Changelog
Source:NEWS.md
rxode2 (development version)
Rework the
tad()
and related functions so they use the same interface as compartments (this way they do not depend on the order of compartments); See #815. For mu-referencing, Also allow dummy variables to ignore state requirements (iepodo(depot)
in a single line will not error when parsing mu-referenced equations).Add
getRxNpars
to api. This allows the development version ofbabelmixr2
to better check what model is loaded and unload/reload as necessary.Add
rxUdfUiControl()
to rxode2 user function to get control information from something likenlmixr2
Bug fix for tracking time after dose when dosing to 2 compartments occur at the exact same time (#804, #819)
Change
transit()
model so that it usestad0()
,podo0()
and related functions for a bit more stable simulation and estimation
rxode2 3.0.2
CRAN release: 2024-10-30
Bug fix for
api
, the censoring function pointer has been updated (#801).Query
rxode2.verbose.pipe
at run time instead of requiring it to be set before loadingrxode2
.Have correct values at boundaries for
logit
,expit
,probit
, andprobitInv
(instead ofNA
). For most cases this does not break anything.Add a new style of user function that modifies the
ui
while parsing or just before using the function (in the presence ofdata
).Used the new user function interface to allow all random functions in
rxode2
ui functions to be named. For example, you can userxnorm(sd=3)
instead of having to userxnorm(0, 3)
, althoughrxnorm()
still works.
rxode2 3.0.1
CRAN release: 2024-09-22
- Explicitly initialize the order vector to stop valgrind warning (requested from CRAN)
rxode2 3.0.0
CRAN release: 2024-09-18
Breaking Changes
The model properties was moved from
$params
to$props
so it does not conflict with the low levelrxode2
model$params
Error when specifying
wd
withoutmodName
With Linear and midpoint of a time between two points, how
rxode2
handles missing values has changed. When the missing value is lower than the requested time, it will look backward until it finds the first non-missing value (or if all are missing start looking forward). When the missing value is higher than the requested time, the algorithm will look forward until it finds the first non-missing value (or if all are missing, start looking backward).The order of ODEs is now only determined by the order of
cmt()
andd/dt()
. Compartment properties,tad()
and other compartment related variables no no longer affect compartment sorting. The optionrxode2.syntax.require.ode.first
no longer does anything.-
The handling of zeros “safely” has changed (see #775)
when
safeZero=TRUE
and the denominator of a division expression is zero, use the Machine’s small number/eps
(you can see this value with.Machine$double.eps
)when
saveLog=TRUE
and the x in thelog(x)
is less than or equal to zero, change this tolog(eps)
when
safePow=TRUE
and the expressionx^y
has a zero forx
and a negative number fory
replacex
witheps
.
Since the protection for divide by zero has changed, the results will also change. This is a more conservative protection mechanism than was applied previously.
Random numbers from
rxode2
are different when usingdop853
,lsoda
orindLin
methods. These now seed the random numbers in the same way asliblsoda
, so the random number provided will be the same with different solving methods.The arguments saved in the
rxSolve
for items likethetaMat
will be the reduced matrices used in solving, not the full matrices (this will likely not break very many items)
Possible breaking changes (though unlikely)
-
iCov
is no longer merged to the event dataset. This makes solving withiCov
slightly faster (#743)
New features
You can remove covariances for every omega by piping with
%>% ini(diag())
you can be a bit more granular by removing all covariances that have eithereta.ka
oreta.cl
by:%>% ini(diag(eta.ka, eta.cl))
or anything with correlations witheta.cl
with%>% ini(diag(eta.cl))
You can also remove individual covariances by
%>% ini(-cov(a, b))
or%>% ini(-cor(a,b))
.-
You can specify the type of interpolation applied for added dosing records (or other added records) for columns that are kept with the
keep=
option inrxSolve()
. This new option iskeepInterpolation
and can belocf
for last observation carried forward,nocb
which is the next observation carried backward, as well asNA
which puts aNA
in all imputed data rows. See #756.Note: when interpolation is linear/midpoint for factors/characters it changes to locf with a warning (#759)
Also note, that the default keep interpolation is
na
-
Now you can specify the interpolation method per covariate in the model:
linear(var1, var2)
says bothvar1
andvar2
would use linear interpolation when they are a time-varying covariate. You could also uselinear(var1)
locf()
declares variables using last observation carried forwardnocb()
declares variables using next observation carried backwardmidpoint()
declares variables using midpoint interpolation
linear()
,locf()
,locb()
,midpoint()
,params()
,cmt()
anddvid()
declarations are now ignored when loading arxode2
model withrxS()
