<20 imports; version bump

nlmixrdevelopment · Mar 7, 2020 · 9e6dae9 · 9e6dae9
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Showing 8 changed files with 41 additions and 29 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,17 +3,33 @@ Type: Package
 Title: Nonlinear Mixed Effects Models in Population Pharmacokinetics
         and Pharmacodynamics
 Depends: R (>= 3.5)
-Imports: Rcpp (>= 0.12.3), brew, lattice, parallel, lbfgs,
-        dparser, methods, ggplot2, memoise, rex, minqa, Matrix,
- 	n1qn1, fastGHQuad,
-        crayon, cli, RcppArmadillo (>= 0.5.600.2.0), vpc (>= 1.0.0),
-	RxODE(>= 0.9.1-9), nlme, magrittr, tidyr, sys, generics,
-	huxtable, digest, flextable, stringr, yaml
+Imports: Rcpp (>= 0.12.3),
+	 brew,
+	 parallel,
+	 methods,
+	 ggplot2,
+	 memoise,
+	 Matrix,
+ 	 n1qn1,
+	 fastGHQuad,
+	 cli,
+	 RcppArmadillo (>= 0.5.600.2.0),
+	 vpc (>= 1.0.0),
+	 RxODE(>= 0.9.1-9),
+	 nlme,
+	 magrittr,
+	 tidyr,
+	 generics,
+	 huxtable,
+	 flextable,
+	 stringr,
+	 yaml
 Suggests: knitr, rmarkdown, dplyr, data.table, lbfgsb3c, testthat,
         madness, devtools, expm, matrixcalc, reshape2, nloptr, ucminf,
 	Rvmmin, broom.mixed, dotwhisker, officer, pkgdown, gridExtra,
-	xpose, lotri
-Version: 1.1.1-5
+	xpose, lotri, rex, minqa, lattice, digest, sys, crayon,
+	lbfgs, dparser
+Version: 1.1.1-6
 Authors@R: c(person("Matthew","Fidler",
       role = "aut", email = "[email protected]",
       comment=c(ORCID="0000-0001-8538-6691")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -264,7 +264,6 @@ importFrom(RxODE,rxPermissive)
 importFrom(RxODE,rxSolve)
 importFrom(RxODE,rxSymPySetupPred)
 importFrom(brew,brew)
-importFrom(dparser,dparse)
 importFrom(generics,augment)
 importFrom(generics,glance)
 importFrom(generics,tidy)
@@ -286,9 +285,6 @@ importFrom(graphics,title)
 importFrom(huxtable,as_hux)
 importFrom(huxtable,as_huxtable)
 importFrom(huxtable,number_format)
-importFrom(lattice,trellis.par.get)
-importFrom(lattice,xyplot)
-importFrom(lbfgs,lbfgs)
 importFrom(magrittr,"%>%")
 importFrom(methods,is)
 importFrom(n1qn1,n1qn1)

diff --git a/R/000.R b/R/000.R
@@ -7,13 +7,14 @@
 #' @return NULL
 #' @export
 nlme_gof <- function(fit, ...){
-	df <- getData(fit)
-	df <- rbind(
-		cbind(df[,c("ID", "TIME", "DV")], grp=0),
-		cbind(df[,c("ID", "TIME")], DV=fit$fitted[,1], grp=1),
-		cbind(df[,c("ID", "TIME")], DV=fit$fitted[,2], grp=2)
-	)
+    RxODE::rxReq("lattice")
+    df <- getData(fit)
+    df <- rbind(
+        cbind(df[,c("ID", "TIME", "DV")], grp=0),
+        cbind(df[,c("ID", "TIME")], DV=fit$fitted[,1], grp=1),
+        cbind(df[,c("ID", "TIME")], DV=fit$fitted[,2], grp=2)
+    )
 
-	p = xyplot(DV~TIME|ID, df, group=grp, type="b", lwd=c(NA, 1, 1), pch=c(1,NA,NA), col=trellis.par.get("superpose.line")$col[c(1,1,2)], ...)
-	p
+    p = lattice::xyplot(DV~TIME|ID, df, group=grp, type="b", lwd=c(NA, 1, 1), pch=c(1,NA,NA), col=lattice::trellis.par.get("superpose.line")$col[c(1,1,2)], ...)
+    p
 }
diff --git a/R/foceiFit.R b/R/foceiFit.R
@@ -800,6 +800,7 @@ foceiControl <- function(sigdig=3,...,
         outerOpt <- match.arg(outerOpt);
         .outerOptTxt <- outerOpt;
         if (outerOpt == "bobyqa"){
+            RxODE::rxReq("minqa")
             outerOptFun <- .bobyqa;
             outerOpt <- -1L;
         } else if (outerOpt == "nlminb"){

diff --git a/R/gnlmm.R b/R/gnlmm.R
@@ -345,7 +345,8 @@ gnlmm <- function(llik, data, inits, syspar=NULL,
 	data.sav = data
 	names(data) <- tolower(names(data))		#needed in ev
 
