign in to comment.