Strings can be assigned to variables in
rxode2
.Strings can now be enclosed with a single quote as well as a double quote. This limitation was only in the rxode2 using string since the R-parser changes single quotes to double quotes. (This has no impact with
rxode2({})
and ui/function form).More robust string encoding for symengine (adapted from
utils::URLencode()
andutils::URLdecode()
)Empty arguments to
rxRename()
give a warning (#688)Promoting from covariates to parameters with model piping (via
ini()
) now allows setting bounds (#692)Added
assertCompartmentName()
,assertCompartmentExists()
,assertCompartmentNew()
,testCompartmentExists()
,assertVariableExists()
testVariableExists()
,assertVariableNew()
,assertVariableName()
, andassertParameterValue()
to verify that a value is a valid nlmixr2 compartment name, nlmixr2 compartment/variable exists in the model, variable name, or parameter value (#726; #733)Added
assertRxUnbounded()
,testRxUnbounded()
,warnRxBounded()
to allownlmixr2
warn about methods that ignore boundaries #760Added functions
tad0()
,tafd0()
,tlast0()
andtfirst0()
that will give0
instead ofNA
when the dose has not been administered yet. This is useful for use in ODEs sinceNA
s will break the solving (so can be used a bit more robustly with models like Weibull absorption).rxode2
is has no more binary link tolotri
, which means that changes in thelotri
package will not requirerxode2
to be recompiled (in most cases) and will not crash the system.rxode2
also has no more binary linkage toPreciseSums
The binary linkage for
dparser
is reduced to C structures only, making changes in dparser less likely to cause segmentation faults inrxode2
if it wasn’t recompiled.A new model property has been added to
$props$cmtProp
and$statePropDf
. Both are data-frames showing which compartment has properties (currentlyini
,f
,alag
,rate
anddur
) in therxode2
ui model. This comes from the lower level model variable$stateProp
which has this information encoded in integers for each state.A new generic method
rxUiDeparse
can be used to deparse meta information into more readable expressions; This currently by default supports lower triangular matrices by lotri, but can be extended to support other types of objects like ’nlmixr2’sfoceiControl()
for instance.
Bug fixes
Fix
ui$props$endpoint
when the ui endpoint is defined in terms of the ode instead of lhs. See #754Fix
ui$props
when the ui is a linear compartment model withoutka
defined.Model extraction
modelExtract()
will now extract model properties. Note that the model property ofalag(cmt)
andlag(cmt)
will give the same value. See #745When assigning reserved variables, the parser will error. See #744
Linear interpolation will now adjust the times as well as the values when
NA
values are observed.Fix when keeping data has
NA
values that it will not crash R; Also fixed some incorrectNA
interpolations. See #756When using
cmt()
sometimes the next statement would be corrupted in the normalized syntax (like for instancelocf
); This bug was fixed (#763)keep
will now error when trying to keep items that are in the rxode2 output data-frame and will be calculated (#764)
Big change
- At the request of CRAN, combine
rxode2parse
,rxode2random
, andrxode2et
into this package; The changes in each of the packages are now placed here:
rxode2et (no changes before merge)
rxode2et 2.0.11
Make the stacking more flexible to help rxode2 have more types of plots
Add
toTrialDuration
by Omar Elashkar to convert event data to trial duration dataFix Issue #23 and prefer variable values over NSE values
rxode2et 2.0.9
Split off
et()
,eventTable()
and related functions.Also split off
rxStack()
andrxCbindStudyIndividual()
in this package.Added a
NEWS.md
file to track changes to the package.
rxode2random (before merge)
- Fix a bug when simulating nested variables (#25)
rxode2random 2.1.0
-
Breaking Change changed distributions from the standard C++
<random>
toboost::random
. Since this is not dependent on the compiler, it makes the random numbers generated from Mac, Windows and Linux the same for every distribution. Unfortunately with a new random number transformation, the simulation results will likely be different than they were before. The exception to this is the uniform number, which was always the same between platforms.
rxode2random 2.0.12
Added function
dfWishart
which gives (by simulation) an approximation of the degrees of freedom of a Wishart to match arse
value.Added function
swapMatListWithCube
which swaps omegaList with omegaCube valuesEnsure that the outputs are integers (instead of long integers) as requested by CRAN for some checking functions.
rxode2parse (fixed before merging)
- As requested by CRAN remove the C code
SET_TYPEOF
which is no longer part of the C R API.
rxode2parse 2.0.19
Added a evid suffix of 60 for cases where evid=2 adds an on event (fixes tad() calculation in certain edge cases)
Initialize all variables to
NA
rxode2parse 2.0.18
Removed linear compartment solutions with gradients from rxode2parse (and rxode2) when compiled with intel c++ compiler (since it crashes while compiling).
