Merge pull request #799 from nlmixr2/doc-pkgdown-fix

Documentation and pkgdown fix

NAMESPACE

@@ -27,6 +27,7 @@ S3method("ini<-",default)
 S3method("model<-",default)
 S3method("rxode2<-","function")
 S3method("rxode2<-",default)
+S3method("units<-",rxEvid)
 S3method(.DollarNames,rxEt)
 S3method(.DollarNames,rxSolve)
 S3method(.DollarNames,rxUi)

R/assert.R

@@ -625,6 +625,7 @@ warnRxBounded <- function(ui, extra="", .var.name=.vname(ui)) {
 #' @return boolean, indicating if the object is a valid initialization data frame
 #' @export
 #' @author Matthew L. Fidler
+#' @family Assertions
 #' @examples
 #' testIniDf(TRUE)
 testIniDf <- function(iniDf) {

R/et.R

@@ -1376,11 +1376,13 @@ as.character.rxEvid <- function(x, ...) {
   as.rxEvid(NextMethod())
 }
 
+#' @rdname rxEvid
+#' @param value It will be an error to set units for evid
+#' @export
 `units<-.rxEvid` <- function(x, value) {
   stop("'evid' is unitless", call. = FALSE)
 }
 
-
 #' @export
 `[<-.rxEvid` <- function(x, i, value) {
   as.rxEvid(NextMethod())

R/linMod.R

@@ -95,9 +95,8 @@ rxUdfUi.default <- function(fun) {
 #'   `rxUdfUi()` for details.
 #'
 #' @export
-#'
+#' @family User functions
 #' @author Matthew L. Fidler
-#'
 #' @examples
 #'
 #' linMod(x, 3)
@@ -239,10 +238,13 @@ linMod <- function(variable, power, dv="dv",
         warning(.dv, "not found in data, so no initial estimates will be set to zero")
       } else {
         names(.dat)[.wdv] <- .dv
-        .model <- stats::lm(as.formula(paste0(.dv, " ~ stats::poly(", .var, ",",
-                                              power, ")",
-                                              ifelse(intercept, "", "+0"))),
-                            data=rxUdfUiData())
+        .model <-
+          stats::lm(
+            stats::as.formula(
+              paste0(.dv, " ~ stats::poly(", .var, ",", power, ")",
+                     ifelse(intercept, "", "+0"))),
+            data=rxUdfUiData()
+          )
         .est <- coef(.model)
       }
     }

R/rudfui.R

@@ -30,12 +30,12 @@ rxUdfUiReset()
 #' UI functions
 #'
 #' @return integer greater than 1L
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples
 #'
 #' rxUdfUiNum()
-#'
 rxUdfUiNum <- function() {
   if (checkmate::testIntegerish(.udfUiEnv$num, lower=1L, len=1L, any.missing=FALSE))  {
     as.integer(.udfUiEnv$num)
@@ -64,6 +64,7 @@ rxUdfUiIniDf <- function() {
 #' Return the lhs parsed language expression
 #'
 #' @return lhs language expression or NULL
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples
@@ -87,6 +88,7 @@ rxUdfUiIniLhs <- function() {
 #'
 #' @return value of the `modelVariables` being processed or `NULL`.
 #'
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples
@@ -113,6 +115,7 @@ rxUdfUiMv <- function(value) {
 #' @return value of the `data.frame` being processed or `NULL`.
 #'
 #' @export
+#' @family User functions
 #' @author Matthew L. Fidler
 #' @examples
 #'
@@ -135,6 +138,7 @@ rxUdfUiData <- function(value) {
 #' @param value when specified, this assigns the character value of
 #'   the estimation method or NULL if there is nothing being estimated
 #' @return value of the estimation method being processed or NULL
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples
@@ -156,6 +160,7 @@ rxUdfUiEst <- function(value) {
 #' Returns if the current ui function is being parsed
 #'
 #' @return logical if the current ui function is being parsed
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples

