Merge pull request #106 from InsightRX/prep-for-cran

prep for CRAN submission

DESCRIPTION

@@ -1,16 +1,16 @@
 Package: PKPDsim
 Type: Package
 Title: Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations
-Version: 1.3.0
-Date: 2023-02-24
+Version: 1.4.0
+Date: 2024-07-17
 Authors@R: c(
         person("Ron", "Keizer", email = "[email protected]", role = c("aut", "cre")),
         person("Jasmine", "Hughes", email = "[email protected]", role = "aut"),
         person("Dominic", "Tong", email = "[email protected]", role = "aut"),
         person("Kara", "Woo", email = "[email protected]", role = c("aut")),
         person("Jordan", "Brooks", email = "[email protected]", role = "aut"),
         person("InsightRX", role = c("cph", "fnd")))
-Depends: R (>= 3.0.2)
+Depends: R (>= 4.0.0)
 Imports: Rcpp (>= 0.12.9), BH, data.table, stringr, MASS,
         randtoolbox, jsonlite, stats, parallel, magrittr
 Suggests: 
@@ -19,7 +19,7 @@ Suggests:
     mockery,
     knitr,
     rmarkdown
-LinkingTo: BH, Rcpp (>= 0.12.9)
+LinkingTo: BH, Rcpp (>= 1.0.13)
 Description: Simulate dose regimens for pharmacokinetic-pharmacodynamic (PK-PD)
         models described by differential equation (DE) systems. Simulation using 
         ADVAN-style analytical equations is also supported (Abuhelwa et al. (2015) 

NEWS.md

@@ -1,3 +1,30 @@
+# PKPDsim 1.4.0
+
+This release fixes an issue introduced with an upgrade in Rcpp (1.0.13), as described here: https://github.com/RcppCore/Rcpp/issues/1311.
+
+Minor other fixes include:
+- Fixed the logic regarding a warning about infusion lengths
+- Added several example model metadata files, and improve functionality for installing example models
+- Ensure that paths with spaces are properly parsed
+- Update debugging informational messages
+- Make it easier to work with model characteristics
+- Make sure infusion length can be used with 'sc' or other non-iv administration types
+- Added feature to allow scaling of the infusion duration
+- Added feature to calculate AUC pre-ss
+- Fix interpolation of time-varying covariates in `pk` blocks.
+- Fix regimen_to_nm() conversion function
+- Added requirement that metadata has `fixed` definition
+- Minor fixes to warnings and messages
+
+## Version 1.3.0
+
+This release addresses the Feb. 16 email from Professor Ripley regarding the use
+of Boost headers that are not compliant with recent C++ versions.
+
+- Regarding note "Package in Depends/Imports which should probably only be in LinkingTo: ‘BH’":
+
+The BH package provides Boost C++ library headers. The BH library is not used in any of the code in /R or /src, but only in the C++ templates that comes with the package (in /inst/cpp). The C++ templates are used when creating a model using the new_ode_model() function, which is then compiled on-the-fly. If the BH package is removed from the Depends field, it won't be installed and hence models cannot be compiled and run. BH cannot be moved to the LinkingTo field.
+
 # PKPDsim 1.1.1
 
 This is the first version of PKPDsim that is released to CRAN. PKPDsim has been

cran-comments.md

@@ -1,3 +1,21 @@
+## Version 1.4.0
+
+This release fixes an issue introduced with an upgrade in Rcpp (1.0.13), as described here: https://github.com/RcppCore/Rcpp/issues/1311.
+
+Minor other fixes include:
+- Fixed the logic regarding a warning about infusion lengths
+- Added several example model metadata files, and improve functionality for installing example models
+- Ensure that paths with spaces are properly parsed
+- Update debugging informational messages
+- Make it easier to work with model characteristics
+- Make sure infusion length can be used with 'sc' or other non-iv administration types
+- Added feature to allow scaling of the infusion duration
+- Added feature to calculate AUC pre-ss
+- Fix interpolation of time-varying covariates in `pk` blocks.
+- Fix regimen_to_nm() conversion function
+- Added requirement that metadata has `fixed` definition
+- Minor fixes to warnings and messages
+
 ## Version 1.3.0
 
 This release addresses the Feb. 16 email from Professor Ripley regarding the use