Fixed
m1mac
string issues as requested by CRAN
rxode2parse 2.0.17
Added ability to query R user functions in a rxode2 model (will force single threaded solve)
Moved core
rxFunParse
andrxRmFunParse
here so that C and R user function clashes can be handledModel variables now tracks which compartments have a lag-time defined
For compartment with steady state doses (NONMEM equivalent SS=1, SS=2), an additional tracking time-point is added at to track the time when the lagged dose is given. As an upshot, the lagged dose will start at the steady state concentration shifted by + ii - lag in
rxode2
(currently for ode systems only)This release calculates non bio-availability adjusted duration for all rates instead of trying to figure the rate duration during solving.
Make double assignment an error, ie
a <- b <-
NA
times are ignored (with warning)Steady state bolus doses with
addl
are treated as non steady state events (like what is observed inNONMEM
)Timsort was upgraded; drop radix support in rxode2 structure
etTrans
now supports keeping logical vectors (with the appropriate version ofrxode2
).Security fixes were applied as requested by CRAN
rxode2parse 2.0.16
- Import
data.table
explicitly in the R code (before was imported only in C/C++ code)
rxode2parse 2.0.14
‘linCmt()’ translations of ‘alpha’, ‘beta’, ‘gamma’, ‘k21’, ‘k31’, ‘vc’ now error instead of ignoring ‘gamma’ and ‘k31’ to give 2 cmt solution
transit compartment internal code now changes dose to 0.0 when no dose has been administered to the depot compartment. This way dosing to the central compartment (without dosing to the transit compartment) will not give a
NA
for the depot compartment (and consequently for the central compartment)Moved
rxDerived
here and added tests for it here as well.-
Moved
etTransParse
here and added tests for it here as well (makes up most ofetTrans
). In addition the following changes were made toetTransParse()
/etTrans()
:The internal translation (
etTrans()
) will not drop times when infusions stop. Before, if the infusion stopped after the last observation the time when the infusion stopped would be dropped. This interferes withlinCmt()
models.Breaking change/bug fix
evid=2
are considered observations when translating data to internalrxode2
event structureFix edge case to find infusion duration when it is the first item of the dosing record at time 0.
Fixed a bug for certain infusions where the
rate
,ii
and/orss
data items were dropped from the output whenaddDosing=TRUE
Also have internal functions to convert between classic NONMEM events and rxode2 events
Have an internal function that gives information on the linear compartmental model translation type, which could be useful for babelmixr2
‘time’ in model is now case insensitive
Use function declaration in
rxode2parseGetTranslation()
to determine thread safety of functions available to rxode2Add check for correct number of function arguments to parser.
Like R, known functions can be assigned as a variable and the function can still be called (while not changing the variable value). For example you can have a variable
gamma
as well as a functiongamma()
.Fix garbled error messages that occur with certain messages.
Fixed errors that occurred when using capitalized AMT variables in the model.
rxode2parse 2.0.12
Bug fix for strict prototypes
Removed
sprintf
as noted by CRANMade
rxode2parse
dll binary independent ofrxode2()
rxode2 2.1.3
CRAN release: 2024-05-28
New features
Create a function to see if a rxode2 solve is loaded in memory (
rxode2::rxSolveSetup()
)Create a new function that fixes the rxode2 population values in the model (and drops them in the initial estimates);
rxFixPop()
rxode2 2.1.2
CRAN release: 2024-01-30
Other changes
rxUi
compression now defaults to fast compressionFixes String literal formatting issues as identified by CRAN (#643)
Removes linear compartment solutions with gradients for intel c++ compiler (since they crash the compiler).
rxode2 2.1.0
CRAN release: 2023-12-11
Breaking changes
Steady state with lag times are no longer shifted by the lag time and then solved to steady state by default. In addition the steady state at the original time of dosing is also back-calculated. If you want the old behavior you can bring back the option with
ssAtDoseTime=FALSE
.“dop853” now uses the
hmax
/h0
values from therxControl()
orrxSolve()
. This may change some ODE solving using “dop853”When not specified (and xgxr is available), the x axis is no longer assumed to be in hours
New features
User defined functions can now be R functions. For many of these R functions they can be converted to C with
rxFun()
(you can see the C code afterwards withrxC("funName")
)Parallel solving of models that require sorting (like modeled lag times, modeled duration etc) now solve in parallel instead of downgrading to single threaded solving
Steady state infusions with a duration of infusions greater than the inter-dose interval are now supported.
