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).
as_data_set()
(#1115, #1196).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 $GLOBAL
(#1125, #1126).
Fixed a bug where modeled event log was not getting reset after simulating the first individual; this resulted in events not getting executed in subsequent individuals when matching events were executed in the first individual; this affects modeled events only, not events coming from the data set (#1117, #1118).
Fixed a bug in detecting which compartments are receiving doses (#1112, #1113).
EPS
draws; this is a change from previous
behavior where records with the same time received the same value for
EPS
(#1110)..x
from matlist
documentation
object per new NOTE output from rdevel (#1103, #1104).Add new functionality for assessing consistency between names on input data set and parameter names (#1078).
check_data_names()
executes the
check.$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 Req
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)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_.ev
filter.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.frame
plot_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 qsim
read_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-class
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
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 >= 0.7.1
ss=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.dplyr
deslist
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 $CAPTURE
s 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 ETA
s. 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.frame
knobs
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.loaded
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)
).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.unload
ed.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 mrgsim
rate > 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
qapply
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)
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 >= 3.1.2
Ops
involving mrgmod
objects are now
deprecatedloadso
now returns the model object (invisibly)init
method with signature
mrgmod
,ANY
, with ANY
getting
coerced to list