# mrgsolve 1.4.1

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

# mrgsolve 1.4.0

- `evtools` is a new plugin providing API for dynamic dosing from within the 
  model; functions and classes are in the `evt` namespace (#1149).
  
- `regimen` is a new class located in the `evt` namespace via the `evtools` 
  plugin; `regimen` objects can execute doses in a regular regimen (#1156).
  
- `mread()` and `mcode()` no longer print a message before the required 
  waiting period on model recompile (#1145).

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

- C++ model code blocks (GLOBAL, PREAMBLE, MAIN/PK, ODE/DES, TABLE/ERROR) are 
  now checked for `<object>.<attribute>` syntax; if found, symbols on both sides
  of the dot become reserved words when loading and compiling that model; 
  specifically, an error will be generated if either side of the dot (`<object>`
  or `<attribute>`) is found in parameter names, compartment names, ETA labels, 
  or EPS labels (#1159).
  
- ETA values are always simulated from OMEGA, even when the user requests they
  get scraped from `data` or `idata` via `etasrc` argument to `mrgsim()`; this 
  ensures `EPS` are reproducible for model runs where `etasrc = "omega"` 
  (default, ETA are simulated) or, for example, where `etaasrc = "data.all"` 
  (scrape ETA from the data set) (#1163).


## Bugs Fixed

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

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

# mrgsolve 1.3.0

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

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

## Bugs Fixed

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

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

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

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

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

# mrgsolve 1.2.0

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

# mrgsolve 1.1.1

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

# mrgsolve 1.1.0

- Add new functionality for assessing consistency between names on input data
  set and parameter names (#1078).
    - New function `check_data_names()` executes the check.
    - New model specification block `$INPUT` for marking parameters as "inputs" 
      and expecting them to be present in the data when `check_data_names()` is
      called.
    - New `$PARAM` block attributes `@input` and `@tag` for adding tags to 
      parameters which will be checked when `check_data_names()` is called.
    - New function `param_tags()` to list parameters and tags for a given model. 

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

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

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

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

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

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

- Kyle Meyer added as contributor (#1096).

- `modlib()` model `1005` re-coded to reflect the "traditional" model
  specification syntax (#1069). 
  
- The model object `update()` method will again issue a warning when 
  unrecognized arguments are passed (#1068).

## Bugs Fixed

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

# mrgsolve 1.0.9

- Fix signatures for `compiled.mrgmod()` and `as_tibble.mrgsims()` based on new
  R-devel check findings (#1065).

# mrgsolve 1.0.8

- `SIGMA()` is a new model macro which allows users to access on-diagonal
  elements of `SIGMA` in the model (e.g. `SIGMA(2)` in `$ERROR`) (#1051, #1052).
  
- `mrgsim()` and `mrgsim_q()` gain an `etasrc` argument, allowing `ETAs` to 
  be either simulated from `OMEGA` (new default and previously the only 
  behavior) or taken from the input data set (new option), similar to the way 
  parameters can be scraped from the data set (#1037).

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

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

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

## Bugs Fixed

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

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

# mrgsolve 1.0.7

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

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

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

## Bugs Fixed

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

# mrgsolve 1.0.6

## Bugs Fixed

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

# mrgsolve 1.0.5

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

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

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

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

## Bugs Fixed

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

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

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

# mrgsolve 1.0.4

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

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

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

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

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

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


# mrgsolve 1.0.3

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

# mrgsolve 1.0.2

- Test class using `inherits()` not `class()` from CRAN check (#943).

# mrgsolve 1.0.1

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

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

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

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

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


# mrgsolve 1.0.0

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



# mrgsolve 0.11.2

- In `pk2iv`, change scaling volume for `CENT` from `V2` (incorrect) to 
  `V1` (#831, #832, #833)
  
- Fix bug collating multiple `$OMEGA` or `$SIGMA` matrices when parsing a 
  model (#863)
  
- Refactor how debugging information is processed when using the `recover` 
  argument to `mread()` (#853)
  
- Fix typo in documentation for `as_cmat()`; the off-diagonals are assumed
  to contain correlations (#856)

- Wrote a `as.data.frame.matrix()` function in Rcpp; all simulation results
  return from the C++ simulation code as a data frame (#857)
  