Added
$symengineModelNoPrune
and$symengineModelPrune
for loading models into rxode2 withrxS()
-
When plotting and creating confidence intervals for multiple endpoint models simulated from a rxode2 ui model, you can plot/summarize each endpoint with
sim
. (ie.confint(model, "sim")
orplot(model, sim)
).If you only want to summarize a subset of endpoints, you can focus on the endpoint by pre-pending the endpoint with
sim.
For example if you wanted to plot/summarize only the endpointeff
you would usesim.eff
. (ieconfint(model, "sim.eff")
orplot(model, sim.eff)
) Added
model$simulationIniModel
which prepend the initial conditions in theini({})
block to the classicrxode2({})
model.Now
model$simulationModel
andmodel$simulationIniModel
will save and use the initialization values from the compiled model, and will solve as if it was the original ui model.Allow
ini(model) <- NULL
to drop ini block andas.ini(NULL)
givesini({})
(Issue #523)Add a function
modelExtract()
to extract model lines to allow modifying them and then changing the model by piping or simply assigning the modified lines withmodel(ui) <- newModifiedLines
Add Algebraic mu-referencing detection (mu2) that allows you to express mu-referenced covariates as:
Instead of the
cl <- exp(tcl + eta.cl + wt_cl * log.WT.div.70.5)
That was previously required (where log.WT.div.70.5
was calculated in the data) for mu expressions. The ui
now has more information to allow transformation of data internally and transformation to the old mu-referencing style to run the optimization.
Allow steady state infusions with a duration of infusion greater than the inter-dose interval to be solved.
Solves will now possibly print more information when issuing a “could not solve the system” error
The function
rxSetPipingAuto()
is now exported to change the way you affect piping in your individual setupAllow covariates to be specified in the model piping, that is
mod %>% model(a=var+3, cov="var")
will add"var"
as a covariate.When calculating confidence intervals for
rxode2
simulated objects you can now useby
to stratify the simulation summary. For example you can now stratify by gender and race by:confint(sim, "sim", by=c("race", "gender"))
When calculating the intervals for
rxode2
simulated objects you can now useci=FALSE
so that it only calculates the default intervals without bands on each of the percentiles; You can also choose not to match the secondary bands limits withlevels
but use your ownci=0.99
for instanceA new function was introduced
meanProbs()
which calculates the mean and expected confidence bands under either the normal or t distributionA related new function was introduced that calculates the mean and confidence bands under the Bernoulli/Binomial distribution (
binomProbs()
)When calculating the intervals for
rxode2
simulated objects you can also usemean=TRUE
to use the mean for the first level of confidence usingmeanProbs()
. For this confidence interval you can override then
used in the confidence interval by usingn=#
. You can also change this to a prediction interval instead usingpred=TRUE
.Also when calculating the intervals for
rxode2
simulated object you can also usemean="binom"
to use the binomial distributional information (and ci) for the first level of confidence usingbinomProbs()
. For this confidence interval you can override then
used in the confidence interval by usingn=#
. You can also change this to a prediction interval instead usingpred=TRUE
. Withpred=TRUE
you can override the number of predicted samples withm=#
When plotting the
confint
derived intervals from anrxode2
simulation, you can now subset based on a simulated value likeplot(ci, Cc)
which will only plot the variableCc
that you summarized even if you also summarizedeff
(for instance).When the rxode2 ui is a compressed ui object, you can modify the ini block with
$ini <-
or modify the model block with$model <-
. These are equivalent toini(model) <-
andmodel(model) <-
, respectively. Otherwise, the object is added to the user defined components in the function (ie$meta
). When the object is uncompressed, it simply assigns it to the environment instead (just like before).When printing meta information that happens to be a
lotri
compatible matrix, uselotri
