Merge branch 'main' into rxode2ui-obj-doc

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: rxode2
-Version: 2.0.13.9000
+Version: 2.0.14.9000
 Title: Facilities for Simulating from ODE-Based Models
 Authors@R: c(
    person("Matthew L.","Fidler",
       role = c("aut", "cre"), email = "matthew.fidler@gmail.com",
       comment=c(ORCID="0000-0001-8538-6691")),
    person("Melissa", "Hallow",
       role = "aut", email = "hallowkm@uga.edu"),
-   person("Wenping", "Wang", 
+   person("Wenping", "Wang",
       role = c("aut"), email = "wwang8198@gmail.com"),
    person("Zufar", "Mulyukov", role="ctb", email="zufar.mulyukov@novartis.com"),
    person("Alan", "Hindmarsh",role="ctb"),
@@ -77,7 +77,7 @@ Imports:
     backports,
     cli (>= 2.0.0),
     checkmate,
-    ggplot2,
+    ggplot2 (>= 3.4.0),
     inline,
     lotri (>= 0.4.0),
     magrittr,
@@ -104,16 +104,16 @@ Description: Facilities for running simulations from ordinary
     Section 6.3, Appendix A, and Appendix D in the "R Administration and
     Installation" manual. Also the code is mostly released under GPL.  The
     'VODE' and 'LSODA' are in the public domain.  The information is available
-    in the inst/COPYRIGHTS. 
+    in the inst/COPYRIGHTS.
 BugReports: https://github.com/nlmixr2/rxode2/issues/
 NeedsCompilation: yes
 VignetteBuilder: knitr
-License: GPL (>= 3) 
+License: GPL (>= 3)
 URL: https://nlmixr2.github.io/rxode2/,
     https://github.com/nlmixr2/rxode2/
 RoxygenNote: 7.2.3
 Biarch: true
-LinkingTo: 
+LinkingTo:
     rxode2parse (>= 2.0.12),
     rxode2random,
     PreciseSums (>= 0.3),

NAMESPACE

@@ -8,6 +8,7 @@ S3method("$",rxSymInvCholEnv)
 S3method("$",rxUi)
 S3method("$<-",rxSolve)
 S3method("$<-",rxSymInvCholEnv)
+S3method("$<-",rxUi)
 S3method("+",rxSolve)
 S3method("+",solveRxDll)
 S3method("[",rxSolve)
@@ -41,6 +42,7 @@ S3method(as.rxUi,rxModelVars)
 S3method(as.rxUi,rxUi)
 S3method(as.rxUi,rxode2)
 S3method(as.rxUi,rxode2tos)
+S3method(binomProbs,default)
 S3method(coef,rxode2)
 S3method(confint,rxSolve)
 S3method(dimnames,rxSolve)
@@ -138,6 +140,7 @@ S3method(rxUiGet,lhsTheta)
 S3method(rxUiGet,lhsVar)
 S3method(rxUiGet,lstChr)
 S3method(rxUiGet,md5)
+S3method(rxUiGet,model)
 S3method(rxUiGet,modelDesc)
 S3method(rxUiGet,modelFun)
 S3method(rxUiGet,muRefTable)
@@ -194,6 +197,7 @@ export(.copyUi)
 export(.expandPars)
 export(.getLastIdLvl)
 export(.handleSingleErrTypeNormOrTFoceiBase)
+export(.iniGetAppendArg)
 export(.iniHandleFixOrUnfix)
 export(.iniHandleLine)
 export(.malert)
@@ -246,6 +250,7 @@ export(assertRxUiPrediction)
 export(assertRxUiRandomOnIdOnly)
 export(assertRxUiSingleEndpoint)
 export(assertRxUiTransformNormal)
+export(binomProbs)
 export(cvPost)
 export(erf)
 export(et)
@@ -469,6 +474,7 @@ export(scale_y_discrete)
 export(setRxThreads)
 export(stat_amt)
 export(stat_cens)
+export(toTrialDuration)
 export(uppergamma)
 export(waiver)
 export(write.template.server)
@@ -529,6 +535,7 @@ importFrom(rxode2et,rxEvid)
 importFrom(rxode2et,rxRateDur)
 importFrom(rxode2et,rxReq)
 importFrom(rxode2et,rxStack)
+importFrom(rxode2et,toTrialDuration)
 importFrom(rxode2parse,.getLastIdLvl)
 importFrom(rxode2parse,forderForceBase)
 importFrom(rxode2parse,rxDerived)

