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Changelog

Source: NEWS.md

mrgsolve 1.5.2

  • Add $EVENT block for writing code related to dosing or other events that are implemented through model code rather than the data set (#1230).

  • Add evt::reset() and evt::reset(self) functions under the evtools plugin; these reset the compartments in a model; overloaded functions are also provided to reset and dose with bolus or infusion (#1222).

  • Completed dosing functionality in evtools plugin; use evt::addl() to schedule additional doses through an evt::ev object; use evt::ii() to set the dosing interval; use evt::ss() to advance the pharmacokinetic system to steady state just prior to dosing; evt::cmt() sets the compartment number; evt::amt() sets the dose amount; evt::rate() sets the infusion rate; see the user guide for the specific signatures that are available (#1227).

  • Add evtools model to modlib(), illustrating how to implement dosing regimens from inside the model a few different ways (#1230).

  • Added more comprehensive checking for duplicate blocks in a model file; duplicate blocks are always handled when allowed; an error message is always issued when duplicates are not allowed (#1238).

  • Code to audit $ODE (or $DES) code, looking for an equation for every model compartment was refactored to use a common approach for both traditional models and models written with the nm-vars plugin; regardless of approach, the user will be warned if mrgsolve does not detect code relevant to every model compartment; the audit system can be bypassed by including the @!audit block option to $ODE (#1235).

  • The autodec plugin was lightly refactored to avoid false positive detection of variables declared as double; plans are in place to narrow the scope of what is detected for declaration in future releases (#1234).

  • R help files (.Rd) reviewed and revised for consistency and formatting (#1246).

mrgsolve 1.5.1

CRAN release: 2024-07-26

  • Fixed yaml_to_cpp() example code to prevent saving the file to the working directory (#1220).

mrgsolve 1.5.0

  • New functions mwrite_yaml() and mwrite_cpp() can write a model object back to a file, accounting for all updates since the model was read from native mrgsolve format using mread() (#1190, #1213).

  • New function mread_yaml() for reading back models written out with mwrite_yaml() (#1190, #1213).

  • New functions in evtools plugin: evt::replace() works like evt::bolus(), but will replace the amount in a given compartment rather than add to it (#1203).

  • The nm-vars plugin now exposes DEXP(), LOG10(), COS() and SIN() for use in the mrgsolve C++ code blocks (#1199).

  • An error is now generated when KA is equal to CL/VC while simulating from the one-compartment model with analytical solution invoked through $PKMODEL (#1179, #1197).

Bugs Fixed

mrgsolve 1.4.2

  • An error will now be issued at simulation time when simulation data sets (data and idata) contain non-numeric data in columns sharing names with parameters; non-numeric data in columns with certain reserved names (like AMT, RATE, II, ADDL, etc.) will also result in an error (#1193).

  • Internal refactoring to improve performance when simulating infusions or doses with lag times when those doses are coded explicitly in the data set (#1186, #1187).

mrgsolve 1.4.1

CRAN release: 2024-02-13

  • Fix bug in evt::regimen.ii(double) where timing of next dose was not as expected (#1170).

mrgsolve 1.4.0

CRAN release: 2024-02-08

  • evtools is a new plugin providing API for dynamic dosing from within the model; functions and classes are in the evt namespace (#1149).

  • regimen is a new class located in the evt namespace via the evtools plugin; regimen objects can execute doses in a regular regimen (#1156).

  • mread() and mcode() no longer print a message before the required waiting period on model recompile (#1145).

  • ev_rep() output rownames are cleaned up before returning (#1158).

  • C++ model code blocks (GLOBAL, PREAMBLE, MAIN/PK, ODE/DES, TABLE/ERROR) are now checked for <object>.<attribute> syntax; if found, symbols on both sides of the dot become reserved words when loading and compiling that model; specifically, an error will be generated if either side of the dot (<object> or <attribute>) is found in parameter names, compartment names, ETA labels, or EPS labels (#1159).

  • ETA values are always simulated from OMEGA, even when the user requests they get scraped from data or idata via etasrc argument to mrgsim(); this ensures EPS are reproducible for model runs where etasrc = "omega" (default, ETA are simulated) or, for example, where etaasrc = "data.all" (scrape ETA from the data set) (#1163).

Bugs Fixed

  • Fixed a bug where modeled doses scheduled to happen now were ignored if the time attribute was set to a value prior to the current simulation time (#1152).