to express it instead of the default R expression.Allow character vectors to be converted to expressions for piping (#552)
rxAppendModel()
will now take an arbitrary number of models and append them together; It also has better handling of models with duplicate parameters and models withoutini()
blocks (#617 / #573 / #575).keep
will now also keep attributes of the input data (with special handling forlevels
); This means a broader variety of classes will be kept carrying more information with it (for example ordered factors, data frame columns with unit information, etc)Piping arguments
append
forini()
andmodel()
have been aligned to perform similarly. Thereforeini(append=)
now can take expressions instead of simply strings andmodel(append=)
can also take strings. Also model piping now can specify the integer line number to be modified just like theini()
could. Alsomodel(append=FALSE)
has been changed tomodel(append=NULL)
. While the behavior is the same when you don’t specify the argument, the behavior has changed to align withini()
when piping. Hencemodel(append=TRUE)
will append andmodel(append=FALSE)
will now pre-pend to the model.model(append=NULL)
will modify lines like the behavior ofini(append=NULL)
. The default ofmodel(line)
modifying a line in-place still applies. While this is a breaking change, most code will perform the same.Labels can now be dropped by
ini(param=label(NULL))
. Also parameters can be dropped with the idiommodel(param=NULL)
orini(param=NULL)
changes the parameter to a covariate to align with this idiom of dropping parametersrxRename
has been refactored to run faster
Internal new features
Add
as.model()
for list expressions, which impliesmodel(ui) <- ui$lstExpr
will assign model components. It will also more robustly work with character vectorsSimulated objects from
rxSolve
now can access the model variables with$rxModelVars
Simulation models from the UI now use
rxerr.endpoint
instead oferr.endpoint
for thesigma
residual error. This is to align with the convention that internally generated variables start withrx
ornlmixr
Sorting only uses timsort now, and was upgraded to the latest version from Morwenn
Bug fixes
Simulating/solving from functions/ui now prefers params over
omega
andsigma
in the model (#632)Piping does not add constants to the initial estimates
When constants are specified in the
model({})
block (likek <- 1
), they will not be to theini
blockBug fix for
geom_amt()
when theaes
transformation hasx
Bug fix for some covariate updates that may affect multiple compartment models (like issue #581)
rxode2 2.0.14
CRAN release: 2023-10-07
CRAN requested that FORTRAN
kind
be changed as it was not portable; This was commented code, and simply removed the comment.Bug-fix for
geom_amt()
; also now useslinewidth
and at leastggplot2 3.4.0
Some documentation was cleaned up from
rxode2
2.0.13
rxode2 2.0.13
CRAN release: 2023-04-22
New features
A new function
zeroRe()
allows simple setting of omega and/or sigma values to zero for a model (#456)Diagonal zeros in the
omega
andsigma
matrices are treated as zeros in the model. The correspondingomega
andsigma
matrices drop columns/rows where the diagonals are zero to create a newomega
andsigma
matrix for simulation. This is the same idiom that NONMEM uses for simulation from these matrices.Add the ability to pipe model estimates from another model by
parentModel %>% ini(modelWithNewEsts)
Add the ability to append model statements with piping using
%>% model(x=3, append=d/dt(depot))
, still supports appending withappend=TRUE
and pre-pending withappend=NA
(the default is to replace lines withappend=FALSE
)rxSolve’s keep argument will now maintain character and factor classes from input data with the same class (#190)
Parameter labels may now be modified via
ini(param = label("text"))
(#351).Parameter order may be modified via the
append
argument toini()
when piping a model. For example,ini(param = 1, append = 0)
orini(param = label("text"), append = "param2")
(#352).
Internal changes
If lower/upper bounds are outside the required bounds, the adjustment is displayed.
When initial values are piped that break the model’s boundary condition reset the boundary to unbounded and message which boundary was reset.
