Fixed error in bmdProfileGrid()

JensBaalkilde · JensBaalkilde · commit 2993a29c173a · 2025-01-29T15:34:58.000+01:00
Fixed object assertion in bmd()
Changed "name" and "alias" in bmdHetVar, drmHetVar and bootDataGenOrdinal manuals
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-cache/
+cache/
+README.Rmd
+README.md
+README_files/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,7 +7,12 @@ Author: Signe M.Jensen, Christian Ritz and Jens Riis Baalkilde
 Maintainer: Signe M. Jensen <smj@plen.ku.dk>
 Description: Benchmark dose analysis for continuous, quantal, count and ordinal dose-response data
 Imports: drc, ggplot2, dplyr
-Suggests: CVXR, multcomp, gridExtra
+Suggests: 
+    CVXR,
+    multcomp,
+    gridExtra,
+    testthat (>= 3.0.0)
 License: GPL
 Encoding: UTF-8
 LazyData: true
+Config/testthat/edition: 3
diff --git a/R/bmd.R b/R/bmd.R
@@ -5,6 +5,11 @@ bmd<-function(object, bmr, backgType = c("modelBased", "absolute", "hybridSD", "
                respTrans = c("none", "log", "sqrt"),
               interval = c("delta", "sandwich", "inv", "profile", "profileGrid"), sandwich.vcov=FALSE, display = TRUE, level=0.95, profileGridSize = NA, profileProgressInfo = TRUE) 
 {
+  if (missing(object)){
+    stop(paste("object is missing", sep=""))
+  } else {
+    if(!inherits(object, "drc")){ stop('object must be of type "drc"')}
+  }
   if (missing(def)) {
     stop(paste("def is missing", sep=""))
   }
diff --git a/R/bmdProfileCIgrid.R b/R/bmdProfileCIgrid.R
@@ -91,6 +91,7 @@ bmdProfileCIgrid <- function(object, bmr, backgType = c("modelBased", "absolute"
     names(object0$coefficients) <- coefNames
     object0$curve[[1]] <- object$pfFct(parmMat = matrix(par, nrow = 1))
     object0$parmMat <- matrix(par, nrow = length(par))
+    colnames(object0$parmMat) <- 1
     
     bmd(object0, bmr = bmr, backgType = backgType, backg = backg, controlSD = controlSD, def = def, interval = "delta", display = FALSE)
   }
diff --git a/man/bmdHetVar.Rd b/man/bmdHetVar.Rd
@@ -1,5 +1,5 @@
-\name{bmd}
-\alias{bmd}
+\name{bmdHetVar}
+\alias{bmdHetVar}
 \title{
 Benchmark dose estimation with heterogeneous variance
 }
diff --git a/man/bootDataGenOrdinal.Rd b/man/bootDataGenOrdinal.Rd
@@ -1,5 +1,5 @@
-\name{bootDataGen}
-\alias{bootDataGen}
+\name{bootDataGenOrdinal}
+\alias{bootDataGenOrdinal}
 \title{
 Help funtion to bmdOrdinal and bmdOrdinalMA
 }
diff --git a/man/drmHetVar.Rd b/man/drmHetVar.Rd
@@ -1,5 +1,5 @@
-\name{bmd}
-\alias{bmd}
+\name{drmHetVar}
+\alias{drmHetVar}
 \title{
 Dose response modeling with heterogeneous variance
 }

Original file line number	Diff line number	Diff line change
`@@ -5,6 +5,11 @@ bmd<-function(object, bmr, backgType = c("modelBased", "absolute", "hybridSD", "`
`5`	`5`	`respTrans = c("none", "log", "sqrt"),`
`6`	`6`	`interval = c("delta", "sandwich", "inv", "profile", "profileGrid"), sandwich.vcov=FALSE, display = TRUE, level=0.95, profileGridSize = NA, profileProgressInfo = TRUE)`
`7`	`7`	`{`
	`8`	`+ if (missing(object)){`
	`9`	`+ stop(paste("object is missing", sep=""))`
	`10`	`+ } else {`
	`11`	`+ if(!inherits(object, "drc")){ stop('object must be of type "drc"')}`
	`12`	`+ }`
`8`	`13`	`if (missing(def)) {`
`9`	`14`	`stop(paste("def is missing", sep=""))`
`10`	`15`	`}`
Original file line number	Diff line number	Diff line change
`@@ -91,6 +91,7 @@ bmdProfileCIgrid <- function(object, bmr, backgType = c("modelBased", "absolute"`
`91`	`91`	`names(object0$coefficients) <- coefNames`
`92`	`92`	`object0$curve[[1]] <- object$pfFct(parmMat = matrix(par, nrow = 1))`
`93`	`93`	`object0$parmMat <- matrix(par, nrow = length(par))`
	`94`	`+ colnames(object0$parmMat) <- 1`
`94`	`95`
`95`	`96`	`bmd(object0, bmr = bmr, backgType = backgType, backg = backg, controlSD = controlSD, def = def, interval = "delta", display = FALSE)`
`96`	`97`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`		`-\name{bmd}`
`2`		`-\alias{bmd}`
	`1`	`+\name{bmdHetVar}`
	`2`	`+\alias{bmdHetVar}`
`3`	`3`	`\title{`
`4`	`4`	`Benchmark dose estimation with heterogeneous variance`
`5`	`5`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`		`-\name{bootDataGen}`
`2`		`-\alias{bootDataGen}`
	`1`	`+\name{bootDataGenOrdinal}`
	`2`	`+\alias{bootDataGenOrdinal}`
`3`	`3`	`\title{`
`4`	`4`	`Help funtion to bmdOrdinal and bmdOrdinalMA`
`5`	`5`	`}`