Add fix/test for 281 compile; Now test with data.

nlmixrdevelopment · Mar 6, 2020 · dac66e1 · dac66e1
1 parent 3dd22f7
commit dac66e1
Show file tree

Hide file tree

Showing 3 changed files with 68 additions and 7 deletions.
diff --git a/R/nlmixr.R b/R/nlmixr.R
@@ -470,12 +470,12 @@ nlmixr_fit0 <- function(uif, data, est=NULL, control=list(), ...,
         model <- uif$saem.model
         inits = uif$saem.init
         if (length(uif$saem.fixed)>0) {
-			nphi = attr(model$saem_mod, "nrhs")
-			m = cumsum(!is.na(matrix(inits$theta, byrow=T, ncol=nphi)))
-			fixid = match(uif$saem.fixed, t(matrix(m,ncol=nphi)))
+            nphi = attr(model$saem_mod, "nrhs")
+            m = cumsum(!is.na(matrix(inits$theta, byrow=T, ncol=nphi)))
+            fixid = match(uif$saem.fixed, t(matrix(m,ncol=nphi)))
 
-			names(inits$theta) = rep("", length(inits$theta))
-			names(inits$theta)[fixid] = "FIXED"
+            names(inits$theta) = rep("", length(inits$theta))
+            names(inits$theta)[fixid] = "FIXED"
         }
         cfg <- configsaem(model=model, data=dat, inits=inits,
                           mcmc=mcmc, ODEopt=ODEopt, seed=seed,

diff --git a/R/ui.R b/R/ui.R
@@ -2624,8 +2624,16 @@ nlmixrUI.saem.fit <- function(obj){
         RxODE::rxLoad(ode);
         message("done.")
         inPars <- obj$saem.inPars;
-        if (length(inPars) == 0) inPars <- NULL
-
+        if (length(inPars) == 0) {
+            inPars <- NULL
+        } else {
+            ## Check for inPars in Covariates in RxODE model
+            .extra <- RxODE::rxModelVars(obj$rxode)
+            .extra <- intersect(obj$saem.all.covs, .extra$params)
+            if (length(.extra) > 0){
+                inPars <- c(inPars, .extra)
+            }
+        }
         saem.fit <- gen_saem_user_fn(model=ode, obj$saem.pars, pred=obj$predSaem, inPars=inPars);
         obj$env$saem.fit <- saem.fit;
         return(obj$env$saem.fit);

diff --git a/tests/testthat/test-281.R b/tests/testthat/test-281.R
@@ -0,0 +1,53 @@
+context("Covs in SAEM covs and model, Issue #281")
+library(nlmixr)
+Lesion7 = function() {
+  ini({
+
+    temaxD = -0.05 # typical value of drug emax
+    tec50  = -0.04 # typical value of ec50
+    temaxT = -0.9 # typical value of emax for placebo effect as a function of time
+    tet50  = 6.64 # typical value of et50
+    tkin   = -7.8
+    tslope = -1 # typical value of growth parameter
+    TRXslope = -0.1
+    tdelay = 7.15
+
+    eta.emaxD ~ 0.3
+    eta.emaxT ~ 0.3
+    eta.slope ~ 0.3
+    eta.delay ~ 0.3
+    add.err  = .1       # add. residual variability
+  })
+  model({
+    Resp(0) = 1 # default Resp(0) = 0
+    emaxD = exp(temaxD + eta.emaxD)
+    ec50  = exp(tec50)
+    emaxT = exp(temaxT + eta.emaxT)
+    et50  = exp(tet50)
+
+    slope = exp(tslope + TRX*TRXslope + eta.slope)
+
+    delay = exp(tdelay + eta.delay)
+    kin   = exp(tkin)
+    kout  = kin
+    GAM   = exp(1)/2 # Hill coef
+    C2 = centr/V;
+    CONC = (C2)^2
+
+    Stim1 = emaxT*(time)/(time+et50) ;
+    Stim2 = emaxD*(CONC^GAM)/(CONC^GAM+ec50^GAM);
+    Stim = Stim1 * ( 1 + TRX * Stim2 )
+
+    Delta = 1/(1 + exp(-20 * (time - delay)))
+    d/dt(depot) =-KA*depot;
+    d/dt(centr) = KA*depot - CL*C2;
+    d/dt(Resp)   = kin * (1 + Delta * slope) - kout * (1 + Stim  ) * Resp;
+
+    Resp ~ add(add.err)
+
+  })
+}
+
+
+tmp <- nlmixr(Lesion7)
+expect_error(tmp$saem.model, NA)