NEWS.md

@@ -11,8 +11,15 @@
 - "dop853" now uses the `hmax`/`h0` values from the `rxControl()` or
   `rxSolve()`.  This may change some ODE solving using "dop853"
 
+- When not specified (and xgxr is available), the x axis is no longer
+  assumed to be in hours
+
 ## New features
 
+- User defined functions can now be R functions.  For many of these R
+  functions they can be converted to C with `rxFun()` (you can see the
+  C code afterwards with `rxC("funName")`)
+
 - Parallel solving of models that require sorting (like modeled lag
   times, modeled duration etc) now solve in parallel instead of downgrading
   to single threaded solving
@@ -90,18 +97,80 @@ mu-referencing style to run the optimization.
   your own `ci=0.99` for instance
 
 - A new function was introduced `meanProbs()` which calculates the
-  mean and expected quantiles under either the normal or t
+  mean and expected confidence bands under either the normal or t
   distribution
 
+- A related new function was introduced that calculates the mean and
+  confidence bands under the Bernoulli/Binomial distribution
+  (`binomProbs()`)
+
 - When calculating the intervals for `rxode2` simulated objects you
   can also use `mean=TRUE` to use the mean for the first level of
-  confidence using `meanProbs()`
+  confidence using `meanProbs()`. For this confidence interval you can
+  override the `n` used in the confidence interval by using `n=#`. You
+  can also change this to a prediction interval instead using
+  `pred=TRUE`.
+
+- Also when calculating the intervals for `rxode2` simulated object
+  you can also use `mean="binom"` to use the binomial distributional
+  information (and ci) for the first level of confidence using
+  `binomProbs()`.  For this confidence interval you can override the
+  `n` used in the confidence interval by using `n=#`. You can also
+  change this to a prediction interval instead using `pred=TRUE`. With
+  `pred=TRUE` you can override the number of predicted samples with
+  `m=#`
 
 - When plotting the `confint` derived intervals from an `rxode2`
   simulation, you can now subset based on a simulated value like
   `plot(ci, Cc)` which will only plot the variable `Cc` that you
   summarized even if you also summarized `eff` (for instance).
 
+- When the rxode2 ui is a compressed ui object, you can modify the ini
+  block with `$ini <-` or modify the model block with `$model <-`.
+  These are equivalent to `ini(model) <-` and `model(model) <-`,
+  respectively. Otherwise, the object is added to the user defined
+  components in the function (ie `$meta`).  When the object is
+  uncompressed, it simply assigns it to the environment instead (just
+  like before).
+
+- When printing meta information that happens to be a `lotri`
+  compatible matrix, use `lotri` to express it instead of the default
+  R expression.
+
+- Allow character vectors to be converted to expressions for piping
+  (#552)
+
+- `rxAppendModel()` will now take an arbitrary number of models and
+  append them together; It also has better handling of models with
+  duplicate parameters and models without `ini()` blocks (#617 / #573
+  / #575).
+
+- `keep` will now also keep attributes of the input data (with special
+  handling for `levels`); This means a broader variety of classes will
+  be kept carrying more information with it (for example ordered
+  factors, data frame columns with unit information, etc)
+
+- Piping arguments `append` for `ini()` and `model()` have been
+  aligned to perform similarly.  Therefore `ini(append=)` now can take
+  expressions instead of simply strings and `model(append=)` can also
+  take strings.  Also model piping now can specify the integer line
+  number to be modified just like the `ini()` could.  Also
+  `model(append=FALSE)` has been changed to `model(append=NULL)`.
+  While the behavior is the same when you don't specify the argument,
+  the behavior has changed to align with `ini()` when piping.  Hence
+  `model(append=TRUE)` will append and `model(append=FALSE)` will now
+  pre-pend to the model.  `model(append=NULL)` will modify lines like
+  the behavior of `ini(append=NULL)`.  The default of `model(line)`
+  modifying a line in-place still applies.  While this is a breaking
+  change, most code will perform the same.
+
+- Labels can now be dropped by `ini(param=label(NULL))`. Also
+  parameters can be dropped with the idiom `model(param=NULL)` or
+  `ini(param=NULL)` changes the parameter to a covariate to align with
+  this idiom of dropping parameters
+
+- `rxRename` has been refactored to run faster
+
 ## Internal new features
 
 - Add `as.model()` for list expressions, which implies `model(ui) <-
@@ -121,6 +190,9 @@ mu-referencing style to run the optimization.
 
