Merge pull request #504 from nlmixr2/503-covariate-and-babelmixr2

Try babelmixr2 back-transform

Author: mattfidler

NEWS.md

@@ -1,7 +1,10 @@
 # nlmixr2est 3.0.3
 
 - Moved data check for covariates and required data items to a
-  pre-processing step. This fixes #499
+  pre-processing step. This fixes #499.  Each method that needs to
+  have a covariate check needs to have a property `covPresent`. For
+  example to apply the covariate data check to the `focei` method you
+  need `attr(nlmixr2Est.focei, "covPresent") <- TRUE`.
 
 - Bug fix for non-mu referenced etas when combined with mu referenced
   covariate values. (See #498)

R/bobyqa.R

@@ -421,5 +421,6 @@ nlmixr2Est.bobyqa <- function(env, ...) {
   on.exit({if (exists("control", envir=.ui)) rm("control", envir=.ui)}, add=TRUE)
   .bobyqaFamilyFit(env,  ...)
 }
+attr(nlmixr2Est.bobyqa, "covPresent") <- TRUE
 
 #minqa::bobyqa()

R/focei.R

@@ -1810,6 +1810,7 @@ nlmixr2Est.focei <- function(env, ...) {
   })
   .foceiFamilyReturn(env, .ui, ..., est="focei")
 }
+attr(nlmixr2Est.focei, "covPresent") <- TRUE
 
 
 #'@rdname nlmixr2Est
@@ -1831,6 +1832,7 @@ nlmixr2Est.foce <- function(env, ...) {
   env$est <- "foce"
   .foceiFamilyReturn(env, .ui, ..., est="focei")
 }
+attr(nlmixr2Est.foce, "covPresent") <- TRUE
 
 #'@rdname nlmixr2Est
 #'@export
@@ -1849,6 +1851,7 @@ nlmixr2Est.posthoc <- function(env, ...) {
   env$est <- "posthoc"
   .foceiFamilyReturn(env, .ui, ..., est="posthoc")
 }
+attr(nlmixr2Est.posthoc, "covPresent") <- TRUE
 
 #' Add objective function line to the return object
 #'
@@ -1916,6 +1919,7 @@ nlmixr2Est.foi <- function(env, ...) {
   .addObjDfToReturn(.ret, .objDf)
   .ret
 }
+attr(nlmixr2Est.foi, "covPresent") <- TRUE
 
 
 #'@rdname nlmixr2Est
@@ -1949,6 +1953,7 @@ nlmixr2Est.fo <- function(env, ...) {
   .addObjDfToReturn(.ret, .objDf)
   .ret
 }
+attr(nlmixr2Est.fo, "covPresent") <- TRUE
 
 #'@rdname nlmixr2Est
 #'@export

R/lbfgsb3c.R

@@ -435,3 +435,4 @@ nlmixr2Est.lbfgsb3c <- function(env, ...) {
   on.exit({if (exists("control", envir=.ui)) rm("control", envir=.ui)}, add=TRUE)
   .lbfgsb3cFamilyFit(env,  ...)
 }
+attr(nlmixr2Est.lbfgsb3c, "covPresent") <- TRUE

R/n1qn1.R

@@ -402,3 +402,4 @@ nlmixr2Est.n1qn1 <- function(env, ...) {
   on.exit({if (exists("control", envir=.ui)) rm("control", envir=.ui)}, add=TRUE)
   .n1qn1FamilyFit(env,  ...)
 }
+attr(nlmixr2Est.n1qn1, "covPresent") <- TRUE

R/newuoa.R

@@ -390,5 +390,6 @@ nlmixr2Est.newuoa <- function(env, ...) {
   on.exit({if (exists("control", envir=.ui)) rm("control", envir=.ui)}, add=TRUE)
   .newuoaFamilyFit(env,  ...)
 }
+attr(nlmixr2Est.newuoa, "covPresent") <- TRUE
 
 #minqa::newuoa()

R/nlm.R

@@ -918,3 +918,4 @@ nlmixr2Est.nlm <- function(env, ...) {
   on.exit({if (exists("control", envir=.ui)) rm("control", envir=.ui)}, add=TRUE)
   .nlmFamilyFit(env,  ...)
 }
+attr(nlmixr2Est.nlm, "covPresent") <- TRUE

