Merge pull request #365 from metrumresearchgroup/next-version

v0.8.11

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mrgsolve
 Type: Package
-Version: 0.8.10.9015
+Version: 0.8.11
 Title: Simulate from ODE-Based Population PK/PD and Systems Pharmacology
     Models
 Authors@R: c(
@@ -42,7 +42,7 @@ LinkingTo:
 Suggests:
     lattice,
     testthat,
-    xml2,
+    xml2 (>= 1.2.0),
     rmarkdown
 LazyLoad: yes
 NeedsCompilation: yes

NAMESPACE

@@ -60,7 +60,6 @@ export(bmat)
 export(cama)
 export(carry.out)
 export(carry_out)
-export(ch)
 export(cmat)
 export(cmtn)
 export(cvec)
@@ -128,7 +127,7 @@ export(relocate)
 export(rename_cols)
 export(req)
 export(revar)
-export(s)
+export(s_)
 export(see)
 export(simargs)
 export(smat)

NEWS.md

@@ -1,3 +1,9 @@
+# mrgsove 0.8.11
+- Internal release
+- Removed the function `s` and replaced with `s_`; this was not a problem 
+created by mrgsolve but rather by ggplot2, which calls `mgcv::s` via 
+`geom_smooth` under certian circumstances
+
 # mrgsolve 0.8.10.9015
 - Re-configured the list of data coming from `as.list.mrgmod` so that
 the names match the names that you would pass to `update.mrgmod`; also

R/class_mrgmod.R

@@ -410,7 +410,6 @@ setMethod("as.list", "mrgmod", function(x, deep = FALSE, ...) {
     project <- project(x)
     model <- model(x)
     fixed <- as.list(x@fixed)
-    fixedp <- names(x@fixed)
     sigma <- as.list(smat(x))
     omega <- as.list(omat(x))
     init <- as.list(init(x))

R/nmxml.R

@@ -78,7 +78,13 @@ nmxml <- function(run=numeric(0), project=character(0),
   }
 
   tree <- xml2::as_list(xml2::read_xml(target))
-  tree <- tree$output$nonmem$problem$estimation
+
+  # https://github.com/r-lib/xml2/blob/master/NEWS.md#xml2-120
+  if(packageVersion("xml2") >= "1.2.0") {
+    tree <- tree[["output"]][["nonmem"]][["problem"]][["estimation"]]      
+  } else {
+    tree <- tree[["nonmem"]][["problem"]][["estimation"]]
+  }
 
   th <- list()
   om <- matrix(0,0,0)

R/utils.R

@@ -244,8 +244,7 @@ tovec <- function(x,concat=TRUE) {
 ##' @examples
 ##'
 ##' cvec("A,B,C")
-##' ch(A,B,C)
-##' s(A,B,C)
+##' s_(A,B,C)
 ##'
 setGeneric("cvec", function(x,...) standardGeneric("cvec"))
 
@@ -255,11 +254,7 @@ setMethod("cvec", "character", as.cvec)
 
 ##' @export
 ##' @rdname cvec
-ch <- function(...) as.character(match.call(expand.dots=TRUE))[-1]
-
-##' @export
-##' @rdname cvec
-s <- ch
+s_ <- function(...) as.character(match.call(expand.dots=TRUE))[-1]
 
 ##' Access or clear arguments for calls to mrgsim
 ##'

inst/maintenance/unit/test-request.R

@@ -45,10 +45,10 @@ test_that("Req gets the right variables", {
   x2 <- names(mod %>% Req(PERIPH,GUT) %>% mrgsim)
   x3 <- names(mod %>% Req(PERIPH,b) %>% mrgsim)
   x4 <- names(mod %>% Req(b,z) %>% mrgsim)
-  expect_identical(x1,s(ID,time,GUT,CENT,PERIPH,b,z))
-  expect_identical(x2,s(ID,time,PERIPH,GUT))
-  expect_identical(x3,s(ID,time,PERIPH,b))
-  expect_identical(x4,s(ID,time,b,z))
+  expect_identical(x1,s_(ID,time,GUT,CENT,PERIPH,b,z))
+  expect_identical(x2,s_(ID,time,PERIPH,GUT))
+  expect_identical(x3,s_(ID,time,PERIPH,b))
+  expect_identical(x4,s_(ID,time,b,z))
 })
 