  • Fixed a bug in how doses were computed using the until argument to ev() (#1154).

mrgsolve 1.3.0

CRAN release: 2023-12-04

  • The evdata object for modeled events now contains a check_unique member; when set to false, the event will be processed without checking for a matching record in the modeled event log (#1119).

  • The amt attribute in evdata modeled event objects is now considered when looking for duplicate records in the modeled event log (#1119).

Bugs Fixed

  • Fixed a bug where multiple lagged doses given at the same time but with different bioavailability were all given the bioavailability of the last dosing record (#1129, #1130).

  • Fixed a bug where modeled infusions given now were never turned off (#1131).

  • Fixed a bug where the self object (type: databox) could not be passed into functions written into header files that were included through $INCLUDE; these header files are now included immediately preceding any user code written into $GLOBAL (#1125, #1126).

  • Fixed a bug where modeled event log was not getting reset after simulating the first individual; this resulted in events not getting executed in subsequent individuals when matching events were executed in the first individual; this affects modeled events only, not events coming from the data set (#1117, #1118).

  • Fixed a bug in detecting which compartments are receiving doses (#1112, #1113).

mrgsolve 1.2.0

  • Data set records at the same time within individual will receive different EPS draws; this is a change from previous behavior where records with the same time received the same value for EPS (#1110).

mrgsolve 1.1.1

CRAN release: 2023-08-16

  • Remove .x from matlist documentation object per new NOTE output from rdevel (#1103, #1104).

mrgsolve 1.1.0

  • Add new functionality for assessing consistency between names on input data set and parameter names (#1078).

    • New function check_data_names() executes the check.
    • New model specification block $INPUT for marking parameters as “inputs” and expecting them to be present in the data when check_data_names() is called.
    • New $PARAM block attributes @input and @tag for adding tags to parameters which will be checked when check_data_names() is called.
    • New function param_tags() to list parameters and tags for a given model.

  • Now checking TIME and time when assessing upper / lower case name consistency of input data sets (#1099).

  • ETAs can now be passed into the problem via idata by passing eta_src as either idata or idata.all to mrgsim() (#1092).

  • Internal refactor of mechanics checking for user interrupt during simulation (#1088).

  • Minor re-factor of mrgsim_nid() and documentation update to be in line with original intent; no meaningful change in functionality (#1086).

  • parameter_list objects can now be passed to param() (#1076).

  • ev_rx() syntax gains & operator allowing specification of multiple events at a single time (#1072).

  • Kyle Meyer added as contributor (#1096).

  • modlib() model 1005 re-coded to reflect the “traditional” model specification syntax (#1069).

  • The model object update() method will again issue a warning when unrecognized arguments are passed (#1068).

Bugs Fixed

  • Fixed bug where ETA in the first column of data was not recognized when using eta_src = "data" or eta_src = "data.all" (#1095).

mrgsolve 1.0.9

CRAN release: 2023-03-10

mrgsolve 1.0.8

CRAN release: 2023-03-04

  • SIGMA() is a new model macro which allows users to access on-diagonal elements of SIGMA in the model (e.g. SIGMA(2) in $ERROR) (#1051, #1052).

  • mrgsim() and mrgsim_q() gain an etasrc argument, allowing ETAs to be either simulated from OMEGA (new default and previously the only behavior) or taken from the input data set (new option), similar to the way parameters can be scraped from the data set (#1037).

  • @etas is a new option for use with the $CAPTURE block to let users name ETAs to be captured into the simulated output; for example, use @etas 1:last to capture all model ETAs in the simulated output (#1055).

  • Drop CXX_STD statement from Makevars file and DESCRIPTION to be consistent with current changes in R-devel; mrgsolve continues to require compiler capable of implementing C++11 standard, but this should be selected automatically by R (#1060).

  • mrgsolve now depends on R >= 3.6.2 (#1060).

Bugs Fixed

  • Fix bug when the path argument is used in the $NMXML or $NMEXT blocks; this bug was introduced through the @cppstem feature in version 1.0.7 (#1046, #1048).

  • Fix bug in mread_cache() where the project directory wasn’t getting rendered properly when passing the complete path to the model specification file (#1056).

mrgsolve 1.0.7

  • $NMXML and $NMEXT now accept the run argument set to "@cppstem" (i.e
    run = "@cppstem"); in this case, the stem of the NONMEM run will be assumed to be the same as the stem of the mrgsolve model file (#1025).