- Fix bug where dynamic capture (via `mread()`) was not allowed for variables
  declared in `$GLOBAL` (#868)

# mrgsolve 0.11.1

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

# mrgsolve 0.11.0

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

# mrgsolve 0.10.9

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

# mrgsolve 0.10.8
- Allow simulation from compartmental models with negative times #778
- Enable dynamic capture of pre-processor directives at compile time #776
- Fix error message when requesting invalid items during dynamic capture #776

# mrgsolve 0.10.7
- Stop testing test_equal using lattice

# mrgsolve 0.10.6
- Fix url endings for check on r-devel
- Adjust test comparing lattice plots based on change in r-devel; passing 
  check.environments now

# mrgsolve 0.10.5
- Suppress warnings when non-numeric columns are dropped when those columns are
  not relevant to the simulation (#709)
- Add `$ERROR` as an alias for `$TABLE` in the model file (#710)
- Fix bug where warning messages during steady-state finding referenced `rtol` 
  and `atol` rather than `ss_rtol` and `ss_atol` (#703)
- Fix annotation parsing bug when the description included semi-colon (#696)
- `loadso` issues a proper error when the model dll doesn't exist (#724)
- Try loading the model with loadso once of the model isn't loaded at the time
  of simulation (#725)
- Throw an error when `addl` or `ss` are negative (#733)
- Internal refactoring so that there is a hard solver reset when parameters that
  are copied from data change (#744)
- Add `tad` plugin to calculate time after dose in a specific compartment
  (#702)
- Internal refactor `carry_out` to respect default `nocb` behavior (#759; see 
  also #744)
- Throw an error when matlist labels are duplicated (#730)
- Add `capture` argument to `mread` to add to `$CAPTURE` when compiling the 
  model (#704)

# mrgsolve 0.10.3

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

# mrgsolve 0.10.1

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

# mrgsolve 0.10.0

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


# mrgsolve 0.9.2

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

# mrgsolve 0.9.1

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

# mrgsolve 0.9.0
- Added `logy` and `logbr` arguments to `plot.mrgsims` so results y-axis
outputs can easily be plotted on log scale
- release

# mrgsolve 0.8.12.9000

## New functions
- Added `numerics_only` function to drop non-numeric columns from 
the input data set after optionally converting logical columns
to integer
- Added `ev_rx` function to write dosing interventions in notation similar
to a prescription 'sig'

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

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

## Bugs fixed
- Fixed bug related to record sort order (#406)

## Deprecated
- `drop.re` and `drop_re`; use `zero_re` instead

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

# mrgsolve 0.8.12
- Minor changes to namespace for CRAN

# mrgsolve 0.8.11
- Internal release
- Removed the function `s` and replaced with `s_`; this was not a problem 
created by mrgsolve but rather by ggplot2, which calls `mgcv::s` via 
`geom_smooth` under certain circumstances

# mrgsolve 0.8.10.9015
- Re-configured the list of data coming from `as.list.mrgmod` so that
the names match the names that you would pass to `update.mrgmod`; also
added some items so that all updatable slots in the model object
are exported by calling `as.list` (#354)

# mrgsolve 0.8.10.9014
- Add OMEGA and SIGMA matrices to `as.list.mrgmod` output under the names
omat and smat, respectively
- It is no longer an error to attempt to update slots for OMEGA
and SIGMA matrices when there is no matrices in the slot as long
as the update is with an empty list or a matrix with zero rows
- Fix segmentation fault when both data set and idata set are used
in a simulation with certain mis-matches in the ID content
between the two (#352)

# mrgsolve 0.8.10.9013
- Removes more mtime code (wasn't in use)

# mrgsolve 0.8.10.9012
- Use `dplyr::filter_` for `filter_.ev`

# mrgsolve 0.8.10.9011
- mtime clear bug

# mrgsolve 0.8.10.9010
- Fixed bug in `filter.ev` method

# mrgsolve 0.8.10.9009
- Added `mutate_sims` and `filter_sims` that work on `mrgsims` (output)
objects, modifying the `data` slot and returning a modified `mrgsims` object
rather than `data.frame`
- Added `plot_sims` function that takes a data frame of simulated output
and generates a plot using the `mrgsims` method