 
@@ -60,10 +60,10 @@ test_that("Req gets the right variables, with request", {
   x2 <- names(mod %>% Req(PERIPH,GUT) %>% mrgsim)
   x3 <- names(mod %>% Req(PERIPH,b) %>% mrgsim)
   x4 <- names(mod %>% Req(z,b) %>% mrgsim)
-  expect_identical(x1,s(ID,time,CENT,b,z))
-  expect_identical(x2,s(ID,time,PERIPH,GUT))
-  expect_identical(x3,s(ID,time,PERIPH,b))
-  expect_identical(x4,s(ID,time,z,b))
+  expect_identical(x1,s_(ID,time,CENT,b,z))
+  expect_identical(x2,s_(ID,time,PERIPH,GUT))
+  expect_identical(x3,s_(ID,time,PERIPH,b))
+  expect_identical(x4,s_(ID,time,z,b))
 })
 
 

tests/testthat/test-as_list_mrgmod.R

@@ -26,46 +26,44 @@ context("test-as_list_mrgmod")
 options(mrgsolve_mread_quiet=TRUE)
 
 test_that("check items in as.list output", {
-  expect_exists <- function(object,name) {
-    expect_true(name %in% names(object))
-  }
   x <- as.list(mrgsolve:::house())  
-  expect_exists(x, "start")
-  expect_exists(x, "end")
-  expect_exists(x, "delta")
-  expect_exists(x, "add")
-  expect_exists(x, "param")
-  expect_exists(x, "init")
-  expect_exists(x, "omega")
-  expect_exists(x, "sigma")
-  expect_exists(x, "request")
-  expect_exists(x, "atol")
-  expect_exists(x, "rtol")
-  expect_exists(x, "hmin")
-  expect_exists(x, "hmax")
-  expect_exists(x, "maxsteps")
-  expect_exists(x, "tscale")
-  expect_exists(x, "digits")
-  expect_exists(x, "code")
-  expect_exists(x, "cmt")
-  expect_exists(x, "neq")
-  expect_exists(x, "pars")
-  expect_exists(x, "npar")
-  expect_exists(x, "preclean")
-  expect_exists(x, "mindt")
-  expect_exists(x, "debug")
-  expect_exists(x, "verbose")
-  expect_exists(x, "envir")
-  expect_exists(x, "cfile")
-  expect_exists(x, "shlib")
-  expect_exists(x, "capture")
-  expect_exists(x, "details")
-  expect_exists(x, "sodll")
-  expect_exists(x, "soloc")
-  expect_exists(x, "covariates")
-  expect_exists(x, "fixedp")
-  expect_exists(x, "plugins")
-  expect_exists(x, "random")
-  expect_exists(x, "model")
-  expect_exists(x, "project")
+  x_names <- names(x)
+  expect_true("start" %in% x_names)
+  expect_true("end" %in% x_names)
+  expect_true("delta" %in% x_names)
+  expect_true("add" %in% x_names)
+  expect_true("param" %in% x_names)
+  expect_true("init" %in% x_names)
+  expect_true("omega" %in% x_names)
+  expect_true("sigma" %in% x_names)
+  expect_true("request" %in% x_names)
+  expect_true("atol" %in% x_names)
+  expect_true("rtol" %in% x_names)
+  expect_true("hmin" %in% x_names)
+  expect_true("hmax" %in% x_names)
+  expect_true("maxsteps" %in% x_names)
+  expect_true("tscale" %in% x_names)
+  expect_true("digits" %in% x_names)
+  expect_true("code" %in% x_names)
+  expect_true("cmt" %in% x_names)
+  expect_true("neq" %in% x_names)
+  expect_true("pars" %in% x_names)
+  expect_true("npar" %in% x_names)
+  expect_true("preclean" %in% x_names)
+  expect_true("mindt" %in% x_names)
+  expect_true("debug" %in% x_names)
+  expect_true("verbose" %in% x_names)
+  expect_true("envir" %in% x_names)
+  expect_true("cfile" %in% x_names)
+  expect_true("shlib" %in% x_names)
+  expect_true("capture" %in% x_names)
+  expect_true("details" %in% x_names)
+  expect_true("sodll" %in% x_names)
+  expect_true("soloc" %in% x_names)
+  expect_true("covariates" %in% x_names)
+  expect_true("fixed" %in% x_names)
+  expect_true("plugins" %in% x_names)
+  expect_true("random" %in% x_names)
+  expect_true("model" %in% x_names)
+  expect_true("project" %in% x_names)
 })