  • Missing values (NA) in input data sets will be replaced with 0 for the following columns: AMT, CMT, EVID, II, ADDL, RATE, SS as well as their lower case counterparts (#1030).

  • Refactored include order when building a model; this is an internal update and not expected to be visible to the user (#1038).

Bugs Fixed

  • Fix bug in generating certain model definitions when using the nm-vars plugin; the bug would have resulted in a warning from the pre-processor and did not affect function of the model (#1039).

mrgsolve 1.0.6

CRAN release: 2022-08-29

Bugs Fixed

  • Fix bug in TOUCH_FUNS where parameter and compartment lists were not getting generated properly when mrgsolve was not loaded; bug was detected and fixed prior to upload to CRAN or MPN (#1013).

mrgsolve 1.0.5

  • Changed behavior for dosing records where EVID = 4 and SS != 0 to match what is done by NONMEM: the system will be advanced to steady-state but will not be reset; behavior prior to 1.0.5 release was to advance to steady-state and then reset (#1011).

  • Any column in an input data set that has a class attribute will now be dropped in addition to non-numeric columns; this includes columns that are integer64 which can be present in data frames derived from data.table::fread() or other .csv readers (#1008).

  • The $MAIN and $TABLE blocks will no longer get called for actual dose administration records with lag times; this could change time after dose calculations or other calculations that could be happening in those blocks when the actual administration is taking place (#992).

  • Code to update the parameter list was re-factored to be much more efficient (#978).

Bugs Fixed

  • Fix bug where apparent dosing events for additional doses with lag times were not getting scheduled (only records for the actual administration); this doesn’t change the simulated output but could change time after dose calculation (#992).

  • Fix bug where special nm-vars variables were not getting recognized as valid capture items during dynamic capture (#987).

  • Fix bug when updating the parameter list with a data frame that included non-numeric columns that were not parameters (#978).

mrgsolve 1.0.4

CRAN release: 2022-05-16

  • Fix bug where as_data_frame() was not properly working when leading event object was evd type (#948, #955).

  • Add uctran() to convert nmtran data names to upper case (#955).

  • Both lctran() and uctran() are generic and work on data.frame or event (ev) objects (#949, #955).

  • Fix bug where data records with EVID = 3 were getting shifted in time by ALAG (#964, #969).

  • Small negative eigenvalues from OMEGA or SIGMA are set to zero in multivariate normal simulation of ETA and EPS, following the pattern seen in MASS::mvrnorm() (#956, #957).

  • Fixed bug where template parameters (T) were getting modified when nm-vars plugin was used in conjunction with mrgx plugin (#965, #968).

mrgsolve 1.0.3

CRAN release: 2022-03-21

  • Removed assert() statement in LSODA code found by CRAN check (#943).

mrgsolve 1.0.2

CRAN release: 2022-03-17

mrgsolve 1.0.1

  • Add LOG(), EXP(), SQRT() macros when nm-vars plugin is invoked (#931, #936).

  • Use evd() to create an event object which renders nmtran names in upper case (e.g. TIME rather than time) (#935, #919).

  • Fixed bug where rate was not getting set for modeled events (#934).

  • Fixed bug where self.stop_id() and self.stop_id_cf() had reversed behavior as documented (#927, #928).

  • Refactored EVID=3 behavior to leave NEWIND as-is (#934).

mrgsolve 1.0.0

CRAN release: 2022-01-20

  • New model syntax: THETA(n) is interpreted as THETAn in the model code; THETA is now a reserved word (#837, #891, #892).

  • New functions collapse_omega(), collapse_sigma() and collapse_matrix() added which help to reshape OMEGA and SIGMA matrix objects with multiple blocks (#897, #900).

  • New plugin nm-vars which implements NONMEM-like syntax for referring to compartments, differential equations, bioavailability factor, infusion duration and rate, and lag time (#904, #891).

  • New plugin autodec which will find user-defined variables in the model code and automatically declare them as type double (#905, #893).

  • Use ii as spacer for setting the between-dose interval when putting event objects in a sequence (c.f. wait) (#906, #901).