# mrgsolve 0.8.10.9008
- Changed `id` argument to `ID` in `ev_rep` and `ev_seq`; a warning
is issued if `id` is used
- Added `data_qsim` for creating input data sets to use with `qsim`
- Fixed a bug where time after dose was not correctly
calculated for additional doses with a lag time #327
- Added `read_nmext` to read in nonmem model output from
the .ext file

# mrgsolve 0.8.10.9007
- Clean up and re-organize Rd files; more-logical grouping and
ordering

# mrgsolve 0.8.10.9006

- Stop importing assertthat and lazyeval

# mrgsolve 0.8.10.9005

## New Features

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

## Bug Fixes

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

## Important changes

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

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

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

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

# mrgsolve 0.8.10.9003

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

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

- Added `qsim_df` function, returning data frame rather than
matrix

- Added `as.list` method for `mrgsims` objects

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

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

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

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

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

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

## Bug Fixes
- Fixed bug preventing simulation with `qsim` with no event

## Functions removed
- `mrgsolve_example` and `mrgsolve_template`; these had been deprecated
previously with warning; use `modlib()` models instead

# mrgsolve 0.8.10.9002
- Added `mrgsim_df` function to return data frame rather than `mrgsims` object

# mrgsolve 0.8.10.9001

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

# mrgsolve 0.8.10
- Release to CRAN

# mrgsolve 0.8.9.9004
- Added `file` argument to `mread` to allow coding model
specification files with any extension.  The current
behavior continues to be assuming that the model
is in a `.cpp` file, but using the `file` argument
allows any file name for model specification.

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

# mrgsolve 0.8.9.9003
- Minor improvements to documentation

# mrgsolve 0.8.9.9002

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

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


# mrgsolve 0.8.6.9000

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

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

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

#  mrgsolve 0.8.4
- Reconfigure use of function pointer in unit tests

#  mrgsolve 0.8.3
- Bug fix that prevented installation on Solaris

#  mrgsolve 0.8.2
- The first release on CRAN

# mrgsolve 0.7.7

## New Authors
- Devin Pastoor is now listed as a contributor.  Thanks for all of your help!

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

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


# mrgsolve 0.7.6

## Important changes
- The `table()` macro in `$TABLE` is now deprecated (#129).  To get derived
values into the simulated output, users should assign
to type `double` and list that variable name in `$CAPTURE`.  See also the
`capture` typedef introduced below.
- The `mrgx` plugin was completely removed.  
- Parameter updates via `param` method with signature `missing` will check
names of input parameters against names of existing parameters.  An error is
generated if a user attempts to update a parameter that doesn't exist.  Note
that this does not apply for the `param` method with signature `list` (#144).
- The git repository was re-organized so that the package lives in the
base directory (#171).  

## Features
- Added `@` macros for indicating block options in model specification file.
- Added `qsim` function for quick(er) simulation runs with just one parameter
set.  
- Added `recmatrix` that creates matrix simulation template for `qsim`.
- Added `mrgsolve:::render` to create a document with overview of model
contents.  Methods for both `mrgmod` objects and `character` strings pointing
to a model file.
- Use `mrgsolve:::details` to extract model annotation.
- Added `capture` typedef in the model specification file.  Variables that are
type `capture` are doubles and are automatically appended to `$CAPTURE`.  
The `capture` typedef is not allowed in `$ODE` and probably should be reserved
for `$TABLE`.
- `simeta` is available in `$MAIN` and `simeps` is available in `$TABLE` by
default, no `$PLUGIN` is required.
- Better support for including `R` objects in the model via `$ENV` (#158).
- Added `assign_ev` function to help build simulation data sets from event
objects (#164).
- Added `as_data_frame` method from the `tibble` package (#166).
- When annotating model blocks, mrgsolve takes the __last__ parens item  as
the "units" and the __last__ bracketed item as "options"
- Added `$` operator for `mrgmod` objects to return the value of a parameter.
- Added `mread_cache` and `mcode_cache` functions to build and cache a model
(#143).

## Bugs fixed
- Fixed documentation issue in `PKMODEL`.  The volumes for two-compartment
model with no depot should be `V1`/`V2`.
- Fixed bug in `knobs` where output column names are malformed when a user
`$CAPTURE`s a parameter that is also being tweaked as a knob.
- Fixed bug in annotated model specification when multiple unit or option
specifications are made.

