v23.1.1.2.4 fixed rel+sd BMD calculations, fixed bug in LMS hybrid, a…

…dded ma_build_priors

.Rbuildignore

@@ -1,2 +1,2 @@
-cran-comments.md
-CHANGELOG.md
+^.*\.Rproj$
+^\.Rproj\.user$

DESCRIPTION

@@ -1,79 +1,99 @@
-Package: ToxicR
-Type: Package
-Title: Analyzing Toxicology Dose-Response Data
-Version: 23.1.1.0.9
-Date: 2023-1-19
-Authors@R:
-    c(
-    person(given = "Matt",
-           family = "Wheeler",
-           role = c("aut", "cre"),
-           email = "matt.wheeler@nih.gov",
-           comment = c(ORCID = "0000-0002-8242-2391")),
-    person(given = "Sooyeong",
-           family = "Lim",
-           role = "aut"),
-    person(given ="Eric",
-           family="Wimberly",
-           role = "ctb"),
-    person(given = "Keith",
-           family = "Shockley",
-           role = "com"),
-    person(given = "Jennifer",
-           family = "Fostel",
-           role = "com"),
-    person(given="Lonlong",
-           family="Yang",
-           role="ctb",
-           comment="Modfied Cochran-Armitage test."),
-    person(given = "Dawan",
-           family = "Taley",
-           role = "com"),
-    person(given = "Cari",
-           family = "Martini",
-           role   = "com"),
-    person(given = "Ashwin",
-           family = "Raghuraman",
-           role   = "ctb",
-           comment = "Modified code for (Jonckheere, Williams etc.) to make them  standalone functions."),
-    person(given = "Steven",
-           family = "Johnson",
-           role = "ctb",
-           comment ="Author of NLOPT."),
-    person(given = "Aymeric",
-           family = "Stamm",
-           role = "ctb",
-           comment ="Maintainer of nloptr Packag 2.0.1 from which all compile scripts were taken."),
-    person(given = "Dirk",
-           family = "Eddelbuettel",
-           role = "ctb",
-           comment ="Contributed script to download GSL, as in RcppGSL."),
-    person("U.S. Deptartment of Health and Human Services (US HHS), National Institute of Environmental Health Sciences (NIEHS)",
-           role="cph",
-           comment ="Owns Copyright for all ToxicR code outside NLOPT and nloptr scripts.")
-           )
-Maintainer: Matt Wheeler <matt.wheeler@nih.gov>
-Copyright: file inst/COPYRIGHTS 
-Description: Toxicology routines for analyzing dose-response data include dose-response analysis 
-    and trend tests. Dose-Response methods are based upon the US EPA's benchmark dose software 3.  Methods have
-    been extended to include additional functionality based on World Health Organization 
-    guidelines.  It further supports the European Food Safety Authority's 
-    draft guidance on model averaging. The dose-response methods and datasets used in this package are 
-    described in Wheeler et al. (2019) <doi:10.1111/risa.13218>, Wheeler et al. (2020) <doi:10.1111/risa.13537>,
-    and Wheeler et al. (2022) <doi:10.1002/env.2728>.  NTP routines are described in 
-    Bailer and Portier (1988) <doi:10.2307/2531856>, Bieler and Williams (1993) <doi:10.2307/2532200>, 
-    Williams (1971) <doi:10.2307/2528930>, and Shirley (1977) <doi:10.2307/2529789>.
-Depends:
-    R (>= 4.1.0)
-License: LGPL (>= 3)
-URL: https://github.com/NIEHS/ToxicR
-LazyData: true
-Imports: Rcpp (>= 1.0.0), ggplot2 (>= 3.3.2), shiny (>= 1.5.0),  coda (>= 0.19-4),
-         scales (>= 1.1.1),  forcats, ggridges (>= 0.5.3), doBy (>= 4.6.11),
-         multcomp (>= 1.4), dplyr (>= 1.0.7) 
-LinkingTo: Rcpp, RcppEigen, RcppGSL
-RoxygenNote: 7.2.1
-VignetteBuilder: knitr
-Suggests: 
-    plotly (>= 4.9.2.1),  rmarkdown, actuar (>= 3.2-0),ggpubr (>= 0.4.0), testthat (>= 3.1.0),gridExtra (>= 2.3),
-    VIM (>= 6.1.1), knitr (>= 1.36), modules
+Package: ToxicR
+Type: Package
+Title: Analyzing Toxicology Dose-Response Data
+Version: 23.1.1.2.4
+Date: 2023-1-23
+Authors@R: 
+    c(
+    person(given = "Matt",
+           family = "Wheeler",
+           role = c("aut", "cre"),
+           email = "matt.wheeler@nih.gov",
+           comment = c(ORCID = "0000-0002-8242-2391")),
+    person(given = "Sooyeong",
+           family = "Lim",
+           role = "aut"),
+    person(given ="Eric",