  • Start deprecatingsimeta(n) and simeps(n), calls to simeta() or simeps() with an integer argument thus limiting the update to just a single ETA(n) or EPS(n); use in model code will generate warning when loading the model that contains the n integer value (#908, #909).

mrgsolve 0.11.2

  • In pk2iv, change scaling volume for CENT from V2 (incorrect) to V1 (#831, #832, #833)

  • Fix bug collating multiple $OMEGA or $SIGMA matrices when parsing a model (#863)

  • Refactor how debugging information is processed when using the recover argument to mread() (#853)

  • Fix typo in documentation for as_cmat(); the off-diagonals are assumed to contain correlations (#856)

  • Wrote a as.data.frame.matrix() function in Rcpp; all simulation results return from the C++ simulation code as a data frame (#857)

  • Fix bug where dynamic capture (via mread()) was not allowed for variables declared in $GLOBAL (#868)

mrgsolve 0.11.1

CRAN release: 2021-05-10

  • mrgsim() will now periodically check for user interrupt signal so that long-running simulations can be stopped using Esc and / or Control-C; the check interval can be modified through the interrupt argument to mrgsim(), but for most applications, this shouldn’t need to be changed (#823)
  • mrgsim() will issue a warning if duplicate columns are found in simulated output and rename duplicates using make.names(); thanks @FelicienLL for the report (#827, #828)
  • Users can now turn compartments to OFF when they have active infusions running; this was previously an error (#822)

mrgsolve 0.11.0

CRAN release: 2021-03-28

  • The absolute paths to nonmem output files (root.xml or root.ext) are now saved in the model object when nonmem results are imported via $NMEXT or $NMXML; paths are accessible by coercing the model object with as.list() and looking at the nm_import item (#802)
  • Add Tim Waterhouse as contributor (#809)
  • Add root argument to $NMEXT and $NMXML so that the nonmem output files are located relative to the working directory (default, previous behavior) or the directory where the cppfile is stored; cppfile will eventually replace working as the default (#803)
  • Models based on $PRED now respect the obsonly option (#811)

mrgsolve 0.10.9

  • Dosing into a compartment that is off at the time of the dose turns the compartment back on regardless of whether bioavailability is zero or non-zero (this is a bug fix where the compartment was not turned on when bioavailability was zero). (#800)
  • simeta() and simeps() now accept an (optional) integer argument to limit re-simulation to single ETA or EPS values (#789)
  • as.list(mod) output now includes a data frame of C++ variables and pre-processor definitions in the cpp_variables slot. (#780)
  • $PARAM, $THETA, $CMT, $INIT, $OMEGA and $SIGMA blocks all include the directives @object and @as_object so that block contents can be specified programmatically. @object names an object that was coded into $ENV and @as_object indicates that the block contains code to realize the object. See ?BLOCK_PARSE help topic for more information on how this all works. (#783)
  • $NMEXT now lets the user select between multiple tables for scraping parameter estimates. (#782)

mrgsolve 0.10.8

  • Allow simulation from compartmental models with negative times #778
  • Enable dynamic capture of pre-processor directives at compile time #776
  • Fix error message when requesting invalid items during dynamic capture #776

mrgsolve 0.10.7

CRAN release: 2020-12-09

  • Stop testing test_equal using lattice

mrgsolve 0.10.6

  • Fix url endings for check on r-devel
  • Adjust test comparing lattice plots based on change in r-devel; passing check.environments now

mrgsolve 0.10.5

  • Suppress warnings when non-numeric columns are dropped when those columns are not relevant to the simulation (#709)
  • Add $ERROR as an alias for $TABLE in the model file (#710)
  • Fix bug where warning messages during steady-state finding referenced rtol and atol rather than ss_rtol and ss_atol (#703)
  • Fix annotation parsing bug when the description included semi-colon (#696)
  • loadso issues a proper error when the model dll doesn’t exist (#724)
  • Try loading the model with loadso once of the model isn’t loaded at the time of simulation (#725)
  • Throw an error when addl or ss are negative (#733)
  • Internal refactoring so that there is a hard solver reset when parameters that are copied from data change (#744)
  • Add tad plugin to calculate time after dose in a specific compartment (#702)
  • Internal refactor carry_out to respect default nocb behavior (#759; see also #744)
  • Throw an error when matlist labels are duplicated (#730)
  • Add capture argument to mread to add to $CAPTURE when compiling the model (#704)

