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.

mrgsolve 0.5.12

Bugs fixed

• Added missing example model specification files (popExample, viralExample, others)
• Added mindt attribute to mrgmod objects with default value of .Machine$double.eps*10. When the problem includes an infusion, the calculated end of the infusion
  may come too close to another record. Usually the solver will fail with the message DLSODA- TOUT(=R1) too close to T(=R2) to start integration.. To fix this, mindt is set to be greater than zero but small. When mindt is greater than zero and tto - tfrom (the times of two adjacent records) is less than mindt, mrgsolve will set tto equal to tfrom (issue 9).
• zero.re didn't properly update the $SIGMA list when one matrix was named and another was unnamed. This has been fixed. (issue 16)
• Fixed a bug where infusions with ss=1 caused mrgsolve/R to crash when the infusion duration was equal to or some multiple of the dosing interval. (issue 19)
• Fixed a bug where setting F_CENT to zero gave undefined behavior. mrgsolve will issue an error if F_CMT is set to zero and the ss flag is set to 1. (issue 22)
• Fixed bug where dosing records with evid=4 (reset the system and dose) and addl > 0 reset the system for all subsequent doses. Additional doses coming from records with evid=4 will not do system reset. (issue 23)

Important changes

• New arguments for $NMXML (see ?nmxml) that are easier to understand and consistent with new prefixes and labels for ETA and EPS. name argument is removed. Use tname (to provide a prefix for THETAs), oname (to name the OMEGA matrix), and sname (to name the SIGMA matrix) instead. In general, set theta to be TRUE to import THETAs, set omega to be TRUE to import OMEGA, and set sigma to be TRUE to import SIGMA. Specifying character names tname, oname, and sname will imply theta=TRUE, omega=TRUE, and sigma=TRUE, respectively.

New features

• New aliases available for setting bioavailability, lag time and infusion duration and rate. For a compartment called DEPOT use: F_DEPOT (bioavailability), ALAG_DEPOT (dosing lag time), D_DEPOT (infusion duration), and / or R_DEPOT (infusion rate). (issue 13)
• Added slightly more informative messages when DLSODA fails, including clear identification if the value of istate, which is 2 when the solver succeeds and negative when the solver fails.
• Added labels and prefix options to $OMEGA and $SIGMA. These allow descriptive aliases for ETAs ... e.g. using ETA_CL rather than ETA(1). (issue 15)
• Added dplyr::slice method for mrgsims objects (issue 11)
• New argument to mread: quiet. Setting quiet to TRUE will prevent printing messages when mread is called. The default is getOptions("mrgsolve_mread_quiet",FALSE) ... so you can call options(mrgsolve_mread_quiet = TRUE) to globally turn off messages from mread.

mrgsolve 0.5.11

Bugs Fixed

• Fixed paths for project (project) and shared object (soloc) so that "short" paths are used when compiling the model on Windows platforms (info issue 4 and here)
• Fixed a bug where bioavailability fraction was not accounted for when setting infusion duration in $MAIN with rate=-2 (see issue 3)
• mrgsolve_example prints a message telling the user to use mrgmod to read and compile the model. The user should use mread. The message has been updated. (info issue 5)
• Fixed bug where parameters were not correctly read from first row of a data set when certain recsort options were selected (issue 6)

New Features

• Added $ADVAN2 and $ADVAN4 for implementing one- and two-compartment PK models with analytical solutions rather than ODEs (thanks to contributions by Bill Gillespie and Charles Margossian)
• Added soloc attribute added to mrgmod and argument added to mread, giving user control over where the shared object is stored; by default it is in tempdir(). soloc needs to be set to local directory when using qapply
• Added generics for various dplyr_ functions so that mrgsims objects can be piped to mutate, group_by, filter, summarise, do, select, and summarise.each (it's a dot not an underscore). So: mod %>% mrgsim %>% mutate(group=1)
• You can now set initial conditions though idata; for compartment CMT, include a column in idata called CMT_0
• Modified update policy for $OMEGA and $SIGMA: if all incoming matrices are unnamed and the signature matches the model object, the update will happen
• Added mcRNG function as alias to base::RNGkind("L'Ecuyer-CMRG")

Under the hood

• Changed dosing lag time mechanism so that lag times are calculated as the simulation progresses and dose times in the simulated output are as in the input data
• Model shared objects are given random names every time the model is compiled and loaded
• Changes to recsort: 1 and 2 will put explicit doses after observations at the same time, 3 and 4 will put explicit doses before observations at the same time. 2 and 4 will put doses scheduled through addl after observations at the same time; 1 and 3 put doses scheduled through addl before observations at the same tile
• Various fixes and expansions to documentation
• Changed R dependency to >= 3.1.2
• All Ops involving mrgmod objects are now deprecated
• loadso now returns the model object (invisibly)
• Compartment names are automatically removed from table map
• Model specification files in need of compilation are detected via md5sum
• Minimum of 2 sec wait time is required before re-compiling a model
• Added init method with signature mrgmod,ANY, with ANY getting coerced to list