

# bage 0.10.2

## Bug fix

* A test was leaving a file behind in the R_USER_CACHE_DIR. Problem
  fixed.
  
## vignettes

* Removed numbers from titles, and used pkgdown yaml, rather than
  numbers in front of files, to control the order of articles in the
  website.

# bage 0.10.1

## vignettes

* All but the first vignette have been changed to 'articles', so that
  they appear on the pkgdown-derived website on GitHub, but are not
  part of the package itself. Rebuilding the vignettes was taking too
  long, and checking times were exceeding CRAN limits.

## datasets

* Fixed bug in `prt_deaths` where deaths and population datasets had
  not merged properly.
* Fixed bug in `usa_deaths`, where the deaths column had class `"ts"`
  rather than `"numeric"`.
* Added a `datasets' overview page.


# bage 0.10.0

## Extending facilities for scaled SVD priors

* Added new scaled SVDs `CSA`, `HIMD_R`, `HIMD_P1`, `HIMD_P5`,
  `WMD_C`, `WMD_E`, for use in modeling school attendance, internal
  migration, and marriage. Also added help page for all scaled SVDs.
* Function `ssvd()`, for creating scaled SVDs is now
  exported. (Previously it was an internal function.)
* Version information has been added to scaled SVDs. Functions for
  creating SVD-based priors, such as [SVD()] and [SVD_AR()] now
  include an argument `v` that can be used to specify a version.
  
## Changes to interface

* `generate()` method for scaled SVDs now use the term `sex` rather
  than`sexgender` in results, for consistency with `components()`.
* `generate()` and `components()` methods for scaled SVDs now default
  to showing results disaggregated by sex/gender. Previously the
  default was to show results for the total population.


# bage 0.9.10

## Changes to internal calculations

* Covariates (as created by `set_covariates()` now use sparse rather
  than dense matrices, which has significantly speeded up
  computations, and reduced memory usage, for models with categorical
  covariates.
* Internal calculations for post-processing results from TMB have been
  refactored to speed them up, and reduce memory usage. (More outputs
  are built piece-by-piece rather than in one go.) Some large models
  now run significantly faster, and models that previously could not
  be fitted because of memory limitations now can.

# bage 0.9.9

## Changes to model behavior

* Up to version 0.9.8, `fit()` silently aggregated rows with
  duplicated values for the predictors (ie the variables to the right
  side of the `~` in the model formula. From 0.9.9 this aggregation
  only occurs with Poisson models where dispersion has been set to 0,
  or with Normal models. Even in these cases, aggregation no longer
  happens if the model includes a data model. In cases where
  aggregation would previously have occurred, `fit()` warns users
  about the behavior change. Thank you to Salah Merad for pointing out
  that the aggregation was leading to unexpected results.

## Changes to interface

* The `"inner-outer"` fitting method can now be used with models that
  include covariates.
* A function called `dispersion()` has been added, which returns prior
  or posterior values of the `disp` parameters. (Previously the only
  ways to obtain values of `disp` was to use function `components()`.)
  
# bage 0.9.8

## Changes to internal calculations

* The update of the TMB to version 1.9.18 appears to have changed
  outputs, which caused a test involving replicate data to fail. The
  test has been make more robust, by generating more draws.
  
## Bug fixes

* Function `unfit()` was not previously removing information on the
  `"inner-outer"` fitting method, making it appear that a model had
  been fit using this method, when it had in fact been re-fit using
  the standard method. This has been corrected.



# bage 0.9.7

## Changes to internal calculations

* The process for carrying out the Cholesky factorization and then
  drawing from the multivariate normal has been made more robust. When
  carrying out the Cholesky decomposition, small values are added to
  the diagonal at each failure, up to a limit that can be controlled
  by the user. Fallbacks (eg to using dense matrix calculations) have
  also been added to the function for generating multiple draws.

# bage 0.9.6


## Data models

* Added data models, also known as measurement error models. The main
  user-visible functions are `set_datamod_exposure()`,
  `set_datamod_miscount()`, `set_datamod_noise()`,
  `set_datamod_over()`, and `set_datamod_under()`. In introduction to
  data models is given in vignette 10. 