mrgsolve 0.10.3

  • The simulation time grid was adjusted so that rendering the grid could result in no times (length 0 vector of times); this is a breaking change from previous behavior where the time grid resolved to 0 when there were no observations to be found. While this is a breaking change, the old behavior was almost always wrong when the desired output was a series of non-observation records (#640)
  • Added 1005 model
  • Added recover mechanism to join items in input data sets to the output (#646)
  • Allow simulation from empty time grid; this would potentially break some existing code; but not common (#648)
  • Add collapse_omega and collapse_sigma arguments to [ set ] block (#651)
  • Add separate tolerances (ss_rtol and ss_atol) to control advance to steady state (#652)
  • Fix bug in realize_addl when addl is zero by ii is not (#653)
  • Fix bug where system did not reset with EVID 4 and infusion dose (#683)
  • NMXML will now take vector for tname to add custom names to imported THETAs (#687)
  • Add NMEXT block that works similar (not identical) to NMXML, but reads from the run.ext file (#509)

mrgsolve 0.10.1

CRAN release: 2020-02-21

  • Add select_sims method for selecting columns in mrgsims object (#585)
  • Fix bug where system was improperly advanced on steady state dosing record with a lag time when the system failed to reach steady state (#596)
  • Add better compartment level control for advancing system to steady state (#598)
  • Allow user to set CXX_FLAGS in $ENV block (#603)
  • Add N_CMT plugin so that the number (index) of every compartment is available by name (e.g. N_CENT for the number index of the central compartment) (#606)
  • Fix bug where blocks() failed when the model was defined in Rmd file (#608)
  • Call ODE block every time the system tries to advance so that variables calculated in ODE are properly calculated in output (#613)
  • Add within method for mrgmod (#616)
  • Access initial compartment values and other model object items with $ operator for mrgmod (#620)
  • Add plot method for signature c("mrgsims", "character"); pass in a character vector of outputs to plot (#630)
  • The house model, previously accessible by mrgsolve:::house() is now an exported function (#625)
  • Exporting outvars function to extract names of current output variables from the model object
  • Now importing lifecycle and glue packages

mrgsolve 0.10.0

CRAN release: 2019-10-15

  • Remove qsim and all associated functions
  • Export new function / workflow as qsim as a simpler, quicker simulation routine (#490)
  • tad calculation (when called through mrgsim() and variants) recognizes evid 4 in addition to evid 1 (#502)
  • Fix bug where $NMXML fails when nm namespace not found in xml file (#510)
  • Arguments to ev constructor are now evaluated; for example, ev(amt = 100, rate = amt/2) (#512)
  • Add $ and [[ operators for event objects (#513)
  • Recalculate rate (from tinf), addl (from total or until) upon mutate (#513)
  • Standardize column order for event objects (#513)
  • mrgsim_e and mrgsim_ei will try to accept data frame and validated data sets
  • Drop ODEPACK solver and implement lsoda in C++ (#504)
  • Add C++11 as system requirement
  • Add constant infusion at steady state (#249)
  • Add outvars argument to update method; this will replace Req
  • Add two arguments to mrgsim: ss_n and ss_fixed to control advance to steady state; a warning will be issued when ss_fixed is FALSE and the system doesn’t reach steady state within ss_n iterations (#533)
  • An error is issued when the first argument to mrgsim and variants is not a model object (#547)
  • Argument xpath is added to nmxml() to handle cases where the nm namespace is not found in the xml file (#510)
  • More informative error messages are included when processing input data sets (#534)
  • When there is a problem when the ODE system is advanced, informative error messages from both lsoda and mrgsolve will be issued along with the value of istate (#457)
  • Add ability to have ss=1 in a dosing record with bioavailability is zero (#497)
  • Error messages will be issued when both of the following are found in input for event object construction: rate/tinf, addl/total, addl/until (#513)
  • When tinf is used to create event object, that item is retained and used to set the infusion rate (along with dose) until it is removed; it is an error to try to set rate when tinf is in the event object (#513)
  • Fix bug related to column identification in expand_observations (#563)
  • Add record position argument to expand_observations to allow control record sort order (#565)

mrgsolve 0.9.2

CRAN release: 2019-07-13

  • Fix bug where system advanced to next time after advancing to steady state on a dosing record with ss=1 with no observation record at the same time but preceding the dosing record (#484)
  • Add AMT and CMT macros for self.amt and self.cmt, respectively (#354)
  • Re-organize DLSODA code to avoid CRAN LTO warning

