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).
yaml_to_cpp() example code to prevent saving the file to the working
directory (#1220).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).
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).
evt::regimen.ii(double) where timing of next dose
was not as expected (#1170).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).
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).
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).
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 $GLOBAL (#1125, #1126).
Fixed a bug where modeled event log was not getting reset after simulating the first individual; this resulted in events not getting executed in subsequent individuals when matching events were executed in the first individual; this affects modeled events only, not events coming from the data set (#1117, #1118).
Fixed a bug in detecting which compartments are receiving doses (#1112, #1113).
EPS draws; this is a change from previous behavior where records with the
same time received the same value for EPS (#1110).Add new functionality for assessing consistency between names on input data set and parameter names (#1078).
check_data_names() executes the check.$INPUT for marking parameters as "inputs"
and expecting them to be present in the data when check_data_names() is
called.$PARAM block attributes @input and @tag for adding tags to
parameters which will be checked when check_data_names() is called.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).
data was not recognized when
using eta_src = "data" or eta_src = "data.all" (#1095).compiled.mrgmod() and as_tibble.mrgsims() based on new
R-devel check findings (#1065).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).
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).
$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).
nm-vars
plugin; the bug would have resulted in a warning from the pre-processor and
did not affect function of the model (#1039).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).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).
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).
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).
assert() statement in LSODA code found by CRAN check (#943).inherits() not class() from CRAN check (#943).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).
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).
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)
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)OFF when they have active infusions
running; this was previously an error (#822)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)root argument to $NMEXT and $NMXML so that the nonmem output files
are located relative to the working directory (default, previous behavior)
or the directory where the cppfile is stored; cppfile will eventually
replace working as the default (#803)$PRED now respect the obsonly option (#811)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)$ERROR as an alias for $TABLE in the model file (#710)rtol
and atol rather than ss_rtol and ss_atol (#703)loadso issues a proper error when the model dll doesn't exist (#724)addl or ss are negative (#733)tad plugin to calculate time after dose in a specific compartment
(#702)carry_out to respect default nocb behavior (#759; see
also #744)capture argument to mread to add to $CAPTURE when compiling the
model (#704)recover mechanism to join items in input data sets to the output
(#646)ss_rtol and ss_atol) to control advance to
steady state (#652)realize_addl when addl is zero by ii is not (#653)tname to add custom names to imported
THETAs (#687)run.ext file (#509)select_sims method for selecting columns in mrgsims object (#585)CXX_FLAGS in $ENV block (#603)N_CMT plugin so that the number (index) of every compartment is available
by name (e.g. N_CENT for the number index of the central compartment) (#606)blocks() failed when the model was defined in Rmd file (#608)within method for mrgmod (#616)$
operator for mrgmod (#620)c("mrgsims", "character"); pass in a character
vector of outputs to plot (#630)mrgsolve:::house() is now an
exported function (#625)qsim and all associated functionsqsim as a simpler, quicker simulation
routine (#490)mrgsim() and variants) recognizes
evid 4 in addition to evid 1 (#502)$NMXML fails when nm namespace not found in xml file (#510)ev constructor are now evaluated; for example,
ev(amt = 100, rate = amt/2) (#512)$ and [[ operators for event objects (#513)mrgsim_e and mrgsim_ei will try to accept data frame and validated data
setsoutvars argument to update method; this will replace Reqss_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)xpath is added to nmxml() to handle cases where the nm namespace
is not found in the xml file (#510)istate (#457)ss=1 in a dosing record with bioavailability is zero (#497)rate/tinf, addl/total, addl/until (#513)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)expand_observations (#563)expand_observations to allow control
record sort order (#565)DLSODA code to avoid CRAN LTO warningmrgsolve_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 retainedvalid_data_set now retain the matrix attribute (#448)simcall to 0 in mrgsim_q@as_object option to the following blocks: PARAM, INIT, CMT,
OMEGA, SIGMA; experimentalODE blocksmtime function to self object for simpler mtime implementation@param block option for ODE blocks; use comma-separated name=value
pairs to add to the parameter list from within ODElogy and logbr arguments to plot.mrgsims so results y-axis
outputs can easily be plotted on log scalenumerics_only function to drop non-numeric columns from
the input data set after optionally converting logical columns
to integerev_rx function to write dosing interventions in notation similar
to a prescription 'sig'$PRED block for models that don't utilize any compartmentspred1 to the internal model library (modlib())mrgsim_q function for simulation from a model object
with quicker turnaround timemread will take soloc and project arguments from options() as
mrgsolve.soloc and mrgsolve.project, respectivelyoutput argument to mrgsim so that e.g. data.frame can be returned,
without creating the usual mrgsims objectsoloc argument of mread (or mcode or
cache versions of both) will be created if it doesn't existpk2iv model as convenience optiontinf argument to ev() constructor functiontime/TIME is no longer required in a data set when $PRED is in usecmt/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)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 listindex 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()).drop.re and drop_re; use zero_re insteadreport 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.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 circumstancesas.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)as.list.mrgmod output under the names
omat and smat, respectivelydplyr::filter_ for filter_.evfilter.ev methodmutate_sims and filter_sims that work on mrgsims (output)
objects, modifying the data slot and returning a modified mrgsims object
rather than data.frameplot_sims function that takes a data frame of simulated output
and generates a plot using the mrgsims methodid argument to ID in ev_rep and ev_seq; a warning
is issued if id is useddata_qsim for creating input data sets to use with qsimread_nmext to read in nonmem model output from
the .ext filemread("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.project path formulations #315The 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
solversettings help topic that identifies some of the
DLSODA inputs you can tweakupdate method as well as
mrgmod-classBioavailability 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
qsim with no eventmrgsolve_example and mrgsolve_template; these had been deprecated
previously with warning; use modlib() models insteadmrgsim_df function to return data frame rather than mrgsims object_env when
mrgx plugin is invokedAdded 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.
