mrgsolve 0.7.7

Important changes

• The table() macro in $TABLE is now deprecated (#129). To get derived values into the simulated output, users should assign
  to type double and list that variable name in $CAPTURE. See also the capture typedef introduced below.
• The mrgx plugin was completely removed.
• Parameter updates via param method with signature missing will check names of
  input parameters against names of existing parameters. An error is generated if a user
  attempts to update a parameter that doesn't exist. Note that this does not apply for the
  param method with signature list (../../issues/144).
• The git repository was re-organized so that the package lives in the base directory (#171).

Features

• Added @ macros for indicating block options in model specification file.
• Added qsim function for quick(er) simulation runs with just one parameter set.
• Added recmatrix that creates matrix simulation template for qsim.
• Added mrgsolve:::render to create a document with overview of model contents. Methods for both mrgmod objects and character strings pointing to a model file.
• Use mrgsolve:::details to extract model annotation.
• Added capture typedef in the model specification file. Variables that are type capture are doubles and are automatically appended to $CAPTURE. The capture typedef is not allowed in $ODE and probably should be reserved for $TABLE.
• simeta is available in $MAIN and simeps is available in $TABLE by default, no $PLUGIN is required.
• Better support for including R objects in the model via $ENV (../../issues/158).
• Added assign_ev function to help build simulation data sets from event objects (#164).
• Added as_data_frame method from the tibble package (../../issues/166).
• When annotating model blocks, mrgsolve takes the last parens item as the "units" and the last bracketed item as "options"
• Added $ operator for mrgmod objects to return the value of a parameter (99748d8).
• Added mread_cache and mcode_cache functions to build and cache a model (#143).

Bugs fixed

• Fixed documentation issue in PKMODEL. The volumes for two-compartment model with no depot should be V1/V2.
• Fixed bug in knobs where output column names are mal-formed when a user $CAPTUREs a parameter that is also being tweaked as a knob.
• Fixed bug in annotated model specification when multiple unit or option specifications are made.

Under the hood

• User-declared double/int/bool in $MAIN, $ODE, $TABLE are kept in unnamed namespace and are local to the file.
• Started to re-organize the .R files.
• mrgsolve:::details returns a data frame of information regardless of whether the model was annotated or not (../../issues/165).
• mrgsolve::details has additional arguments to help control output.
• Removed pkevent class; all records are datarecord.

mrgsolve 0.7.6

Features

• Added annotated code blocks for $PARAM, $FIXED, $THETA, $CMT, $INIT, and $VCMT. (#107)
• mrgsolve:::house() model re-coded as an annotated model.
• Re-implemented $ENV to allow users to create R objects that can be used at certain points
  when parsing the model. (#115)
• Added >> signifier to code blocks that allow options; >> at the beginning of the line indicates that the name=value statements that follow are to be parsed as block options.
• Added object argument for the following blocks: $PARAM, $OMEGA, $SIGMA, $FIXED, $CMT. When object is set to a character string naming an object in $ENV, that object will be used to form the output from the block.

Bugs fixed

• Fixed a bug which caused simulation run to hang when implementing a dose with a very small lag time. (#109)
• Fixed a bug where valid.numericlist wasn't returning FALSE for improperly-formed objects.

Under the hood

• Now using an environment to collect objects when parsing the model specification file.
• Some small changes to C++ code that calculates compartment amounts for closed form one- and two-compartment models resulting in faster simulation runs.

The source package (built) is attached as mrgsolve_0.7.6.tar.gz. But the recommended installation method is with devtools::install_github("metrumresearchgroup/[email protected]", subdir="rdev")

mrgsolve 0.7.5

• The modmrg package was discontinued. All of the pre-coded models are now available in mrgsolve. Simply call mread with the model stem (e.g. pk1cmt, irm3, etc ...) and call modlib() as the project argument. For example: mod <- mread("emax", modlib()) will compile the emax model and return the model object.

The source package (built) is attached as mrgsolve_0.7.5.tar.gz. But the recommended installation method is with devtools::install_github("metrumresearchgroup/[email protected]", subdir="rdev")

mrgsolve 0.7.4

• Tests re-configured
• Fixed issue with record sorting for lagged doses when using full data_setand obsaug=TRUE (#102)
• Fixed issue where idata_set wasn't handled properly when it was passed in as tbl (#100)

The source package (built) is attached as mrgsolve_0.7.4.tar.gz. But the recommended installation method is with devtools::install_github("metrumresearchgroup/[email protected]", subdir="rdev")

mrgsolve 0.7.3

• Addressed an issue where model compilation on Windows systems failed when certain symbol names were used in the model (#97). In this release, a dllname-win.def file is created in soloc to export only the functions that mrgsolve needs to use.
• Added a check on the project argument to mread: if newline(s) are found, an error is generated and the user is prompted to use mcode instead.
• Several changes under the hood (#99)

The source package (built) is attached as mrgsolve_0.7.3.tar.gz. But the recommended installation method is with devtools::install_github("metrumresearchgroup/[email protected]", subdir="rdev")

mrgsolve 0.7.2

• Fix bug in #96

mrgsolve 0.7.1

• Minor change to build process; no longer need to cwd to build dir to build.

mrgsolve 0.7.0

Features

• Added as_data_set to convert one or more event objects into a data frame that can be passed to data_set. Does something similar to expand.ev, but more control.
• For special column names (time, amt, rate, evid, ii, addl ,ss, cmt) either lower case or upper case names are recognized. The determination is made on the time / TIME column (always required when using a data set). If time mrgsolve will continue looking for lower case names; if TIME it will look for upper case names. A warning is issued in case both upper and lower case names are included.
• Added $PLUGIN to let users extend their model specification file. Valid plugins include simeta, Rcpp, RcppArmadillo, and BH. When a plugin is used, mrgsolve will link back the the appropriate package and possibly include appropriate header files when compiling the model. For example, simeta will link back to mrgsolve and RcppArmadillo and allow the modeler to simulate a new set of ETAs. Use Rcpp plugin to simulate random variates from common distibutions in R(e.g. rnorm, rexp etc ... ).