mrgsolve 0.9.1

CRAN release: 2019-06-14

  • Fix bug in TAD plugin where time of last dose never moved from default
  • Add option in mrgsolve_q to call the standard mrgsolve simulation rather than the streamlined function; a decision will have to be made about whether or not the streamlined function will be retained
  • Fix bug in the model parser where commented lines with (all) leading spaces were not handled properly (#450)
  • Objects of class valid_data_set now retain the matrix attribute (#448)
  • Block names are now coerced to upper case letters
  • Change default for simcall to 0 in mrgsim_q
  • Add recover argument to mread
  • Add @as_object option to the following blocks: PARAM, INIT, CMT, OMEGA, SIGMA; experimental
  • Allow multiple ODE blocks
  • Add mtime function to self object for simpler mtime implementation
  • Add @param block option for ODE blocks; use comma-separated name=value pairs to add to the parameter list from within ODE
  • Remove BLAS code embedded in ODEPACK fortran files per CRAN request

mrgsolve 0.9.0

CRAN release: 2019-01-23

  • Added logy and logbr arguments to plot.mrgsims so results y-axis outputs can easily be plotted on log scale
  • release

mrgsolve 0.8.12.9000

New functions

  • Added numerics_only function to drop non-numeric columns from the input data set after optionally converting logical columns to integer
  • Added ev_rx function to write dosing interventions in notation similar to a prescription ‘sig’

New features

  • Added $PRED block for models that don’t utilize any compartments
  • Added pred1 to the internal model library (modlib())
  • Added mrgsim_q function for simulation from a model object with quicker turnaround time
  • mread will take soloc and project arguments from options() as mrgsolve.soloc and mrgsolve.project, respectively
  • Added output argument to mrgsim so that e.g. data.frame can be returned, without creating the usual mrgsims object
  • The directory name passed to the soloc argument of mread (or mcode or cache versions of both) will be created if it doesn’t exist
  • Added pk2iv model as convenience option
  • Added tinf argument to ev() constructor function

New behavior

  • time/TIME is no longer required in a data set when $PRED is in use
  • cmt/CMT is no longer required in a data set; a default value of 0 will be assigned in case it is missing and an error will continue to be generated when dosing into an invalid compartment (0 is always an invalid index for dosing compartment)
  • An error will be generated if missing values (NA) are detected in an input data set with the following names: ID, time/TIME, or any column that shares a name with an item in the parameter list
  • An index argument was added to the $NMXML block to allow results selection when multiple estimation blocks were used. The new default is to use the last result.
  • modlib is now able to function as a wrapper to mread for models in the model library so that, for example, modlib("pk1") is equivalent to mread("pk1", modlib()).

Bugs fixed

  • Fixed bug related to record sort order (#406)

Deprecated

  • drop.re and drop_re; use zero_re instead

Breaking changes

  • An undocumented function called report was previously available to use in model code. This function has been moved to a namespace and is now available as mrg::report. This feature continues to be undocumented.

mrgsolve 0.8.12

CRAN release: 2018-04-27

  • Minor changes to namespace for CRAN

mrgsolve 0.8.11

CRAN release: 2018-04-26

  • Internal release
  • Removed the function s and replaced with s_; this was not a problem created by mrgsolve but rather by ggplot2, which calls mgcv::s via geom_smooth under certain circumstances

mrgsolve 0.8.10.9015

  • Re-configured the list of data coming from as.list.mrgmod so that the names match the names that you would pass to update.mrgmod; also added some items so that all updatable slots in the model object are exported by calling as.list (#354)

mrgsolve 0.8.10.9014

  • Add OMEGA and SIGMA matrices to as.list.mrgmod output under the names omat and smat, respectively
  • It is no longer an error to attempt to update slots for OMEGA and SIGMA matrices when there is no matrices in the slot as long as the update is with an empty list or a matrix with zero rows
  • Fix segmentation fault when both data set and idata set are used in a simulation with certain mis-matches in the ID content between the two (#352)

mrgsolve 0.8.10.9013

  • Removes more mtime code (wasn’t in use)

mrgsolve 0.8.10.9012

mrgsolve 0.8.10.9011

  • mtime clear bug

mrgsolve 0.8.10.9010

  • Fixed bug in filter.ev method

mrgsolve 0.8.10.9009

  • Added mutate_sims and filter_sims that work on mrgsims (output) objects, modifying the data slot and returning a modified mrgsims object rather than data.frame
  • Added plot_sims function that takes a data frame of simulated output and generates a plot using the mrgsims method