self object was not correctly updated for the
first record for an individual (#273)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.addl. The previous behavior had bioavailability parameter locked at the
value at the time the initiating dose was implementedRcpp >= 0.12.12 and dplyr >= 0.7.1ss=2 are recognized, allowing combining of
steady-state dosing regimens under linear kinetics (e.g. 10 mg QAM and 20 mg
QPM) (#221)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.dplyrdeslist implementation (#222)tad) in the simulated
output. Use mrgsim(tad=TRUE).$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.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.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 $PKMODEL.cols argument to as_bmat and as_dmat so that a character vector
of names can be specified (rather than regular expression) to select data for
creating matrix.preclean argument now causes unlink to be called on the model build
directory.$ENV: ls_env, get_env,
re_eval_env, update_env.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.mrgx plugin was completely removed.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).@ macros for indicating block options in model specification file.qsim function for quick(er) simulation runs with just one parameter
set.recmatrix that creates matrix simulation template for qsim.mrgsolve:::render to create a document with overview of model
contents. Methods for both mrgmod objects and character strings pointing
to a model file.mrgsolve:::details to extract model annotation.capture typedef in the model specification file. Variables that are
type capture are doubles and are automatically appended to $CAPTURE.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.R objects in the model via $ENV (#158).assign_ev function to help build simulation data sets from event
objects (#164).as_data_frame method from the tibble package (#166).$ operator for mrgmod objects to return the value of a parameter.mread_cache and mcode_cache functions to build and cache a model
(#143).PKMODEL. The volumes for two-compartment
model with no depot should be V1/V2.knobs where output column names are malformed when a user
$CAPTUREs a parameter that is also being tweaked as a knob.double/int/bool in $MAIN, $ODE, $TABLE are kept in
unnamed namespace and are local to the file..R files.mrgsolve:::details returns a data frame of information regardless of
whether the model was annotated or not (#165).mrgsolve::details has additional arguments to help control output.pkevent class; all records are datarecord.$PARAM, $FIXED, $THETA, $CMT,
$INIT, and $VCMT. (#107)mrgsolve:::house() model re-coded as an annotated model.$ENV to allow users to create R objects that can be used
at certain points
when parsing the model. (#115)>> 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.object argument for the following blocks: $PARAM, $OMEGA,
$SIGMA, $FIXED, $CMT. When object is set to a character string
naming an object in $ENV, that object will be used to form the output from
the block.valid.numericlist wasn't returning FALSE for
improperly-formed objects.environment to collect objects when parsing the model
specification file.C++ code that calculates compartment amounts for
closed form one- and two-compartment models resulting in faster simulation runs.modmrg package was discontinued. All of the pre-coded models are
now available in mrgsolve. Simply call mread with the model stem (e.g.
pk1cmt, irm3, etc ...) and call modlib() as the project argument.mod <- mread("emax", modlib()) will compile the emax model
and return the model object.data_set and obsaug=TRUE (#102)idata_set wasn't handled properly when it was passed
in as tbl (#100)Windows systems failed when
certain symbol names were used in the model (#97). In this release, a
dllname-win.def file is created in soloc to export only the functions that
mrgsolve needs to use. This is only relevant to Windows platform.project argument to mread: if newline(s) are found,
an error is generated and the user is prompted to use mcode instead.cwd to soloc is not required to
build the model. This was only required on Windows systems where there was
a space in the file name. Correctly rendering the path for the build
directory now.as_data_set to convert one or more event objects into a data frame
that can be passed to data_set. Does something similar to expand.ev,
but more control.time, amt, rate, evid, ii, addl ,ss,
cmt) either lower case or upper case names are recognized. The determination
is made on the time / TIME column (always required when using a data set).