tests/testthat/test-nmxml.R

@@ -229,8 +229,8 @@ test_that("Model compiles", {
 })
 
 test_that("Labels are assigned to $OMEGA and $SIGMA", {
-  expect_equivalent(mod@omega@labels, list(s(a,b,c,d),s(x,y,z)))
-  expect_equivalent(mod@sigma@labels, list(s(e,f), s(h,i,j,k,l)))
+  expect_equivalent(mod@omega@labels, list(s_(a,b,c,d),s_(x,y,z)))
+  expect_equivalent(mod@sigma@labels, list(s_(e,f), s_(h,i,j,k,l)))
 })
 
 
@@ -256,7 +256,7 @@ $OMEGA
 mod <- mcode("label2", code,warn=FALSE, compile = FALSE)
 
 test_that("Mixed labels / no labels and prefix", {
-  expect_equivalent(mod@omega@labels, list(s(x_a,x_b),s(.,.,.)))
+  expect_equivalent(mod@omega@labels, list(s_(x_a,x_b),s_(.,.,.)))
 })
 
 

tests/testthat/test-rename.R

@@ -32,26 +32,26 @@ mod <- mod %>% data_set(df)
 ## "Rename via carry.out #30"
 test_that("tran item is renamed", {
   out <- mod %>% carry.out(EVID=evid) %>% mrgsim
-  expect_true(all(is.element(s(RESP,CENT,EVID), names(out))))
+  expect_true(all(is.element(c("RESP","CENT","EVID"), names(out))))
   out <- mod %>% carry.out(EVID=evid,addl) %>% mrgsim
-  expect_true(all(is.element(s(RESP,CENT,EVID,addl), names(out))))
+  expect_true(all(is.element(c("RESP","CENT","EVID","addl"), names(out))))
   out <- mod %>% carry.out(X=addl) %>% mrgsim
-  expect_true(all(is.element(s(RESP,CENT,X), names(out))))
+  expect_true(all(is.element(c("RESP","CENT","X"), names(out))))
   out <- mod %>% carry.out(EVID=evid,addl) %>% mrgsim
-  expect_false(all(is.element(s(evid), names(out))))
+  expect_false(all(is.element("evid", names(out))))
 })
 
 
 test_that("Item carried from data set is renamed", {
   out <- mod %>% carry.out(Dose,WEIGHT = WT) %>% mrgsim
-  expect_true(all(is.element(s(RESP,CENT,WEIGHT), names(out))))
-  expect_true(all(is.element(s(Dose,WEIGHT), names(out))))
+  expect_true(all(is.element(s_(RESP,CENT,WEIGHT), names(out))))
+  expect_true(all(is.element(s_(Dose,WEIGHT), names(out))))
 })
 
 
 test_that("Item carried from data set is renamed", {
   out <- mod %>% carry.out(FOO=BAR) %>% mrgsim
-  expect_equal(s(ID,time,CENT,RESP), names(out))
+  expect_equal(c("ID","time","CENT","RESP"), names(out))
 })