mrgsolve 0.8.10.9008

  • Changed id argument to ID in ev_rep and ev_seq; a warning is issued if id is used
  • Added data_qsim for creating input data sets to use with qsim
  • Fixed a bug where time after dose was not correctly calculated for additional doses with a lag time #327
  • Added read_nmext to read in nonmem model output from the .ext file

mrgsolve 0.8.10.9007

  • Clean up and re-organize Rd files; more-logical grouping and ordering

mrgsolve 0.8.10.9006

  • Stop importing assertthat and lazyeval

mrgsolve 0.8.10.9005

New Features

  • Added better support for writing model files with any extension. For example, mread("mymodel.txt") will read from the file mymodel.txt if it exists. However, the default behavior remains unchanged so that mread("mymodel") will expect to find the model in the file mymodel.cpp.

Bug Fixes

  • Fixed bug where the MD5 value on the model file could not be calculated under certain project path formulations #315

Important changes

  • The realize_addl function was re-factored to better account for time-varying data items; more option are provided for seeing where rows were inserted into the data set and whether to make assumptions about other data in those rows or not

  • mrgsolve no longer utilizes any functions from the XML package. All previous functionality that depended on XML now depends on xml2. As such, xml2 is listed under the Suggests dependency.

  • When using $NMXML, the $OMEGA and $SIGMA matrices are now loaded by default; see new default arguments to mrgsolve:::nmxml

Documentation

  • Added solversettings help topic that identifies some of the DLSODA inputs you can tweak
  • Improved documentation for update method as well as mrgmod-class

mrgsolve 0.8.10.9003

New Features

  • Bioavailability specified in $MAIN is accounted for when simulating with qsim; there is still no bioavailability adjustment for infusions or lag times adjustments to doses

  • Added capability to rename data items in $CAPTURE; also, names are partially sanitized, removing parens and brackets.
    For example $CAPTURE WT = WGT ETA(1) TVCL = THETA1

  • Added qsim_df function, returning data frame rather than matrix

  • Added as.list method for mrgsims objects

  • Added deep argument for as.list method for mrgmod object; it was taking a lot of time to return the function set, so now you only get it if deep = TRUE

  • Added mrgsim variant functions with explicit input requirements written into the function name. For example, call mrgsim_e to simulate from an event object, mrgsim_d to simulate from a data frame. All of these functions are called by mrgsim.

  • Added method so that event objects can be passed to data_set; also, coercing event objects to data_set when passed in as data

  • Added all.equal.mrgmod function to compare two model objects. The function returns logical (only)

  • Added env_get_env that always just returns the model environment; it has identical result as env_get(mod, tolist = FALSE)

  • Change mread_cache and mcode_cache so that the cache is invalidated when preclean argument is TRUE

Bug Fixes

  • Fixed bug preventing simulation with qsim with no event

Functions removed

  • mrgsolve_example and mrgsolve_template; these had been deprecated previously with warning; use modlib() models instead

mrgsolve 0.8.10.9002

  • Added mrgsim_df function to return data frame rather than mrgsims object

mrgsolve 0.8.10.9001

  • The model environment is automatically imported as _env when mrgx plugin is invoked

mrgsolve 0.8.10

CRAN release: 2017-11-01

  • Release to CRAN

mrgsolve 0.8.9.9004

  • Added file argument to mread to allow coding model specification files with any extension. The current behavior continues to be assuming that the model is in a .cpp file, but using the file argument allows any file name for model specification.

  • Added nocb argument to mrgsim. If nobc is TRUE (default), mrgsim continues to use next observation carried forward to advance the system when there are time-varying parameters (including covariates). If nocb is FALSE, mrgsim will use last observation carried forward (locf) to advance the system when there are time-varying parameters.

mrgsolve 0.8.9.9003

  • Minor improvements to documentation

mrgsolve 0.8.9.9002

Bug Fix

  • Fixed bug where deslist was created in the wrong order
  • Fixed bug where infusion duration was incorrect when paired with non-zero lag time (test added)
  • Fixed bug where self object was not correctly updated for the first record for an individual (#273)

Important changes

  • Add support for dosing records with both lag time and ss flag; an error message will be generated if lag time is greater than ii or if lag time + infusion duration is greater than ii.
  • The behavior of ev_assign is changed so that the unique values of evgroup are sorted prior to making event assignments. Details about the new behavior are now included in the R help topic.