If time mrgsolve will continue looking for lower case names; if TIME it
will look for upper case names. A warning is issued in case both upper and
lower case names are included.$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 ... ).ev where no rows were returned if amt wasn't supplied
(#44)..cpp.cpp
file when compiling.touch_funs when large number (> 25) of ETAs in the model
(#68).$PKMODEL with ncmt=2 and depot=FALSE, the default PK
parameters are CL, V1 (central volume), Q, V2 (peripheral volume).V2 (central) and V3
(peripheral).$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.$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.dplyr, now requiring dplyr >= 0.5.0 (#69)data slot in mrgsims objects is now data.frameknobs function and plot method has been re-written. Overall behavior
for most applications should be the same.C++ symbols for model functions are now stored in the model object
(funs slot)mrgsolve:::funset(mod)funs can be found with is.loadedsoloc 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)).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.getLoadedDLLs()), are attempted to be dyn.unloaded.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).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.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.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.mread.complog system, including:
comp_forget a message is issuedcomplog no message is issuedtrequest argument to mrgsimrate > 0 and amt==0.amt (#43).evid 4 were not properly
implemented. While investigating that issue, also found similar issue with
evid 4 infusions getting scheduled with addl (#31).ev to avoid unintended
issues in evaluation (#29).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.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.Req when you want to change the names of compartments or
output variables specified in $TABLE / $CAPTURE.pkmodel function for easy loading and simulating from 1- and
2-compartment models (#39).$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).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.get_tokens), a wrapper for the boost tokenizer)
to help checking the model specification file.$FIXED are now implemented as C++ preprocessor
directives by default rather than const double variables. Use $SET fixed_type = "define" or $SET fixed_type = "const" to select between
the approaches.mindt attribute to mrgmod objects with default value of
.Machine$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 $SIGMA list when one matrix was
named and another was unnamed. This has been fixed. (#16)ss=1 caused mrgsolve/R to crash when
the infusion duration was equal to or some multiple of the dosing interval.
(#19)F_CENT to zero gave undefined behavior.F_CMT is set to zero and the ss flag is
set to 1. (#22)evid=4 (reset the system and dose)addl > 0 reset the system for all subsequent doses. Additional doses
coming from records with evid=4 will not do system reset. (#23)$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.tname, oname, and sname will imply
theta=TRUE, omega=TRUE, and sigma=TRUE, respectively.DEPOT use: F_DEPOT
(bioavailability), ALAG_DEPOT (dosing lag time), D_DEPOT (infusion
duration), and / or R_DEPOT (infusion rate). (#13)DLSODA fails, including
clear identification if the value of istate, which is 2 when the solver
succeeds and negative when the solver fails.labels and prefix options to $OMEGA and $SIGMA. These allow
descriptive aliases for ETAs ... e.g. using ETA_CL rather than ETA(1).dplyr::slice method for mrgsims objects (#11)mread: quiet. Setting quiet to TRUE will prevent
printing messages when mread is called. The default is
getOptions("mrgsolve_mread_quiet",FALSE) ... so you can call
options(mrgsolve_mread_quiet = TRUE) to globally turn off messages
from mread.project) and shared object (soloc) so that
"short" paths are used when compiling the model on Windows platforms (#4).$MAIN with rate=-2(#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 (#5).recsort options were selected (#6).$ADVAN2 and $ADVAN4 for implementing one- and two-compartment PK
models with analytical solutions rather than ODEs (thanks to contributions by
Bill Gillespie and Charles Margossian)soloc attribute added to mrgmod and argument added to mread,
giving user control over where the shared object is stored; by default it is
in tempdir(). soloc needs to be set to local directory when using qapplydplyr_ functions so that mrgsims objects can
be piped to mutate, group_by, filter, summarise, do, select, and
summarise.each (it's a dot not an underscore). So:
mod %>% mrgsim %>% mutate(group=1)idata; for compartment
CMT, include a column in idata called CMT_0$OMEGA and $SIGMA: if all incoming
matrices are unnamed and the signature matches the model object, the update
will happenmcRNG function as alias to base::RNGkind("L'Ecuyer-CMRG")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.R dependency to >= 3.1.2Ops involving mrgmod objects are now deprecatedloadso now returns the model object (invisibly)init method with signature mrgmod,ANY, with ANY getting coerced
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