## Interface

* Extra checking of inputs for model constructor functions, eg
  checking that factors have at least two levels.

## Changes to internal calculations

* Improved efficiency of some C++ code in the TMB template, through
  greater use of call by reference.



# bage 0.9.5


## Interface

* Added method `n_draw()` for querying the `n_draw` value of a model
  object.
* Deprecated the use of formulas for specifying exposure, size, or
  weights. Formulas complicate measurement error models and forecasts.
  Formulas will be completely removed in future.
* In `replicate_data()`, changed the default for `condition_on` to
  `"fitted"` in cases where dispersion is zero, since the
  `"expected"` option is not permitted in these cases.
* Extra checking of inputs for model constructor functions, eg
  checking that factors have at least two levels.

## Documentation 

* Extended documentation of `Lin()` prior in Mathematical Details
  vignette, and on online help, to describe case where `s = 0`. Also
  updated description of prior in online help to match current
  implementation.
  
## Bug fixes

* Fixed bug in RR3, where values for rates were being calculated from
  confidentialized values of the outcome variable, rather than
  (imputed) true values.
* Fixed bug in aggregation of exposure for Poisson where `exposure =
  1`, and aggregation of weights in normal models where `weights = 1`.
  

# bage 0.9.4

## Interface

* Modified help for `mod_pois()`, `mod_binom()`, `mod_norm()` to
  clarify prior for dispersion. Added default value (of 1) to
  `set_disp()`. This does not affect behaviour, but is a bit clearer
  for users. (#94)
* In `set_covariates()`, added paragraph in online documentation to
  note that calling `set_covariates()` on a model that already has
  covariates deletes the existing covariates. Also added a warning
  message to `set_covariates()` when covariates being
  overwritten. (#95).
* `mod_pois()` emits message (not warning) if one or more rates are
  suspiciously high (which is often a sympton of inaccurate
  exposures.) (#96)
* Added a guarded version of `rpois_rvec()`, which sets x[i] equal to
  lambda[i] for lambda[i] > 1e8. This avoids numeric problems which
  can lead to valgrind errors. The guarded version is called by
  `augment()` and by `replicate_data()`. The user is warned when the
  threshold of 1e8 is exceeded.
  

## Bug fix

* Fixed bug in `set_n_draw()`, which was failing to thin covariate
  coefficient draws. (#97)
  


# bage 0.9.3

## Interface

* In the online help for `mod_norm()` and in the Mathematical Details
  vignette (vignette 2), give a new parameterisation of the
  `mod_norm()` model, expressed on the original scale, not the
  transformed scale (and closer to the paramterisation used by
  `mod_pois()` and `mod_binom()`.)

## Bug fix

* Modify the `bage_mod_norm` method for `replicate_data()` so that it
  returns results on the original scale.
* Modify the `bage_mod_norm` methods for the helper functions for
  `augment()` so that they properly incorporate weights.

# bage 0.9.2

## Interface

* Added `original_scale` argument to `components()`, to be used with
  normal models. Also added message remining users that, with normal
  models, components were on a log scale (#88)
* Added more information on progress.
* Tidied printing of model objects.
* Added new checks for outcome variable: no `NaN` and no `Inf`
  permitted.

## Bug fixes

* Fixed bug introducted when `fit_default()` refactored in 0.9.1. Bug
  meant that when optimizer switched from `nlminb()` to `optim()` on
  non-convergence, `optim()` was not starting from old parameter
  values.

## Documentation

* Added entry for `RW2_Infant()` to priors table. Hat-tip to Luke
  Morris for noticing that entry was missing. (#87)

  

# bage 0.9.1

## Changes to interface

* Added function `set_covariates()`. Models can now include
  covariates. Covariates are predictors other than the
  cross-classifying dimensions such as age, sex, or time -- though
  covariates can be formed from these dimensions.
* Added variables `gdp_pc_2023` and `dens_2020` to dataset
  `kor_births`.
* Added `prt_deaths` dataset.
* Added `set_seeds()` function, allowing users to reset random seeds
  (though this would be uncommon in normal use.)