mrgsolve 0.8.6.9000

Important changes

  • The bioavailability parameter now gets updated with each and every dose, regardless of whether it was explicitly coded in the data set or implicitly via addl. The previous behavior had bioavailability parameter locked at the value at the time the initiating dose was implemented
  • Updated package dependency requirements. Notably, mrgsolve now requires Rcpp >= 0.12.12 and dplyr >= 0.7.1

New Features

  • Dosing records with ss=2 are recognized, allowing combining of steady-state dosing regimens under linear kinetics (e.g. 10 mg QAM and 20 mg QPM) (#221)
  • Added function (inventory) that reconciles model parameters with names in an object (e.g. a simulation data set) verify that required parameters can be found in the data object.

Bugs fixed

  • PR #214 from @dastoor fixes compatibility issue with new dplyr
  • Fixed bug in deslist implementation (#222)
  • PR #238 fixes incorrect steady-state values when dose is associated with lagtime (#239)

mrgsolve 0.8.4

  • Reconfigure use of function pointer in unit tests

mrgsolve 0.8.3

  • Bug fix that prevented installation on Solaris

mrgsolve 0.8.2

CRAN release: 2017-03-11

  • The first release on CRAN

mrgsolve 0.7.7

New Authors

  • Devin Pastoor is now listed as a contributor. Thanks for all of your help!

New Features

  • Added automatic, on-demand output of time-after-dose (tad) in the simulated output. Use mrgsim(tad=TRUE).
  • Several new functions added to $PLUGIN mrgx, including mrgx::get<T> for getting objects out of $ENV or a package namespace and mrgx::mt_fun() that is just a function that you can assign when declaring Rcpp::Function.
  • Added object argument to idata_set and data_set to get a data.frame (or function to call that returns data.frame) out of $ENV to use for simulation.

Changes / additions

  • Added cmt argument to $PKMODEL. When cmt is set to a character vector or a comma-separated string, $PKMODEL infers the number of compartments and declares them in the model. This means a separate $CMT block is not required when using $PKMODEL.
  • Added cols argument to as_bmat and as_dmat so that a character vector of names can be specified (rather than regular expression) to select data for creating matrix.
  • The preclean argument now causes unlink to be called on the model build directory.
  • Added several functions to help work with $ENV: ls_env, get_env, re_eval_env, update_env.
  • When a dose is administered into a compartment that is off, the compartment is now turned on and the dosing is allowed to proceed. This is a change from previous behavior, where an error was generated.

mrgsolve 0.7.6

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 (#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 (#158).
  • Added assign_ev function to help build simulation data sets from event objects (#164).
  • Added as_data_frame method from the tibble package (#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.
  • 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 malformed 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 (#165).
  • mrgsolve::details has additional arguments to help control output.
  • Removed pkevent class; all records are datarecord.

mrgsolve 0.7.5

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.

mrgsolve 0.7.4

  • 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.

mrgsolve 0.7.3

  • 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)

mrgsolve 0.7.2

  • 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. This is only relevant to Windows platform.
  • 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)

mrgsolve 0.7.1

  • Fixed bug where requested columns were not properly named in certain circumstances (#86).

mrgsolve 0.7.0

  • Revert back to previous behavior where cwd to soloc is not required to build the model. This was only required on Windows systems where there was a space in the file name. Correctly rendering the path for the build directory now.

mrgsolve 0.6.1

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 distributions in R(e.g. rnorm, rexp etc … ).

Bugs fixed

  • Fixed issue with ev where no rows were returned if amt wasn’t supplied (#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 (#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 (#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 modified 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 0.6.0

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 (#43).

mrgsolve 0.5.12

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 (#31).
  • Removed NSE evaluation for arguments passed into ev to avoid unintended issues in evaluation (#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 specified in $TABLE / $CAPTURE.
  • Added pkmodel function for easy loading and simulating from 1- and 2-compartment models (#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 (#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 0.5.11

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, set mindt to be greater than zero but small … maybe 1E-12. 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 (#9).
  • zero.re didn’t properly update the $SIGMA list when one matrix was named and another was unnamed. This has been fixed. (#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. (#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. (#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. (#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). (#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).
    (#15)
  • Added dplyr::slice method for mrgsims objects (#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.