Added
as.rxUi()
function to convert the following objects torxUi
objects:rxode2
,rxModelVars
,function
. Converting nlmixr2 fits torxUi
will be placed in thes3
method in the corresponding package.assertRxUi(x)
now usesas.rxUi()
so that it can be extended outside ofrxode2
/nlmixr2
.rxode2
now supportsaddl
withss
dosesMoved
rxDerived
torxode2parse
(and re-exported it here).Added test for transit compartment solving in absence of dosing to the transit compartment (fixed in
rxode2parse
but solving tested here)Using
ini()
without any arguments on arxode2
type function will return theini()
block. Also added a methodini(mod) <- iniBlock
to modify theini
block is you wish.iniBlock
should be an expression.Using
model()
without any arguments on arxode2
type function will return themodel()
block. Also added a new methodmodel(mod) <- modelBlock
Added a new method
rxode2(mod) <- modFunction
which allows replacing the function with a new function while maintaining the meta information about the ui (like information that comes fromnonmem2rx
models). ThemodFunction
should be the body of the new function, the new function, or a newrxode2
ui.rxode2
ui objects now have a$sticky
item inside the internal (compressed) environment. This$sticky
tells what variables to keep if there is a “significant” change in the ui during piping or other sort of model change. This is respected during model piping, or modifying the model withini(mod)<-
,model(mod)<-
,rxode2(mod)<-
. A significant change is a change in the model block, a change in the number of estimates, or a change to the value of the estimates. Estimate bounds, weather an estimate is fixed or estimate label changes are not considered significant.Added
as.ini()
method to convert various formats to an ini expression. It is used internally withini(mod)<-
. If you want to assign something new that you can convert to an ini expression, add a method foras.ini()
.Added
as.model()
method to convert various formats to a model expression. It is used internally withmodel(mod)<-
. If you want to assign something new that you can convert to a model expression, add a method foras.model()
.
rxode2 2.0.11
CRAN release: 2022-11-01
Give a more meaningful error for ‘rxode2’ ui models with only error expressions
Break the ABI requirement between
roxde2()
andrxode2parse()
The new
rxode2parse
will fix thesprintf
exclusion shown on CRAN.
rxode2 2.0.10
CRAN release: 2022-10-20
Time invariant covariates can now contain ‘NA’ values.
When a column has ‘NA’ for the entire id, now ‘rxode2’ warns about both the id and column instead of just the id.
To fix some CRAN issues in ‘nlmixr2est’, make the version dependency explicit.
rxode2 2.0.9
CRAN release: 2022-10-19
Remove log likelihoods from ‘rxode2’ to reduce compilation time and increase maintainability of ‘rxode2’. They were transferred to ‘rxode2ll’ (requested by CRAN).
Remove the parsing from ‘rxode2’ and solved linear compartment code and move to ‘rxode2parse’ to reduce the compilation time (as requested by CRAN).
Remove the random number generation from ‘rxode2’ and move to ‘rxode2random’ to reduce the compilation time (as requested by CRAN).
Remove the event table translation and generation from ‘rxode2’ and move to ‘rxode2et’ to reduce the compilation time (as requested by CRAN).
Change the
rxode2
ui object so it is a compressed, serialized object by default. This could reduce theC stack size
problem that occurs with too many environments in R.Warn when ignoring items during simulations
Export a method to change ‘rxode2’ solve methods into internal integers
Bug fix for time invariant covariates identified as time variant covariate when the individual’s time starts after
0
.
rxode2 2.0.8
CRAN release: 2022-09-23
Breaking changes
rxgamma
now only allows arate
input. This aligns with the internalrxode2
version ofrxgamma
and clarifies how this will be used. It is also aligned with thellikGamma
function used for generalized likelihood estimation.ui
cauchy
simulations now follow the ui fornormal
andt
distributions, which means you can combine with transformations. This is because thecauchy
is at
distribution with one degree of freedom.ui
dnorm()
andnorm()
are no longer equivalent toadd()
. Now it allows you to use the loglikllikNorm()
instead of the standardnlmixr2
style focei likelihood. This is done by addingdnorm()
at the end of the line. It also meansdnorm()
now doesn’t take any arguments.Vandercorput normal removed (non-random number generator)
New features
Allow models in the
nlmixr2
form without anini({})
blockAllow model piping of an omega matrix by
f %>% ini(omegaMatrix)
Standard models created with
rxode2()
can no be piped into a model functionFamilies of log-likelihood were added to
rxode2
so that mixed likelihood nonlinear mixed effects models may be specified and run.The memory footprint of a
rxode2
solving has been reducedPiping now allow named strings (issue #249)
Bug fixes
rxode2
’s symengine would convertsqrt(2)
toM_SQRT_2
when it should beM_SQRT2
. This has been fixed; it was most noticeable in nlmixr2 log-likelihood estimation methodsrxode2
treatsDV
as a non-covariate withetTran
(last time it would duplicate if it is in the model). This is most noticeable in the nlmixr2 log-likelihood estimation methods.