## Changes to documentation

* Added covariates vignette.
  
## Changes to internal calculations

* More careful handling of `NA`s in offset and predictor variables.
  
  
# bage 0.9.0

* From 0.9.0 onwards we will use a formal deprecation make any
  breaking changes
* Tweaks to printing of `"bage_mod"` objects
* Started vignette replicating analyses from the book *Bayesian
  Demographic Estimation and Forecasting*

# bage 0.8.6

## Changes to interface

* Added `"multi"` option for `optimizer` argument to `fit()`. With
  `"multi"`, the `fit()` function first tries `nlminb()` and if that
  fails switches to `optim()` with method `"BFGS"`. 
* Added a warning if the calculations do not converge
* Modified the printout for `"bage_mod"` objects to show the time
  spent by `TMB::sdreport` rather than the time spent by drawing from
  the multivariate normal (which, since **bage** started using
  **sparseMVN**, is very short).
* Finished vignette 1.
* Added covariates
* Added `gdp_pc_2023` and `dens_2020` variables to `kor_births`



# bage 0.8.5

## Changes to internal calculations

* `report_sim()` excludes comparisons of `"hyper"` parameters (eg
  standard deviations) if the simulation model and estimation model
  use different priors with different classes for that term. For
  instance if the simulation model uses a `RW()` prior for age and the
  estimation model uses a `RW2()` prior for age, then `report_sim()`
  will not report on the standard deviation parameter for age.
* Added warning to documentation for `report_sim()` stating that the
  interface is still under development.

# bage 0.8.4

## Changes to interface

* Changed `zero_sum` argument to `con` (short for "constraint"). `con
  = "none"` corresponds to `zero_sum = FALSE`, and `con = "by"`
  corresponds to `zero_sum = TRUE`. Additional options will be added
  in future.
* Added `sd` argument to `RW()`, `RW2()`, `SVD_RW()` and
  `SVD_RW2()`. The initial value of the random walks are drawn from a
  `N(0, sd^2)` prior. By default `sd` equals `1`, but it can be set to
  0.
* Loosened restrictions in `AR()` and `Lin_AR()` priors so that the
  coefficients no longer need to be consistent with stationarity. The
  Stan user guide recommends against building in stationarity:
  https://mc-stan.org/docs/stan-users-guide/time-series.html#autoregressive.section
  Also, testing for stationarity often causes numerical problems.


# bage 0.8.3

## Changes to internal calculations

* Corrected bug in forecasting of `AR()` and `Lin_AR()` priors. 
* Modified prior for coefficients of `AR()` and `Lin_AR()` priors, so
  that partical autocorrelation function (PACF), rather than the AR
  coefficients themselves, are restricted to (-1, 1). Restricting the
  PACF to (-1,1) ensures stationarity.


# bage 0.8.2

## Changes to interface

* Check to see that model object was created using current version of
  'bage'.
* Added `optimizer` argument to `fit()`, giving choice between three
  ways of optimizing
* Modifed behaviour of `quiet` argument to `fit()` so that when it is
  `TRUE`, trace output from the optimizer is shown.
* Added `start_oldpar` argument to `fit()`, to allow calculations to
  be restarted on a model that has already been fitted.
* Modified printing of `"bage_mod"` object.


# bage 0.8.1

## Changes to interface

* Modified construction of `computations` part of models so that it
  works with models fitted using the "inner-outer" method. Extended
  the `print()` method for `"bage_mod"` so that it shows extra output
  for models fitted using the `"inner-outer"` method.


