Merge pull request #30 from JensBaalkilde/master

V2.7.1

Author: JensBaalkilde

.DS_Store

@@ -1,2 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+cache/
+README.Rmd
+README.md
+README_files/

.Rbuildignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+cache/

.gitignore

@@ -1,13 +1,26 @@
 Package: bmd
 Type: Package
 Title: Benchmark dose estimation for dose-response data
-Version: 2.6.5
-Date: 2024-12-11
+Version: 2.7.1
+Date: 2025-03-24
 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
+Suggests: 
+    sandwich,
+    CVXR,
+    multcomp,
+    gridExtra,
+    isotone,
+    reshape2,
+    dplyr,
+    car,
+    Matrix,
+    RLRsim,
+    scales,
+    testthat (>= 3.0.0)
 License: GPL
 Encoding: UTF-8
-LazyData: true
+LazyData: true
+Config/testthat/edition: 3

DESCRIPTION

@@ -1,12 +1,15 @@
 import(drc, ggplot2, dplyr)
 export(bmd, bmdBoot, bmdIso, bmdIsoBoot, PAV, bmdMA, bootDataGen, bmdMACurve, BCa, invBmd, expandBinomial, 
-       getStackingWeights, drmOrdinal, bmdOrdinal, bmdOrdinalMA, expandOrdinal, bootDataGenOrdinal,
-       qplotDrc, qplotBmd, MACurve)
+       getStackingWeights, drmOrdinal, bmdOrdinal, bmdOrdinalMA,
+       expandOrdinal, bootDataGenOrdinal,
+       qplotDrc, qplotBmd, MACurve, monotonicityTest, trendTest, bmdHetVar, drmHetVar)
 
 ## S3 methods
 S3method(logLik, drcOrdinal)
 S3method(AIC, drcOrdinal)
+S3method(BIC, drcOrdinal)
 S3method(plot, drcOrdinal)
 S3method(print, drcOrdinal)
 S3method(print, bmdOrdinal)
-S3method(plot, bmd)
+S3method(plot, bmd)
+S3method(plot, drcHetVar)

NAMESPACE

@@ -0,0 +1,5 @@
+BIC.drcOrdinal <- function(object, epsilon = 10^(-16)){
+  n.parameters <- sum(sapply(object$drmList, function(mod) length(mod$coefficients)))
+  n.obs <- sum(object$data[[object$weights]])
+  n.parameters * log(n.obs) - 2 * logLik(object, epsilon) 
+}