## Under the hood
- User-declared `double/int/bool` in `$MAIN`, `$ODE`, `$TABLE` are kept in
unnamed namespace and are local to the file.
- Started to re-organize the `.R` files.
- `mrgsolve:::details` returns a data frame of information regardless of
whether the model was annotated or not (#165).
- `mrgsolve::details` has additional arguments to help control output.
- Removed `pkevent` class; all records are `datarecord`.

# mrgsolve 0.7.5

## Features

- Added annotated code blocks for `$PARAM`, `$FIXED`, `$THETA`, `$CMT`,
`$INIT`, and `$VCMT`. (#107)
- `mrgsolve:::house()` model re-coded as an annotated model.
- Re-implemented `$ENV` to allow users to create `R` objects that can be used
at certain points
when parsing the model. (#115)
- Added `>>` signifier to code blocks that allow options; `>>` at the
beginning of the line indicates that the `name=value` statements that follow
are to be parsed as block options.
- Added `object` argument for the following blocks: `$PARAM`, `$OMEGA`,
`$SIGMA`, `$FIXED`, `$CMT`.  When `object` is set to a character string
naming an object in `$ENV`, that object will be used to form the output from
the block.

## Bugs fixed

- Fixed a bug which caused simulation run to hang when implementing a dose
with a __very__ small lag time. (#109)
- Fixed a bug where `valid.numericlist` wasn't returning `FALSE` for
improperly-formed objects.

## Under the hood

- Now using an `environment` to collect objects when parsing the model
specification file.
- Some small changes to `C++` code that calculates compartment amounts for
closed form one- and two-compartment models resulting in faster simulation runs.

# mrgsolve 0.7.4
- The `modmrg` package was discontinued.  All of the pre-coded models are
now available in mrgsolve.  Simply call `mread` with the model stem (e.g.
`pk1cmt`, `irm3`, etc ...) and call `modlib()` as the `project` argument.  
For example: `mod <- mread("emax", modlib())` will compile the `emax` model
and return the model object.

# mrgsolve 0.7.3
- Tests re-configured
- Fixed issue with record sorting for lagged doses when using full `data_set
`and `obsaug=TRUE` (#102)
- Fixed issue where `idata_set` wasn't handled properly when it was passed
in as `tbl` (#100)


# mrgsolve 0.7.2
- Addressed an issue where model compilation on `Windows` systems failed when
certain symbol names were used in the model (#97).  In this release, a
`dllname-win.def` file is created in `soloc` to export only the functions that
mrgsolve needs to use.  This is *only* relevant to `Windows` platform.
- Added a check on the `project` argument to `mread`: if newline(s) are found,
an error is generated and the user is prompted to use `mcode` instead.
- Several changes under the hood (#99)


# mrgsolve 0.7.1
- Fixed bug where requested columns were not properly named in certain
circumstances (#86).

# mrgsolve 0.7.0
- Revert back to previous behavior where `cwd` to `soloc` is not required to
build the model.  This was only required on `Windows` systems where there was
a space in the file name.   Correctly rendering the path for the build
directory now.

# mrgsolve 0.6.1

## Features
* Added `as_data_set` to convert one or more event objects into a data frame
that can be passed to `data_set`.  Does something similar to `expand.ev`,
but more control.
* For special column names (`time`, `amt`, `rate`, `evid`, `ii`, `addl` ,`ss`,
`cmt`) either lower case or upper case names are recognized.  The determination
is made on the `time` / `TIME` column (always required when using a data set).
If `time` mrgsolve will continue looking for lower case names; if `TIME` it
will look for upper case names.  A warning is issued in case both upper and
lower case names are included.
* Added `$PLUGIN` to let users extend their model specification file.  Valid
plugins include `simeta`, `Rcpp`, `RcppArmadillo`, and `BH`.  When a plugin
is used, mrgsolve will link back the the appropriate package and possibly
include appropriate header files when compiling the model.  For example,
`simeta` will link back to mrgsolve and `RcppArmadillo` and allow the modeler
to simulate a new set of `ETA`s.  Use `Rcpp`  plugin to simulate random variates
from common distributions in `R`(e.g. `rnorm`, `rexp` etc ... ).  

