Merge pull request #16 from nlmixr2/articles

Articles

.Rbuildignore

@@ -2,5 +2,7 @@
 ^README\.Rmd$
 ^bad-library.md$
 ^pkgdown$
+^_pkgdown.yml$
 ^.github$
 ^vignettes/articles$
+^cran-comments\.md$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: monolix2rx
 Title: 'monolix2rx' Converts 'Monolix' Models to 'rxode2'
-Version: 0.0.0.9000
+Version: 0.0.1
 Authors@R:
    c(person("Matthew","Fidler", role = c("aut", "cre"), email = "[email protected]", comment=c(ORCID="0000-0001-8538-6691")),
      person("Justin", "Wilkins", role = "ctb", email = "[email protected]", comment=c(ORCID="0000-0002-7099-9396")))
@@ -40,7 +40,7 @@ Imports:
     crayon,
     lotri,
     magrittr,
-    rxode2 (> 2.0.13),
+    rxode2 (>= 3.0.0),
 Suggests:
     devtools,
     testthat (>= 3.0.0),

NAMESPACE

@@ -69,13 +69,8 @@ export(logit)
 export(lotri)
 export(mlxTxt)
 export(mlxtran)
-export(mlxtranGetMutate)
 export(model)
 export(monolix2rx)
-export(monolixDataImport)
-export(monolixEndpoints)
-export(monolixEtaImport)
-export(monolixPredIpred)
 export(rxRename)
 export(rxSolve)
 export(rxUiGet)

NEWS.md

@@ -0,0 +1,3 @@
+# monolix2rx 0.0.1
+
+* Initial CRAN submission.

R/dataCov.R

@@ -3,7 +3,7 @@
 #'
 #' @param mlxtran input mlxtran file
 #' @return mlxtran string that can be applied to a model (by evaluating it)
-#' @export
+#' @noRd
 #' @author Matthew L. Fidler
 #' @examples
 #'

R/dataImport.R

@@ -211,7 +211,7 @@
 #' @inheritParams utils::read.table
 #' @return Dataset appropriate for using with the rxode2 model for
 #'   simulations
-#' @export
+#' @noRd
 #' @author Matthew L. Fidler
 #' @examples
 #'

R/endpointInfo.R

@@ -4,7 +4,7 @@
 #' @param mlxtran This is the parsed mlxtran or imported rxode2 model from monolix
 #'
 #' @return nothing, called for side effects
-#' @export
+#' @noRd
 #' @author Matthew L. Fidler
 monolixEndpoints <- function(mlxtran) {
   mlxtran <- .monolixGetMlxtran(mlxtran)

R/etaImport.R

@@ -3,7 +3,7 @@
 #' @param mlxtran mlxtran file where data input is specified
 #' @inheritParams utils::read.table
 #' @author Matthew L Fidler
-#' @export
+#' @noRd
 monolixEtaImport <- function(mlxtran, na.strings=c("NA", ".")) {
   mlxtran <- .monolixGetMlxtran(mlxtran)
   if (is.null(mlxtran)) return(NULL)

R/indDef.R

@@ -156,13 +156,7 @@
                         return(.c)
                       })
       .ret$cov <- .monolix2rx$cov
-      .ret$coef <- lapply(seq_along(.coef),
-                          function(i) {
-                            .cur <- .coef[[i]]
-                            .w <- which(grepl("^rxCov_", .cur))
-                            if (length(.w) >= 1) .cur <- .cur[-.w]
-                            .cur
-                          })
+      .ret$coef <- .coef
       .rx <- paste0(.rx, " + ",
                     paste(vapply(seq_along(.ret$coef),
                                  function(i) {
@@ -184,10 +178,20 @@
                                                                     .coef[.w])
                                        .coef <- .coef[-.w]
                                        .ref <- .ref[-.w]
+                                       .w <- which(grepl("^rxCov_", .coef))
+                                       if (length(.w) > 0) {
+                                         .coef <- .coef[-.w]
+                                         .ref <- .ref[-.w]
+                                       }
                                        return(paste(paste0(.coef, " * (", .cov, " == '", .ref, "')"), collapse=" + "))
                                      }
-                                    }
-                                   paste(paste0(.ret$coef[[i]], "*", .ret$cov[i]), collapse=" + ")
+                                   }
+                                   .coef <- .ret$coef[[i]]
+                                   .w <- which(grepl("^rxCov_", .coef))
+                                   if (length(.w) > 0) {
+                                     .coef <- .coef[-.w]
+                                   }
+                                   paste(paste0(.coef, "*", .ret$cov[i]), collapse=" + ")
                                  }, character(1), USE.NAMES=FALSE),
                           collapse=" + "))
     }

R/ipredImport.R

@@ -53,7 +53,7 @@
 #' @param mlxtran mlxtran file where data input is specified
 #' @inheritParams utils::read.table
 #' @author Matthew L Fidler
-#' @export
+#' @noRd
 monolixPredIpred <- function(mlxtran, na.strings=c("NA", ".")) {
   mlxtran <- .monolixGetMlxtran(mlxtran)
   withr::with_dir(.monolixGetPwd(mlxtran), {

R/rxSolve.R

@@ -6,7 +6,7 @@ rxSolve.monolix2rx <- function(object, params = NULL, events = NULL,
     maxsteps = 70000L, hmin = 0, hmax = NA_real_, hmaxSd = 0, 
     hini = 0, maxordn = 12L, maxords = 5L, ..., cores, covsInterpolation = c("locf", 
         "linear", "nocb", "midpoint"), naInterpolation = c("locf", 
-        "nocb"), keepInterpolation = c("locf", "nocb", "na"), 
+        "nocb"), keepInterpolation = c("na", "locf", "nocb"), 
     addCov = TRUE, sigma = NULL, sigmaDf = NULL, sigmaLower = -Inf, 
     sigmaUpper = Inf, nCoresRV = 1L, sigmaIsChol = FALSE, sigmaSeparation = c("auto", 
         "lkj", "separation"), sigmaXform = c("identity", "variance", 

