From f55ca284b013574724150193dd71ddea02d3bdfe Mon Sep 17 00:00:00 2001 From: Andrew Hooker Date: Fri, 4 Oct 2024 17:14:51 +0200 Subject: [PATCH] Preparing for CRAN release. --- DESCRIPTION | 2 +- NEWS.md | 17 ++++++++++++++--- R/ed_laplace_ofv.R | 2 +- R/start_parallel.R | 2 +- README.Rmd | 1 + README.md | 1 + man/PopED-package.Rd | 2 +- man/ed_laplace_ofv.Rd | 2 +- man/start_parallel.Rd | 2 +- revdep/.gitignore | 7 +++++++ revdep/README.md | 25 +++++++++++++++++++++++++ revdep/cran.md | 7 +++++++ revdep/failures.md | 1 + revdep/problems.md | 1 + 14 files changed, 63 insertions(+), 9 deletions(-) create mode 100644 revdep/.gitignore create mode 100644 revdep/README.md create mode 100644 revdep/cran.md create mode 100644 revdep/failures.md create mode 100644 revdep/problems.md diff --git a/DESCRIPTION b/DESCRIPTION index 2b5ca80..18816ba 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -54,7 +54,7 @@ Description: Optimal experimental designs for both population and individual . 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 diff --git a/NEWS.md b/NEWS.md index 161dc19..7a1b655 100644 --- a/NEWS.md +++ b/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. diff --git a/R/ed_laplace_ofv.R b/R/ed_laplace_ofv.R index 27a6f34..c517170 100644 --- a/R/ed_laplace_ofv.R +++ b/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. diff --git a/R/start_parallel.R b/R/start_parallel.R index 8928239..ca7e5d7 100644 --- a/R/start_parallel.R +++ b/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 diff --git a/README.Rmd b/README.Rmd index 48f446c..46fc5fa 100644 --- a/README.Rmd +++ b/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: andrew.hooker@farmaci.uu.se diff --git a/README.md b/README.md index 5abb6ce..f63c8da 100644 --- a/README.md +++ b/README.md @@ -47,6 +47,7 @@ PopED](https://andrewhooker.github.io/PopED/articles/intro-poped.html) You are welcome to: +- Ask questions at: - submit suggestions and bug-reports at: - send a pull request on: diff --git a/man/PopED-package.Rd b/man/PopED-package.Rd index aea21f8..dc1f686 100644 --- a/man/PopED-package.Rd +++ b/man/PopED-package.Rd @@ -197,7 +197,7 @@ experimental design in population kinetics", Computer Methods and Programs in Bi Useful links: \itemize{ \item \url{https://andrewhooker.github.io/PopED/} - \item \url{https://github.com/andrewhooker/PopED,} + \item \url{https://github.com/andrewhooker/PopED} \item Report bugs at \url{https://github.com/andrewhooker/PopED/issues} } diff --git a/man/ed_laplace_ofv.Rd b/man/ed_laplace_ofv.Rd index 587fa3b..226e44d 100644 --- a/man/ed_laplace_ofv.Rd +++ b/man/ed_laplace_ofv.Rd @@ -61,7 +61,7 @@ can also just supply the diagonal parameter values (variances) as a \code{c()}.} \item{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.} \item{return_gradient}{Should the gradient be returned.} diff --git a/man/start_parallel.Rd b/man/start_parallel.Rd index 84ca0e7..d2aa123 100644 --- a/man/start_parallel.Rd +++ b/man/start_parallel.Rd @@ -18,7 +18,7 @@ start_parallel( \item{parallel}{Should the parallel functionality start up?} \item{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.} \item{parallel_type}{Which type of parallelization should be used? Can be "snow" or "multicore". "snow" works on Linux-like systems & Windows. diff --git a/revdep/.gitignore b/revdep/.gitignore new file mode 100644 index 0000000..111ab32 --- /dev/null +++ b/revdep/.gitignore @@ -0,0 +1,7 @@ +checks +library +checks.noindex +library.noindex +cloud.noindex +data.sqlite +*.html diff --git a/revdep/README.md b/revdep/README.md new file mode 100644 index 0000000..78a925f --- /dev/null +++ b/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 + diff --git a/revdep/cran.md b/revdep/cran.md new file mode 100644 index 0000000..d07935b --- /dev/null +++ b/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 + diff --git a/revdep/failures.md b/revdep/failures.md new file mode 100644 index 0000000..9a20736 --- /dev/null +++ b/revdep/failures.md @@ -0,0 +1 @@ +*Wow, no problems at all. :)* \ No newline at end of file diff --git a/revdep/problems.md b/revdep/problems.md new file mode 100644 index 0000000..9a20736 --- /dev/null +++ b/revdep/problems.md @@ -0,0 +1 @@ +*Wow, no problems at all. :)* \ No newline at end of file