## Bugs fixed
* Fixed issue with `ev` where no rows were returned if `amt` wasn't supplied
(#44).
* Shortened the path for both the shared object and the name of the `.cpp.cpp`
file when compiling.
* Fixed bug in `touch_funs` when large number (`> 25`) of ETAs in the model
(#68).

## Important changes
* When using `$PKMODEL` with `ncmt=2` and `depot=FALSE`, the default PK
parameters are `CL`, `V1` (central volume), `Q`, `V2` (peripheral volume).  
This is a change where the previous volumes were `V2` (central) and `V3`
(peripheral).
* `$CAPTURE` now saves output items to slots in `std::vector<double>`, rather
than `std::map<std::string,double>`.  We've known for a while that the
`std::map` wasn't very efficient especially with large simulations.  
Currently, items in `$TABLE` are still saved into `std::map` with `table()`
macro.  The plan going forward is to eliminate that `table` `map` and force
output variables into `$CAPTURE`.
* Due to major changes to `dplyr`, now requiring `dplyr >= 0.5.0` (#69)
* The `data` slot in `mrgsims` objects is now `data.frame`
* The `knobs` function and `plot` method has been re-written.  Overall behavior
for most applications should be the same.

## Under the hood
* `C++` symbols for model functions are now stored in the model object
(`funs` slot)
* The status of the model object (function names and compile status) can be
checked with `mrgsolve:::funset(mod)`
* A model is considered to be loaded and ready to go if all functions in
`funs` can be found with `is.loaded`
* Model shared objects are still stored within the `soloc` directory (by
default `tempdir()`), but mrgsolve will create a subdirectory structure to
organize compilation artifacts.  The outer directory is keyed based on the
current mrgsolve version number and the computer platform.  Inner directories
are based on the model name (`model(mod)`).  
* A source file is created based on the `model` name and the shared object is
created based on that name.  If the compilation is successful, the shared
object (`.so` on mac/unix, `.dll` on Windows) is copied to a `.so` or `.dll`
file with a unique stem (e.g. `model2lj239wsfo.so`).  This unique shared object
is loaded into the `R` process for use with the model.  
* Every time the model is rebuilt, the build directory is scanned for shared
object files.  Excluding the main model shared object (unchanging name based
on the model), old shared object files are deleted and, if currently loaded
(`getLoadedDLLs()`), are attempted to be `dyn.unload`ed.
* Upon model rebuild (via `mread` or `mcode`), if there are no changes to the
source `.cpp` file, the source is not overwritten.  In that case, `make` will
not re-build the shared object.  Using the `preclean` argument will force
re-compilation (see `R CMD SHLIB`).
* The header files `modelheader.h` and `mrgsolv.h` are no longer copied into
the project directory.  But `CLINK_CPPFLAGS` environment variable is modified
to include `<path-to-mrgsolve-package>/inst/base` so that these may be linked.
* The `R CMD SHLIB` build process always uses `intern=TRUE` so that output is
suppressed on both `Windows` and `mac/unix`.  The user may still request to
view build output with the `ignore.stdout` argument.
* Model build always links-to the `project` directory to look for `C++` header
files.  When including a header file that may change from build to build,
always run with `preclean=TRUE`.
* mrgsolve now changes the working directory prior to building a model.  
The working directory is restored on exit from `mread`.

## Deprecated
* The entire `complog` system, including:
    * `comp_forget` a message is issued
    * `complog` no message is issued
* `trequest` argument to `mrgsim`


# mrgsolve 0.6.0

## Bugs fixed
* Fixed a bug when an infusion was attempted with `rate > 0` and `amt==0`.  
Additionally, an error is generated when an infusion is attempted with zero
`amt` (#43).

# mrgsolve 0.5.12

## Bugs fixed
* Fixed a bug where infusion dosing events with `evid 4` were not properly
implemented.  While investigating that issue, also found similar issue with
`evid 4` infusions getting scheduled with `addl` (#31).
* Removed NSE evaluation for arguments passed into  `ev` to avoid unintended
issues in evaluation (#29).