R/validate.R

@@ -180,9 +180,22 @@
     .qai <- stats::quantile(with(.both, abs(ipred-monolixIpred)), .q, na.rm=TRUE)
     .qp <- stats::quantile(with(.both, 100*abs((pred-monolixPred)/monolixIpred)), .q, na.rm=TRUE)
     .qap <- stats::quantile(with(.both, abs(pred-monolixPred)), .q, na.rm=TRUE)
+
     .qw <- stats::quantile(with(.both, 100*abs((iwres-monolixIwres)/monolixIwres)), .q, na.rm=TRUE)
     .qaw <- stats::quantile(with(.both, abs(iwres-monolixIwres)), .q, na.rm=TRUE)
 
+    .ui$ipredAtol <- .qai[3]
+    .ui$ipredRtol <- .qi[3]/100
+    .ui$ipredCompare <- .both[,grepl("(id|time|monolixIpred|ipred|cmt)", names(.both), ignore.case=TRUE)]
+
+    .ui$predAtol <- .qap[3]
+    .ui$predRtol <- .qp[3]/100
+    .ui$predCompare <- .both[,grepl("^(id|time|monolixPred|pred|cmt)$", names(.both), ignore.case=TRUE)]
+
+    .ui$iwresAtol <- .qaw[3]
+    .ui$iwresRtol <- .qw[3]/100
+    .ui$iwresCompare <- .both[,grepl("(id|time|monolixIwres|iwres|cmt)", names(.both), ignore.case=TRUE)]
+
     .msg <- c(paste0("ipred relative difference compared to Monolix ipred: ", round(.qi[3], 2),
                      "%; ", .ci0 * 100,"% percentile: (",
                      round(.qi[2], 2), "%,", round(.qi[4], 2), "%); rtol=",

README.Rmd

@@ -41,6 +41,37 @@ You can install the development version of monolix2rx from
 # install.packages("devtools")
 devtools::install_github("nlmixr2/monolix2rx")
 ```
+## What you can do with `monolix2rx`/`babelmixr2`
+
+You can do many useful tasks directly converting between nlmixr2 and
+NONMEM models; you can:
+
+-	[Convert a Monolix model to a rxode2/nlmixr2 model](https://nlmixr2.github.io/monolix2rx/articles/convert-nlmixr2.html)
+
+Then with nlmixr2 fit models and monolix2rx models coming from both conversions, you can:
+
+-	[Perform simulations of new
+    dosing](https://nlmixr2.github.io/monolix2rx/articles/simulate-new-dosing.html) from the Monolix model or even [simulate using the uncertainty in your model to simulate new scenarios](https://nlmixr2.github.io/monolix2rx/articles/simulate-uncertainty.html)
+
+-	[Modify the model to calculate derived parameters](https://nlmixr2.github.io/monolix2rx/articles/simulate-extra-items.html) (like AUC). These parameters slow down Monolix’s optimization, but can help in your simulation scenario.
+
+-  [Simulating with Covariates/Input PK
+   parameters](https://nlmixr2.github.io/monolix2rx/articles/simulate-new-dosing-with-covs.html). This example shows approaches to resample from the input dataset for covariate selection.
+
+With nonmem2rx and babelmixr2, convert the imported rxode2 model to a nlmixr2 object, allowing:
+
+-	[Generation of Word and PowerPoint plots with
+      nlmixr2rpt](https://nlmixr2.github.io/monolix2rx/articles/create-office.html)
+
+-	[Easy VPC
+      creation](https://nlmixr2.github.io/monolix2rx/articles/create-vpc.html)
+      (with `vpcPlot()`)
+
+-	[Easy Individual plots with extra solved
+      points](https://nlmixr2.github.io/monolix2rx/articles/create-augPred.html). This
+      will show the curvature of individual and population fits for
+      sparse data-sets (with `augPred()`)
+
 
 ## Example
 

_pkgdown.yml

@@ -0,0 +1,44 @@
+url: ~
+template:
+  bootstrap: 5
+  params:
+    bootswatch: flatly
+reference:
+  - title: Importing Monolix to rxode2
+    contents:
+      - monolix2rx
+  - title: Reading in `mlxtran`
+    contents:
+      - mlxtran
+      - mlxTxt
+navbar:
+  left:
+  - text: Converting
+    icon: fa-arrow-right
+    href: articles/convert-nlmixr2.html
+  - text: "Qualify"
+    icon: fa-check
+    href: articles/rxode2-validate.html
+  - text: "Simulation"
+    icon: fa-dice
+    menu:
+      - text: "New Dosing Scenarios"
+        href: articles/simulate-new-dosing.html
+      - text: "Simulating with Uncertainty"
+        href: articles/simulate-uncertainty.html
+      - text: "Simulating with Derived Variables"
+        href: articles/simulate-extra-items.html
+  - text: "Reporting"
+    menu:
+      - text: "Creating word and powerpoint documents"
+        href: articles/create-office.html
+      - text: "Easily create VPC plots"
+        href: articles/create-vpc.html
+      - text: "Create enriched Individual plots"
+        href: articles/create-augPred.html
+  - text: "Functions"
+    icon: fa-file-code-o
+    href: reference/index.html
+  - text: "News"
+    icon: fas fa-rss
+    href: news/index.html

cran-comments.md

@@ -0,0 +1,8 @@
+
+This adds monolix import to the nlmixr2 ecosystem
+
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.