 ## Bug fixes
 
+- Simulating/solving from functions/ui now prefers params over `omega`
+  and `sigma` in the model (#632)
+
 - Piping does not add constants to the initial estimates
 
 - When constants are specified in the `model({})` block (like `k <- 1`), they will not
@@ -131,6 +203,19 @@ mu-referencing style to run the optimization.
 - Bug fix for some covariate updates that may affect multiple compartment
   models (like issue #581)
 
+## Maintenance fixes
+
+- Modify plot code to work with development `xgxr`
+
+# rxode2 2.0.14
+
+- CRAN requested that FORTRAN `kind` be changed as it was not portable;
+  This was commented code, and simply removed the comment.
+
+- Bug-fix for `geom_amt()`; also now uses `linewidth` and at least `ggplot2 3.4.0`
+
+- Some documentation was cleaned up from `rxode2` 2.0.13
+
 # rxode2 2.0.13
 
 ## Bug fixes

R/RcppExports.R

@@ -40,7 +40,7 @@ etTrans <- function(inData, obj, addCmt = FALSE, dropUnits = FALSE, allTimeVar =
 #' @param c1 character vector of items to be expanded
 #' @param c2 second character vector of items to be expanded
 #' @param type 0 for a typical data frame, 1 for symengine sensitivity expansion
-#' @return data frame (when type = 0) or symengine string (when type=1) 
+#' @return data frame (when type = 0) or symengine string (when type=1)
 #' @export
 #' @keywords internal
 rxExpandGrid_ <- function(c1, c2, type) {
@@ -74,17 +74,18 @@ rxExpandSens2_ <- function(state, s1, s2) {
 #'
 #' @param state is the state to expand
 #' @param neta is the number of etas
-#' @param pred type of prediction 
+#' @param pred type of prediction
+#' @param isTheta logical, is the expansion actually for thetas instead of etas
 #' @keywords internal
 #' @return String of symengine expressions to evaluate to calculate df/deta
 #' @export
-rxExpandFEta_ <- function(state, neta, pred) {
-    .Call(`_rxode2_rxExpandFEta_`, state, neta, pred)
+rxExpandFEta_ <- function(state, neta, pred, isTheta = FALSE) {
+    .Call(`_rxode2_rxExpandFEta_`, state, neta, pred, isTheta)
 }
 
 #' Rep R0 for foce
 #'
-#' @param number ETA to substitute
+#' @param neta ETA to substitute
 #'
 #' @return Returns a string of R code to substitute the rx_r expression in the symengine environment .s
 #'
@@ -260,7 +261,7 @@ rxSetupIni <- function(obj, inits = NULL) {
 #'
 #' @param obj rxode2 object
 #'
-#' @param inits A numeric vector of initial conditions.
+#' @param scale A numeric vector scales
 #'
 #' @param extraArgs A list of extra args to parse for initial conditions.
 #'
@@ -589,7 +590,15 @@ rxErf <- function(v) {
     .Call(`_rxode2_rxErf`, v)
 }
 
-meanProbs_ <- function(x, probs, naRm, useT) {
-    .Call(`_rxode2_meanProbs_`, x, probs, naRm, useT)
+binomProbsPredVec_ <- function(n, m, Y, M, doP = TRUE, tol = 1e-7) {
+    .Call(`_rxode2_binomProbsPredVec_`, n, m, Y, M, doP, tol)
+}
+
+binomProbs_ <- function(x, probs, naRm, nIn, cont) {
+    .Call(`_rxode2_binomProbs_`, x, probs, naRm, nIn, cont)
+}
+
+meanProbs_ <- function(x, probs, naRm, useT, pred, nIn) {
+    .Call(`_rxode2_meanProbs_`, x, probs, naRm, useT, pred, nIn)
 }