+           family="Wimberly",
+           role = "ctb"),
+    person(given = "Keith",
+           family = "Shockley",
+           role = "com"),
+    person(given = "Jennifer",
+           family = "Fostel",
+           role = "com"),
+    person(given="Lonlong",
+           family="Yang",
+           role="ctb",
+           comment="Modfied Cochran-Armitage test."),
+    person(given = "Dawan",
+           family = "Taley",
+           role = "com"),
+    person(given = "Cari",
+           family = "Martini",
+           role   = "com"),
+    person(given = "Ashwin",
+           family = "Raghuraman",
+           role   = "ctb",
+           comment = "Modified code for (Jonckheere, Williams etc.) to make them  standalone functions."),
+    person(given = "Steven",
+           family = "Johnson",
+           role = "ctb",
+           comment ="Author of NLOPT."),
+    person(given = "Aymeric",
+           family = "Stamm",
+           role = "ctb",
+           comment ="Maintainer of nloptr Packag 2.0.1 from which all compile scripts were taken."),
+    person(given = "Dirk",
+           family = "Eddelbuettel",
+           role = "ctb",
+           comment ="Contributed script to download GSL, as in RcppGSL."),
+    person("U.S. Deptartment of Health and Human Services (US HHS), National Institute of Environmental Health Sciences (NIEHS)",
+           role="cph",
+           comment ="Owns Copyright for all ToxicR code outside NLOPT and nloptr scripts.")
+           )
+Maintainer: Matt Wheeler <matt.wheeler@nih.gov>
+Copyright: file inst/COPYRIGHTS
+Description: Toxicology routines for analyzing dose-response data include dose-response analysis 
+    and trend tests. Dose-Response methods are based upon the US EPA's benchmark dose software 3.  Methods have
+    been extended to include additional functionality based on World Health Organization 
+    guidelines.  It further supports the European Food Safety Authority's 
+    draft guidance on model averaging. The dose-response methods and datasets used in this package are 
+    described in Wheeler et al. (2019) <doi:10.1111/risa.13218>, Wheeler et al. (2020) <doi:10.1111/risa.13537>,
+    and Wheeler et al. (2022) <doi:10.1002/env.2728>.  NTP routines are described in 
+    Bailer and Portier (1988) <doi:10.2307/2531856>, Bieler and Williams (1993) <doi:10.2307/2532200>, 
+    Williams (1971) <doi:10.2307/2528930>, and Shirley (1977) <doi:10.2307/2529789>.
+Depends: R (>= 4.1.0)
+License: LGPL (>= 3)
+URL: https://github.com/NIEHS/ToxicR
+LazyData: true
+Imports: Rcpp (>= 1.0.0), ggplot2 (>= 3.3.2), shiny (>= 1.5.0), coda
+        (>= 0.19-4), scales (>= 1.1.1), forcats, ggridges (>= 0.5.3),
+        doBy (>= 4.6.11), multcomp (>= 1.4), dplyr (>= 1.0.7)
+LinkingTo: Rcpp, RcppEigen, RcppGSL
+RoxygenNote: 7.2.3
+Encoding: UTF-8
+VignetteBuilder: knitr
+Suggests: plotly (>= 4.9.2.1), rmarkdown, actuar (>= 3.2-0),ggpubr (>=
+        0.4.0), testthat (>= 3.1.0),gridExtra (>= 2.3), VIM (>= 6.1.1),
+        knitr (>= 1.36), modules
+NeedsCompilation: yes
+Packaged: 2023-04-11 20:00:54 UTC; Brian.kidd
+Author: Matt Wheeler [aut, cre] (<https://orcid.org/0000-0002-8242-2391>),
+  Sooyeong Lim [aut],
+  Eric Wimberly [ctb],
+  Keith Shockley [com],
+  Jennifer Fostel [com],
+  Lonlong Yang [ctb] (Modfied Cochran-Armitage test.),
+  Dawan Taley [com],
+  Cari Martini [com],
+  Ashwin Raghuraman [ctb] (Modified code for (Jonckheere, Williams etc.)
+    to make them standalone functions.),
+  Steven Johnson [ctb] (Author of NLOPT.),
+  Aymeric Stamm [ctb] (Maintainer of nloptr Packag 2.0.1 from which all
+    compile scripts were taken.),
+  Dirk Eddelbuettel [ctb] (Contributed script to download GSL, as in
+    RcppGSL.),
+  U.S. Deptartment of Health and Human Services (US HHS), National
+    Institute of Environmental Health Sciences (NIEHS) [cph] (Owns
+    Copyright for all ToxicR code outside NLOPT and nloptr scripts.)

NAMESPACE

@@ -86,4 +86,3 @@ S3method(MAdensity_plot, BMDdichotomous_MA_mcmc, .plot.density.BMDdichotomous_MA
 S3method(MAdensity_plot, BMDcontinuous_MA_mcmc, .plot.density.BMDcontinous_MA_MCMC)
 
 
-