New features
A new flag (
rxFlag
) has been created to tell you where in therxode2
solving process you are. This is useful for debugging. If outputting this variable it will always be11
or calculating the left handed equations. If you are using in conjunction with theprintf()
methods, it is a double variable and should be formatted with"%f"
.An additional option of
fullPrint
has been added torxode2()
which allowsrprintf()
to be used in almost all ofrxode2()
steps (inductive linearization and matrix exponential are the exception here) instead of just the integrationddt
step. It defaults toFALSE
.
rxode2 2.0.7
CRAN release: 2022-05-17
Removed accidental
^S
from news as requested by CRAN.Bug fix for more complicated mu-referencing.
Change rxode2 md5 to only depend on the C/C++/Fortran code and headers not the R files. That way if there is binary compatibility between
nlmixr2est
andrxode2
, a new version ofnlmixr2est
will not need to be submitted to CRAN.
rxode2 2.0.6
CRAN release: 2022-05-09
Breaking changes
Solving controls
The options for
rxControl
andrxSolve
are more strict.camelCase
is now always used. Old options likeadd.cov
andtransit_abs
are no longer supported, onlyaddCov
is supported.A new option,
sigdig
has been added torxControl()
, which controls some of the more common significant figure options likeatol
,rtol
,ssAtol
,ssRtol
, with a single option.
Simulations
For simulations,
$simulationSigma
now assumes a diagonal matrix. The sigma values are assumed to be standard normal, and uncorrelated between endpoints. Simulation with uncertainty will still draw from this identity diagonal matrixParallel solving now seeds each simulation per each individual based on the initial seed plus the simulation id. This makes the simulation reproducible regardless of the number of cores running the simulation.
Other breaking changes
Solved objects now access the underlying rxode model with
$rxode2
instead of$rxode
Since this change names,
rxode2
,rxode
andRxODE
all perform the same function.Options were changed from
RxODE.syntax
torxode2.syntax
.Assigning states with
rxode2.syntax.assign.state
(wasRxODE.syntax.assign.state
) is no longer supported.Enforcing “pure” assignment syntax with
=
syntax is no longer supported sorxode2.syntax.assign
is no longer supported (wasRxODE.syntax.assign
).Since R supports
**
as an exponentiation operator, the pure syntax without**
can no longer be enabled. Hencerxode2.syntax.star.pow
(wasRxODE.syntax.star.pow
) no longer has any effect.The “pure” syntax that requires a semicolon can no longer be enabled. Therefore
rxode2.syntax.require.semicolon
(wasRxODE.syntax.require.semicolon
) no longer has any effect.The syntax
state(0)
can no longer be turned off.rxode2.syntax.allow.ini0
(wasRxODE.syntax.allow.ini0
) has been removed.Variable with dots in variable and state names like
state.name
works in R. Therefore, “pure” syntax of excluding.
values from variables cannot be enforced withrxode2.syntax.allow.dots
(wasRxODE.syntax.allow.dots
).The mnemonic
et(rate=model)
andet(dur=model)
mnemonics have been removed.rate
needs to be set to-1
and-2
manually instead.The function
rxode2Test()
has been removed in favor of using testthat directly.Transit compartments need to use a new
evid
,evid=7
. That being said, thetransitAbs
option is no longer supported.ID
columns in input parameter data frames are not sorted or merged with original dataset any more; The underlying assumption of ID order should now be checked outside ofrxode2()
. Note that the event data frame is still sorted.
Additional features
The UI functions of
nlmixr
have been ported to work inrxode2
directly.rxModelVars({})
is now supported.You may now combine 2 models in
rxode2
withrxAppendModel()
. In fact, as long as the first value is a rxode2 evaluated ui model, you can usec
/rbind
to bind 2 or more models together.You may now append model lines with piping using
%>% model(lines, append=TRUE)
you can also pre-pend lines by%>% model(lines, append=NA)
You may now rename model variables, states and defined parameters with
%>% rxRename(new=old)
or ifdplyr
is loaded:%>% rename(new=old)
You can fix parameters with
%>% ini(tcl=fix)
or%>% ini(fix(tcl))
as well as unfix parameters with%>% ini(tcl=unfix)
or%>% ini(unfix(tcl))
Internal changes
Strict R headers are enforced more places
Since there are many changes that could be incompatible, this version has been renamed to
rxode2
rxode2()
printout no longer uses rules and centered headings to make it display better on a larger variety of systems.