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Simplify eta_agd_arm_noRE #31

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Simplify eta_agd_arm_noRE #31

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24 changes: 7 additions & 17 deletions inst/stan/binomial_1par.stan
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Original file line number Diff line number Diff line change
Expand Up @@ -30,11 +30,11 @@ transformed parameters {

// -- AgD model (arm-based) --
if (ni_agd_arm) {
if (nint_max > 1) { // -- If integration points are used --
vector[nint_max * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;
vector[nint_max * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;

if (nint_max > 1) { // -- If integration points are used --
if (RE) {
if (link == 1) { // logit link
for (i in 1:ni_agd_arm) {
Expand Down Expand Up @@ -81,10 +81,6 @@ transformed parameters {
}
} else { // -- If no integration --
if (RE) {
vector[nint * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;

if (link == 1) { // logit link
for (i in 1:ni_agd_arm) {
if (which_RE[narm_ipd + i])
Expand All @@ -109,17 +105,11 @@ transformed parameters {
}
} else {
if (link == 1) // logit link
theta_agd_arm_bar = has_offset ?
inv_logit(X_agd_arm * beta_tilde + offset_agd_arm) :
inv_logit(X_agd_arm * beta_tilde);
theta_agd_arm_bar = inv_logit(eta_agd_arm_noRE);
else if (link == 2) // probit link
theta_agd_arm_bar = has_offset ?
Phi(X_agd_arm * beta_tilde + offset_agd_arm) :
Phi(X_agd_arm * beta_tilde);
theta_agd_arm_bar = Phi(eta_agd_arm_noRE);
else if (link == 3) // cloglog link
theta_agd_arm_bar = has_offset ?
inv_cloglog(X_agd_arm * beta_tilde + offset_agd_arm) :
inv_cloglog(X_agd_arm * beta_tilde);
theta_agd_arm_bar = inv_cloglog(eta_agd_arm_noRE);
}
}
}
Expand Down
24 changes: 7 additions & 17 deletions inst/stan/binomial_2par.stan
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Original file line number Diff line number Diff line change
Expand Up @@ -33,11 +33,11 @@ transformed parameters {

// -- AgD model (arm-based) --
if (ni_agd_arm) {
if (nint_max > 1) { // -- If integration points are used --
vector[nint_max * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;
vector[nint_max * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;

if (nint_max > 1) { // -- If integration points are used --
if (RE) {

if (link == 1) { // logit link
Expand Down Expand Up @@ -88,10 +88,6 @@ transformed parameters {
}
} else { // -- If no integration --
if (RE) {
vector[nint * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;

if (link == 1) { // logit link
for (i in 1:ni_agd_arm) {
if (which_RE[narm_ipd + i])
Expand All @@ -116,17 +112,11 @@ transformed parameters {
}
} else {
if (link == 1) // logit link
theta_agd_arm_bar = has_offset ?
inv_logit(X_agd_arm * beta_tilde + offset_agd_arm) :
inv_logit(X_agd_arm * beta_tilde);
theta_agd_arm_bar = inv_logit(eta_agd_arm_noRE);
else if (link == 2) // probit link
theta_agd_arm_bar = has_offset ?
Phi(X_agd_arm * beta_tilde + offset_agd_arm) :
Phi(X_agd_arm * beta_tilde);
theta_agd_arm_bar = Phi(eta_agd_arm_noRE);
else if (link == 3) // cloglog link
theta_agd_arm_bar = has_offset ?
inv_cloglog(X_agd_arm * beta_tilde + offset_agd_arm) :
inv_cloglog(X_agd_arm * beta_tilde);
theta_agd_arm_bar = inv_cloglog(eta_agd_arm_noRE);
}

theta2_agd_arm_bar = theta_agd_arm_bar .* theta_agd_arm_bar;
Expand Down
20 changes: 6 additions & 14 deletions inst/stan/normal.stan
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Original file line number Diff line number Diff line change
Expand Up @@ -35,11 +35,11 @@ transformed parameters {

// -- AgD model (arm-based) --
if (ni_agd_arm) {
if (nint_max > 1) { // -- If integration points are used --
vector[nint_max * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;
vector[nint_max * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;

if (nint_max > 1) { // -- If integration points are used --
if (RE) {

if (link == 1) { // identity link
Expand Down Expand Up @@ -77,10 +77,6 @@ transformed parameters {
}
} else { // -- If no integration --
if (RE) {
vector[nint * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;

if (link == 1) { // identity link
for (i in 1:ni_agd_arm) {
if (which_RE[narm_ipd + i])
Expand All @@ -98,13 +94,9 @@ transformed parameters {
}
} else {
if (link == 1) // identity link
theta_agd_arm_bar = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;
theta_agd_arm_bar = eta_agd_arm_noRE;
else if (link == 2) // log link
theta_agd_arm_bar = has_offset ?
exp(X_agd_arm * beta_tilde + offset_agd_arm) :
exp(X_agd_arm * beta_tilde);
theta_agd_arm_bar = exp(eta_agd_arm_noRE);
}
}
}
Expand Down
16 changes: 5 additions & 11 deletions inst/stan/poisson.stan
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Original file line number Diff line number Diff line change
Expand Up @@ -30,11 +30,11 @@ transformed parameters {

// -- AgD model (arm-based) --
if (ni_agd_arm) {
if (nint_max > 1) { // -- If integration points are used --
vector[nint_max * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;
vector[nint_max * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;

if (nint_max > 1) { // -- If integration points are used --
if (RE) {

if (link == 1) { // log link
Expand Down Expand Up @@ -62,10 +62,6 @@ transformed parameters {
}
} else { // -- If no integration --
if (RE) {
vector[nint * ni_agd_arm] eta_agd_arm_noRE = has_offset ?
X_agd_arm * beta_tilde + offset_agd_arm :
X_agd_arm * beta_tilde;

if (link == 1) { // log link
for (i in 1:ni_agd_arm) {
if (which_RE[narm_ipd + i])
Expand All @@ -76,9 +72,7 @@ transformed parameters {
}
} else {
if (link == 1) // log link
theta_agd_arm_bar = has_offset ?
exp(X_agd_arm * beta_tilde + offset_agd_arm) :
exp(X_agd_arm * beta_tilde);
theta_agd_arm_bar = exp(eta_agd_arm_noRE);
}
}
}
Expand Down
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