## New features
* Added `mcode` function as alternative to using `mread` when your model is
written in an `R` string.  Note the order of the arguments:
first `model`, then `code`, then `project`.  `project` defaults to `tempdir`.  
So the call is: `mod <- mcode("mymodel", code)`.  The
equivalent `mread` call is: `mod <- mread("mymodel", tempdir(),code)`.
* `carry.out()` and `Req()` now take `newname = oldname` as input.  Use this
syntax in `carry.out` when you want to copy a column from the input data set
into the simulated data set, changing the column to `newname` from `oldname`.  
Use this syntax in `Req` when you want to change the names of compartments or
output variables specified in `$TABLE` / `$CAPTURE`.
* Added `pkmodel` function for easy loading and simulating from 1- and
2-compartment models (#39).
* Added new code block: `$PKMODEL` for simulating PK model with analytical
solutions.  The main option for this block is `ncmt`, which picks the number
of compartments for the pk model.  See `?PKMODEL` for more information and
other options (#34).

## Under the hood
* Added `code` attribute to `mrgmod` objects.  The actual source code stays
with the model object. `see` was modified to look at `x@code` first when
showing the model code.
* Added a tokenizer function (`get_tokens`), a wrapper for the boost tokenizer)
to help checking the model specification file.
* Data items entered in `$FIXED` are now implemented as C++ preprocessor
directives by default rather than `const double` variables.  Use `$SET
fixed_type = "define"` or `$SET fixed_type = "const"` to select between
the approaches.


# mrgsolve 0.5.11
## Bugs fixed
* Added missing example model specification files (popExample, viralExample,
others)
* Added `mindt` attribute to `mrgmod` objects with default value of
`.Machine$double.eps*10`. When the problem includes an infusion, the
calculated end of the infusion may come too close to another record.  Usually
the solver will fail with the message `DLSODA- TOUT(=R1) too close to T(=R2)
to start integration.`.  To fix this, set `mindt` to be greater than zero but
small ... maybe 1E-12.  When `mindt` is greater than zero and `tto - tfrom`
(the times of two adjacent records) is less than `mindt`, mrgsolve will set
`tto` equal to `tfrom` (#9).
* `zero.re` didn't properly update the `$SIGMA` list when one matrix was
named and another was unnamed.  This has been fixed.  (#16)
* Fixed a bug where infusions with `ss`=1 caused mrgsolve/`R` to crash when
the infusion duration was equal to or some multiple of the dosing interval.
(#19)
* Fixed a bug where setting `F_CENT` to zero gave undefined behavior.  
mrgsolve will issue an error if `F_CMT` is set to zero and the `ss` flag is
set to 1. (#22)
* Fixed bug where dosing records with `evid=4` (reset the system and dose)  
and `addl > 0` reset the system for all subsequent doses. Additional doses
coming from records with `evid=4` will not do system reset. (#23)

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


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

# 0.5.001

## Bugs Fixed
* Fixed paths for project (`project`) and shared object (`soloc`) so that
"short" paths are used when compiling the model on Windows  platforms (#4).
* Fixed a bug where bioavailability fraction was not accounted for when
setting infusion duration in `$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).
* Fixed bug where parameters were not correctly read from first row of a
data set when certain `recsort` options were selected (#6).

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

## Important changes
* Changes to `recsort`: 1 and 2 will put explicit doses after observations at
the same time, 3 and 4 will put explicit doses before observations at the same
time.  2 and 4 will put doses scheduled through `addl` after observations at
the same time; 1 and 3 put doses scheduled through `addl` before observations
at the same tile.

## Under the hood
* Changed dosing lag time mechanism so that lag times are calculated as the
simulation progresses and dose times in the simulated output are as in the input
data
* Model shared objects are given random names every time the model is
compiled and loaded
* Various fixes and expansions to documentation
* Changed `R` dependency to `>= 3.1.2`
* All `Ops` involving `mrgmod` objects are now deprecated
* `loadso` now returns the model object (invisibly)
* Compartment names are automatically removed from table map
* Model specification files in need of compilation are detected via md5sum
* Minimum of 2 sec wait time is required before re-compiling a model
* Added `init` method with signature `mrgmod`,`ANY`, with `ANY` getting coerced
to `list`