# bage 0.8.0

## Changes to interface

* Added 'along' column to tidy and print methods for `"bage_mod"`
  objects. (Thank you to Andrew Taylor for suggesting this.)
* Allow `s = 0` in `Lin()` priors
* Added `zero_sum` argument to priors with an `along` dimension. When
  `zero_sum` is `TRUE`, values for each combination of a `by` variable
  and the `along` variable are constrained to sum to zero. This can
  allow better identification of higher-level terms in complicated
  models. It can also slow computations, and has virtually no effect on
  estimates of the lowest-level rates, probabilities, and means.
* Removed post-estimation standardization. We now rely on explicit
  constraints instead to give interpretable values for main effects
  and interactions.
* Added `RW2_Infant()` prior for modelling age-patterns of mortality
  rates.
* The `s_seas` parameter in `RW_Seas()` and `RW2_Seas()` now defaults
  to 0, rather than 1, so that seasonal effects are by default fixed
  over time rather than varying. Using varying seasonal effects can
  greatly increase computation times.
* Moved **rvec** from Imports to Depends, so that it loads when
  **bage** is loaded. Manipulating results from **bage** models
  without **rvec** loaded can lead to strange errors.
* Added information on computations to printout from fitted model
  objects.
* Added function `computations()`, which can be used to extract this
  information from fitted model objects.
* Added `quiet` argument to `fit()`. When `quiet` is `TRUE` (the
  default), warnings generated by `nlminb()` are suppressed. (These
  warnings are virtually always about NAs early in the optimization
  process and are nothing to worry about.)

## Changes to internal calculations

* Removed some unnecessary coercion of sparse matrices to dense
  matrices (which could sometimes cause memory problems)
* Added extra constraints to some priors - eg the first element of
  random walks is now zero. This often (but not always) helps make raw
  estimates of main effects and interactions more interpretable, and
  can speed up computations slightly.
* In the normal model, we now rescale the weights so that they have a
  mean of 1. This allows us to use the same default prior
  for dispersion (an exponential prior with mean 1), regardless of the
  original weights. The rescaling of the weights affects the estimated
  value for dispersion, but does not affect the estimates for any
  other parameters.
* Generation of posterior sample now using fast methods from package
  **sparseMVN** where possible.
  

# bage 0.7.8

## Datasets

* Added `HFD`, a scaled SVD object holding data from the Human
  Fertiltiy Database
* Changed names of data objects:
  - `deaths` --> `isl_deaths`
  - `expenditure` --> `nld_expenditure`
  - `divorces` --> `nzl_divorces`
  - `injuries` --> `nzl_injuries`
  - `us_acc_deaths` --> `usa_deaths`
* Added new data object `kor_births`, births in South Korea


# bage 0.7.7

## Bug fixes

* `report_sim()` now works on fitted models. Thank you to Ollie Pike
  for pointing out that it previously did not.
* Removed redundant levels from `age` variable in `divorces`.

## Changes to internal calculations

* Removed internal **bage** function `rr3()`. Call **poputils**
  function `rr3()` instead.


# bage 0.7.6

## Changes to interface

* Added `newdata` argument to `forecast()`.
* Added minimum version numbers for **rvec** and **poputils**.


# bage 0.7.5.1

## Bug fixes

* Fixed bug in code for simulating from `Lin()` and `Lin_AR()` priors.


# bage 0.7.5

## Changes to interface

* Added arguments `method` and `vars_inner` to `fit()`. When
  `method` is `"standard"` (the default) `fit()` uses the existing
  calculation methods. When `method` is `"inner-outer"`, `fit()` uses
  a new, somewhat experimental calculation method that involves
  fitting an inner model using a subset of variables, and then an
  outer model using the remaining variables. With big datasets,
  `"inner-outer"` can be faster, and use less memory, but give very
  similar results.
* Added information on numbers of parameters, and standard deviations
  to output for print. Thank you to Duncan Elliot for suggesting
  printing numbers of parameters.
  
## Changes to calculations

* `fit()` now internally aggregates input data before fitting, so that
  cells with the same combinations of predictor variables are
  combined. This increases speed and reduces memory usage.
  