R/nlme.R

@@ -537,3 +537,4 @@ nlmixr2Est.nlme <- function(env, ...) {
   on.exit({if (exists("control", envir=.ui)) rm("control", envir=.ui)}, add=TRUE)
   .uiFinalizeMu2(.nlmeFamilyFit(env,  ...), .model)
 }
+attr(nlmixr2Est.nlme, "covPresent") <- TRUE

R/nlminb.R

@@ -566,3 +566,4 @@ nlmixr2Est.nlminb <- function(env, ...) {
   on.exit({if (exists("control", envir=.ui)) rm("control", envir=.ui)}, add=TRUE)
   .nlminbFamilyFit(env,  ...)
 }
+attr(nlmixr2Est.nlminb, "covPresent") <- TRUE

R/nls.R

@@ -1079,3 +1079,4 @@ nlmixr2Est.nls <- function(env, ...) {
   on.exit({if (exists("control", envir=.ui)) rm("control", envir=.ui)}, add=TRUE)
   .nlsFamilyFit(env,  ...)
 }
+attr(nlmixr2Est.nls, "covPresent") <- TRUE

R/optim.R

@@ -625,3 +625,4 @@ nlmixr2Est.optim <- function(env, ...) {
   on.exit({if (exists("control", envir=.ui)) rm("control", envir=.ui)}, add=TRUE)
   .optimFamilyFit(env,  ...)
 }
+attr(nlmixr2Est.optim, "covPresent") <- TRUE

R/preProcessCovariatesPresent.R

@@ -8,7 +8,8 @@
 .nlmixr0preProcessCovariatesPresent <- function(ui, est, data, control) {
   # Could possibly use to stack data or use an DV or IDV different
   # than what is present in the data
-  if (!missing(data)) {
+  if (!missing(data) &&
+        isTRUE(attr(utils::getS3method("nlmixr2Est", est), "covPresent"))) {
     .covNames <- ui$covariates
     colnames(data) <- vapply(names(data), function(x) {
       if (any(x == .covNames)) {

R/rxsolve.R

@@ -152,6 +152,7 @@ nlmixr2Est.rxSolve <- function(env, ...) {
                                   events = .events, inits = NULL), .rxSolveGetControlForNlmixr(env),
                              list(theta = NULL, eta = NULL)))
 }
+attr(nlmixr2Est.rxSolve, "covPresent") <- TRUE
 
 #'@rdname nlmixr2Est
 #'@export
@@ -162,6 +163,7 @@ nlmixr2Est.simulate <- function(env, ...) {
                                   events = .events, inits = NULL), .rxSolveGetControlForNlmixr(env),
                              list(theta = NULL, eta = NULL)))
 }
+attr(nlmixr2Est.simulate, "covPresent") <- TRUE
 
 #'@rdname nlmixr2Est
 #'@export
@@ -179,6 +181,8 @@ nlmixr2Est.simulation <- function(env, ...) {
                                   events = .events, inits = NULL), .rxControl,
                              list(theta = NULL, eta = NULL)))
 }
+attr(nlmixr2Est.simulation, "covPresent") <- TRUE
+
 
 #'@rdname nlmixr2Est
 #'@export
@@ -199,6 +203,8 @@ nlmixr2Est.predict <- function(env, ...) {
   nlmixr2(object=get("ui", envir=env), data=.events,
           est="rxSolve", control=.rxControl)
 }
+attr(nlmixr2Est.predict, "covPresent") <- TRUE
+
 #' Get new data
 #'
 #'

R/saem.R

@@ -805,6 +805,8 @@ nlmixr2Est.saem <- function(env, ...) {
   }, add=TRUE)
   .uiFinalizeMu2(.saemFamilyFit(env,  ...), .doMu2)
 }
+attr(nlmixr2Est.saem, "covPresent") <- TRUE
+
 
 #' @rdname nmObjGet
 #' @export

R/uobyqa.R

@@ -397,5 +397,5 @@ nlmixr2Est.uobyqa <- function(env, ...) {
   }, add=TRUE)
   .uobyqaFamilyFit(env,  ...)
 }
-
+attr(nlmixr2Est.uobyqa, "covPresent") <- TRUE
 #minqa::uobyqa()