_pkgdown.yml

@@ -55,6 +55,7 @@ reference:
   - rxUiCompress
   - rxUiDecompress
   - rxode2<-
+  - testIniDf
   - testRxLinCmt
   - testRxUnbounded
   - update.rxUi
@@ -160,6 +161,18 @@ reference:
   - rxSymInvChol
   - swapMatListWithCube
   - uppergamma
+- title: User functions
+  contents:
+  - linMod
+  - rxIntToBase
+  - rxIntToLetter
+  - rxUdfUiData
+  - rxUdfUiEst
+  - rxUdfUiIniDf
+  - rxUdfUiIniLhs
+  - rxUdfUiMv
+  - rxUdfUiNum
+  - rxUdfUiParsing
 - title: Internal Functions
   contents:
   - .cbindOme

man-roxygen/etExamples.R

@@ -1,6 +1,6 @@
 #' @examples
 #'
-#' \donttest{
+#' \dontrun{
 #'
 #' library(rxode2)
 #' library(units)
@@ -32,16 +32,17 @@
 #' ## These are making the more complex regimens of the rxode2 tutorial
 #'
 #' ## bid for 5 days
-#' bid <- et(timeUnits="hr") %>%
+#' bid <- et(timeUnits="hr") |>
 #'        et(amt=10000,ii=12,until=set_units(5, "days"))
 #'
 #' ## qd for 5 days
-#' qd <- et(timeUnits="hr") %>%
+#' qd <- et(timeUnits="hr") |>
 #'       et(amt=20000,ii=24,until=set_units(5, "days"))
 #'
 #' ## bid for 5 days followed by qd for 5 days
 #'
-#' et <- seq(bid,qd) %>% et(seq(0,11*24,length.out=100))
+#' et <- seq(bid,qd) |>
+#'       et(seq(0,11*24,length.out=100))
 #'
 #' bidQd <- rxSolve(mod1, et)
 #'
@@ -51,11 +52,12 @@
 #' ## Now Infusion for 5 days followed by oral for 5 days
 #'
 #' ##  note you can dose to a named compartment instead of using the compartment number
-#' infusion <- et(timeUnits = "hr") %>%
+#' infusion <- et(timeUnits = "hr") |>
 #'       et(amt=10000, rate=5000, ii=24, until=set_units(5, "days"), cmt="centr")
 #'
 #'
-#' qd <- et(timeUnits = "hr") %>% et(amt=10000, ii=24, until=set_units(5, "days"), cmt="depot")
+#' qd <- et(timeUnits = "hr") |>
+#'   et(amt=10000, ii=24, until=set_units(5, "days"), cmt="depot")
 #'
 #' et <- seq(infusion,qd)
 #'
@@ -65,9 +67,10 @@
 #'
 #' ## 2wk-on, 1wk-off
 #'
-#' qd <- et(timeUnits = "hr") %>% et(amt=10000, ii=24, until=set_units(2, "weeks"), cmt="depot")
+#' qd <- et(timeUnits = "hr") |>
+#'       et(amt=10000, ii=24, until=set_units(2, "weeks"), cmt="depot")
 #'
-#' et <- seq(qd, set_units(1,"weeks"), qd) %>%
+#' et <- seq(qd, set_units(1,"weeks"), qd) |>
 #'      add.sampling(set_units(seq(0, 5.5,by=0.005),weeks))
 #'
 #' wkOnOff <- rxSolve(mod1, et)
@@ -76,10 +79,11 @@
 #'
 #' ## You can also repeat the cycle easily with the rep function
 #'
-#' qd <-et(timeUnits = "hr") %>% et(amt=10000, ii=24, until=set_units(2, "weeks"), cmt="depot")
+#' qd <-et(timeUnits = "hr") |>
+#'      et(amt=10000, ii=24, until=set_units(2, "weeks"), cmt="depot")
 #'
-#' et <- etRep(qd, times=4, wait=set_units(1,"weeks")) %>%
-#'      add.sampling(set_units(seq(0, 12.5,by=0.005),weeks))
+#' et <- etRep(qd, times=4, wait=set_units(1,"weeks")) |>
+#'       add.sampling(set_units(seq(0, 12.5,by=0.005),weeks))
 #'
 #' repCycle4 <- rxSolve(mod1, et)
 #'