Preparing for CRAN release.

DESCRIPTION

@@ -54,7 +54,7 @@ Description: Optimal experimental designs for both population and individual
     <doi:10.1016/S0169-2607(03)00073-7>.
 License: LGPL (>= 3)
 ByteCompile: true
-URL: https://andrewhooker.github.io/PopED/, https://github.com/andrewhooker/PopED, 
+URL: https://andrewhooker.github.io/PopED/, https://github.com/andrewhooker/PopED 
 BugReports: https://github.com/andrewhooker/PopED/issues
 Copyright: 2014-2021 Andrew C. Hooker
 Encoding: UTF-8

NEWS.md

@@ -1,6 +1,17 @@
-# PopED 0.6.0.900x (new updates in the current development version)
+# PopED 0.7.0
+
+* `create.poped.database()` now uses a better method of identifying the total number of parameters of each type (bpop, d, sigma, etc.) in a user defined model parameter function (the `ff_fun` argument in `create.poped.database()`) (#73).
+
+* `create.poped.database()` has a new option `reorder_parameter_vectors`, which is turned off by default. When turned on, if you use named arguments in `bpop` or `d` then PopED will try to figure out the order of the parameters based on what is found in the `fg_fun`. See the resulting `poped_db$parameters` and make sure the order matches with `fg_fun`.
+
+* `start_parallel()` has a new default for`num_cores`, which is now one less than the number of cores available from `parallel::detectCores()`.
+
+* `model_prediction()` and therefore `plot_model_prediction()` allow for log-normal distributions when using the PI option. This makes sense if you expect the prediction interval of the model will be approximately log-normally distributed, which might often be the case in pop PK models. The new default is now `PI_ln_dist = TRUE`.
+
+* `poped_optim()` now has an explicit argument allowing for the specification of Ds-optimal parameters of interest. The option is `ds_index`.
+
+* Minor bug fixes 
 
-* Nothing yet
 
 # PopED 0.6.0
 
@@ -73,7 +84,7 @@ how to handle covariate distributions in optimal design, an example on how to in
 
 * Updates to `optim_ARS()` for when to stop search.
 
-* Extended functionality of `plot.model.prediction()` (#23, @martin-gmx).
+* Extended functionality of `plot_model_prediction()` (#23, @martin-gmx).
 
 * Bug fixing.  See https://github.com/andrewhooker/PopED/commits/master for more information.
 

R/ed_laplace_ofv.R

@@ -22,7 +22,7 @@
 #' @param aopto the continuous design variables
 #' @param method If 0 then use an optimization routine translated from PopED code written in MATLAB to
 #'        optimize the parameters in the Laplace approximation.  If 1 then use \code{\link{optim}} to compute both
-#'        k and the hessian of k (see Dodds et al, JPP, 2005 for more information). If 2 then use \code{\link{fdHess}}
+#'        k and the hessian of k (see Dodds et al, JPP, 2005 for more information). If 2 then use \code{\link[nlme]{fdHess}}
 #'        to compute the hessian.
 #' @param return_gradient Should the gradient be returned.
 #' @param ... Arguments passed through from other functions, does not pass anything to another function.

R/start_parallel.R

@@ -6,7 +6,7 @@
 #' 
 #' @param parallel Should the parallel functionality start up?
 #' @param num_cores How many cores to use.  Default is
-#'   \code{parallel::detectCores()}. See \code{\link[parallel]{detectCores}} for more information.
+#'   \code{parallel::detectCores()}-1 . See \code{\link[parallel]{detectCores}} for more information.
 #' @param parallel_type Which type of parallelization should be used? Can be
 #'   "snow" or "multicore".  "snow"  works on Linux-like systems & Windows.
 #'   "multicore" works only on Linux-like systems.  By default this is chosen

README.Rmd

@@ -53,6 +53,7 @@ Learn more in this [introduction to PopED](https://andrewhooker.github.io/PopED/
 
 You are welcome to:
 
+* Ask questions at: https://github.com/andrewhooker/PopED/discussions
 * submit suggestions and bug-reports at: https://github.com/andrewhooker/PopED/issues 
 * send a pull request on: https://github.com/andrewhooker/PopED
 * compose a friendly e-mail to: [email protected] 

README.md

@@ -47,6 +47,7 @@ PopED](https://andrewhooker.github.io/PopED/articles/intro-poped.html)
 
 You are welcome to:
 
+- Ask questions at: <https://github.com/andrewhooker/PopED/discussions>
 - submit suggestions and bug-reports at:
   <https://github.com/andrewhooker/PopED/issues>
 - send a pull request on: <https://github.com/andrewhooker/PopED>

revdep/.gitignore

@@ -0,0 +1,7 @@
+checks
+library
+checks.noindex
+library.noindex
+cloud.noindex
+data.sqlite
+*.html

revdep/README.md

@@ -0,0 +1,25 @@
+# Platform
+
+|field    |value                                      |
+|:--------|:------------------------------------------|
+|version  |R version 4.4.1 (2024-06-14)               |
+|os       |macOS Sonoma 14.7                          |
+|system   |aarch64, darwin20                          |
+|ui       |RStudio                                    |
+|language |(EN)                                       |
+|collate  |en_US.UTF-8                                |
+|ctype    |en_US.UTF-8                                |
+|tz       |Europe/Stockholm                           |
+|date     |2024-10-04                                 |
+|rstudio  |2024.09.0+375 Cranberry Hibiscus (desktop) |
+|pandoc   |3.4 @ /opt/homebrew/bin/ (via rmarkdown)   |
+
+# Dependencies
+
+|package |old   |new        |Δ  |
+|:-------|:-----|:----------|:--|
+|PopED   |0.6.0 |0.6.0.9005 |*  |
+|glue    |NA    |1.8.0      |*  |
+
+# Revdeps
+

revdep/cran.md

@@ -0,0 +1,7 @@
+## revdepcheck results
+
+We checked 2 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages
+

revdep/failures.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*

revdep/problems.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*