-    #model
+    ##model
+    RxODE::rxReq("lbfgs")
     if (is.null(system)) {}
     else if (class(system) == "RxODE") {}
     else if (class(system) == "character") {
@@ -525,7 +526,7 @@ gnlmm <- function(llik, data, inits, syspar=NULL,
 			}
 
 			pvd = NULL; nfcall = 0
-			..fit.inner = lbfgs(f, g, starts[.wh,], invisible=T, epsilon=10000*con$reltol.inner)
+			..fit.inner = lbfgs::lbfgs(f, g, starts[.wh,], invisible=T, epsilon=10000*con$reltol.inner)
 			..fit.inner$hessian = optimHess(..fit.inner$par, f, g)
 			} else {
 			..fit.inner = optim(par=starts[.wh,], ..g.fn, method=con$optim.inner,

diff --git a/R/nlmixr.R b/R/nlmixr.R
@@ -53,8 +53,6 @@ nlmixrForget <- function(){
 ##' @importFrom stats predict logLik na.fail pchisq
 ##' @importFrom n1qn1 n1qn1
 ##' @importFrom brew brew
-##' @importFrom lattice xyplot
-##' @importFrom lattice trellis.par.get
 ##' @importFrom nlme nlme fixed.effects random.effects
 ##' @importFrom nlme groupedData
 ##' @importFrom nlme getData
@@ -64,10 +62,8 @@ nlmixrForget <- function(){
 ##' @importFrom stats as.formula nlminb optimHess rnorm terms predict anova optim sd var AIC BIC asOneSidedFormula coef end fitted resid setNames start simulate nobs qnorm quantile time
 ##' @importFrom utils assignInMyNamespace getFromNamespace head stack sessionInfo tail str
 ##' @importFrom parallel mclapply
-##' @importFrom lbfgs lbfgs
 ##' @importFrom methods is
 ##' @importFrom Rcpp evalCpp
-##' @importFrom dparser dparse
 ##' @importFrom vpc vpc
 ##' @importFrom ggplot2 ggplot aes geom_point facet_wrap geom_line geom_abline xlab geom_smooth aes_string
 ##' @importFrom RcppArmadillo armadillo_version

diff --git a/R/simulate.R b/R/simulate.R
@@ -221,7 +221,7 @@ nlmixrSim <- function(object, ...){
         .dataName  <- ifelse(is.null(object$uif$data.name),"",paste0(object$uif$data.name,"-"));
         if (.dataName==".-") .dataName <- ""
         .digest <- digest::digest(list(gsub("<-","=",gsub(" +","",object$uif$fun.txt)),
-                                       as..data.frame(object$uif$ini),
+                                       as.data.frame(object$uif$ini),
                                        .xtra,
                                        as.character(utils::packageVersion("nlmixr")),
                                        as.character(utils::packageVersion("RxODE"))))
@@ -483,7 +483,7 @@ nlmixrAugPred <- function(object, ..., covsInterpolation = c("linear", "locf", "
         .dataName  <- ifelse(is.null(object$uif$data.name),"",paste0(object$uif$data.name,"-"));
         if (.dataName==".-") .dataName <- ""
         .digest <- digest::digest(list(gsub("<-","=",gsub(" +","",object$uif$fun.txt)),
-                                       as..data.frame(object$uif$ini),
+                                       as.data.frame(object$uif$ini),
                                        covsInterpolation,
                                        primary, minimum, maximum, length.out,
                                        as.character(utils::packageVersion("nlmixr")),

diff --git a/R/utils.R b/R/utils.R
@@ -307,7 +307,8 @@ dynmodel = function(system, model, evTable, inits, data, fixPars=NULL,
 		fit = mymin(as.vector(inits), obj, control=control)
 		fit$message=c("NON-CONVERGENCE", "NELDER_FTOL_REACHED")[1+fit$convergence]
 	} else if (method=="L-BFGS-B") {
-		fit = lbfgs(as.vector(inits), obj, control=control)
+            RxODE::rxReq("lbfgs")
+            fit = lbfgs::lbfgs(as.vector(inits), obj, control=control)
 	} else {
 		if ("ftol_rel" %in% names(control)) {
 			control$rel.tol = control$ftol_rel