Bugs fixed

• Fixed issue with ev where no rows were returned if amt wasn't supplied (issue 44).
• Shortened the path for both the shared object and the name of the .cpp.cpp file when compiling.
• Fixed bug in touch_funs when large number (> 25) of ETAs in the model (issue 68).

Important changes

• When using $PKMODEL with ncmt=2 and depot=FALSE, the default PK parameters are CL, V1 (central volume), Q, V2 (peripheral volume). This is a change where the previous volumes were V2 (central) and V3 (peripheral).
• $CAPTURE now saves output items to slots in std::vector<double>, rather than std::map<std::string,double>. We've known for a while that the std::map wasn't very efficient especially with large simulations. Currently, items in $TABLE are still saved into std::map with table() macro. The plan going forward is to eliminate that table map and force output variables into $CAPTURE.
• Due to major changes to dplyr, now requiring dplyr >= 0.5.0 (issue 69)
• The data slot in mrgsims objects is now data.frame
• The knobs function and plot method has been re-written. Overall behavior for most applications should be the same.

Under the hood

• C++ symbols for model functions are now stored in the model object (funs slot)
• The status of the model object (function names and compile status) can be checked with mrgsolve:::funset(mod)
• A model is considered to be loaded and ready to go if all functions in funs can be found with is.loaded
• Model shared objects are still stored within the soloc directory (by default tempdir()), but mrgsolve will create a subdirectory structure to organize compilation artifacts. The outer directory is keyed based on the current mrgsolve version number and the computer platform. Inner directories are based on the model name (model(mod)).
• A source file is created based on the model name and the shared object is created based on that name. If the compilation is successful, the shared object (.so on mac/unix, .dll on Windows) is copied to a .so or .dll file with a unique stem (e.g. model2lj239wsfo.so). This unique shared object is loaded into the R process for use with the model.
• Every time the model is rebuilt, the build directory is scanned for shared object files. Excluding the main model shared object (unchanging name based on the model), old shared object files are deleted and, if currently loaded (getLoadedDLLs()), are attempted to be dyn.unloaded.
• Upon model rebuild (via mread or mcode), if there are no changes to the source .cpp file, the source is not overwritten. In that case, make will not re-build the shared object. Using the preclean argument will force re-compilation (see R CMD SHLIB).
• The header files modelheader.h and mrgsolv.h are no longer copied into the project directory. But CLINK_CPPFLAGS environment variable is modlifed to include <path-to-mrgsolve-package>/inst/base so that these may be linked.
• The R CMD SHLIB build process always uses intern=TRUE so that output is suppressed on both Windows and mac/unix. The user may still request to view build output with the ignore.stdout argument.
• Model build always links-to the project directory to look for C++ header files. When including a header file that may change from build to build, always run with preclean=TRUE.
• mrgsolve now changes the working directory prior to building a model. The working directory is restored on exit from mread.

Deprecated

• The entire complog system, including:
  • comp_forget a message is issued
  • complog no message is issued
• trequest argument to mrgsim

mrgsolve 0.6.1

Bugs fixed

• Fixed a bug when an infusion was attempted with rate > 0 and amt==0. Additionally, an error is generated when an infusion is attempted with zero amt (issue 43).

mrgsolve 0.6.0

Bugs fixed

• Fixed a bug where infusion dosing events with evid 4 were not properly implemented. While investigating that issue, also found similar issue with evid 4 infusions getting scheduled with addl (issue 31).
• Removed NSE evaluation for arguments passed into ev to avoid unintended issues in evaluation (issue 29).

New features

• Added mcode function as alternative to using mread when your model is written in an R string. Note the order of the arguments:
  first model, then code, then project. project defaults to tempdir. So the call is: mod <- mcode("mymodel", code). The
  equivalent mread call is: mod <- mread("mymodel", tempdir(),code).
• carry.out() and Req() now take newname = oldname as input. Use this syntax in carry.out when you want to copy a column from the input data set into the simulated data set, changing the column to newname from oldname. Use this syntax in Req when you want to change the names of compartments or output variables spcified in $TABLE / $CAPTURE.
• Added pkmodel function for easy loading and simulating from 1- and 2-compartment models (issue 39).
• Added new code block: $PKMODEL for simulating PK model with analytical solutions. The main option for this block is ncmt, which picks the number of compartments for the pk model. See ?PKMODEL for more information and other options (issue 34).

Under the hood

• Added code attribute to mrgmod objects. The actual source code stays with the model object. see was modified to look at x@code first when showing the model code.
• Added a tokenizer function (get_tokens), a wrapper for the boost tokenizer) to help checking the model specification file.
• Data items entered in $FIXED are now implemented as C++ preprocessor directives by default rather than const double variables. Use $SET fixed_type = "define" or $SET fixed_type = "const" to select between the approaches.