## Changes to documentation

* Added help for `print.bage_mod`

# bage 0.7.4

## Changes to interface

* Function `ssvd()` no longer exported. Will export once package
  **bssvd** matures.
* **bage** released on to CRAN


# bage 0.7.3

## Changes to data and examples

* Modified example for `augment()` so it runs faster
* Reduced size of `divorces` dataset


# bage 0.7.2

## Changes to interface

* Added first data model. New function is `set_datamod_outcome_rr3()`,
  which deals with the case where the outcome variable has been
  randomly rounded to base 3.
* `augment()` now creates a new version of the outcome variable if (i)
  the outcome variable has `NA`s, or (ii) a data model is being
  applied to the outcome variable. The name of the new variable is
  created by added a `.` to the start of the name of the outcome
  variable.
* A help page summarising available data models

# bage 0.7.1

## Changes to interface

* There are now three choices for the `standardization` argument:
  `"terms"`, `"anova"`, and `"none"`. With `"terms"`, all effects,
  plus assoicated SVD coefficients, and trend, cyclical, and
  seasonal terms, are centered independently. With `"anova"`, the type
  of standardization descibed in Section 15.6 of Gelman et al (2014)
  Bayesian Data Analysis, is applied to the effects.


# bage 0.7.0 

## Changes to calculations

* Further simplification of standardization, but likely in future
  to split into two types of standardization: one that gives an 
  ANOVA-style decomposition of effects, and one that helps with
  understanding the dynamics of each term.
  
## Changes to infrastructure

* Added Makevars file.

## Changes to documentation

* Stopped referring to second-order walks as equivalent to random
  walks with drift. (A second-order random walk differs from a random
  walk in that the implied drift term in a second-order random walk
  can vary over time.)


# bage 0.6.3

## Changes to calculations

* Changed standardization of forecasts so that forecasts are
  standardized along the 'along' dimension by choosing the values that
  makes them consistent with time trends in the estimation period, and
  then standardizing within each value of the along dimensions.



# bage 0.6.2

## Changes to interface

* Removed `SVDS()`, `SVDS_AR()`, `SVDS_AR1()`, `SVDS_RW()`, and
  `SVDS_RW2()` priors. Added `indep` argument to corresponding `SVD`
  priors. `SVD` priors now choose between 'total', 'independent' and
  'joint' models based on (1) the value of `indep` argument, (2) the
  value of `var_sexgender` and the name of the term.
  
## Changes to data

* Object `HMD` now contains 5 components, rather than 10.


# bage 0.6.1

## Changes to calculations

* Fixed problems with standardization of forecast
* Added an intercept term to `Lin()` and `LinAR()` priors

# bage 0.6.0

## Issues

* Standardization of forecasts not working correctly.

## Changes to interface

* Added priors `SVD_AR()`, `SVDS_AR()`, `SVD_AR1()`, `SVDS_AR1()`,
  `SVD_RW()`, `SVDS_RW()`, `SVD_RW2()`, `SVDS_RW2()`

## Internal calculations

* Changed values that are stored in object: removed `draws_linpred`, added
 `draws_effectfree`, `draws_spline`, and `draws_svd`. Modified/added
 downstream functions.
* Calculation of 'along_by' and 'agesex' matrices pushed downwards
  into lower-level functions.

# bage 0.5.1

## Changes to interface

* Moved HMD code to package **bssvd**.

# bage 0.5.0

## Changes to interface

* Combined interaction (eg ELin) and main effect (eg Lin) versions of
  priors
* Removed function `compose_time()`
* Added priors RWSeas and RW2Seas
* Improved `report_sim()`


# bage 0.4.2

## Changes to interface

* Tidying of online help (not yet complete).

# bage 0.4.1

## New functions

* Added 'bage_ssvd' method for `components()`.

## Changes to interface

* `augment()` method for `bage_mod` objects now calculated value for
  `.fitted` in cases where the outcome or exposure/size is NA, rather
  than setting the value of `.fitted` to `NA`.
  
## Internal calculations

* Standardization of effects only done if `components()` is
  called. `augment()` uses the linear predictor (which does not need
  standardization.)
* Internally, draws for the linear predictor, the hyper-parameters and
  (if included in model) `disp` are stored, rather than the full
  standardized components.
* Standardization algorithm repeats up to 100 times, or until all
  residuals are less than 0.0001.
* With the new configuration, calculations for large matrices that
  previously failed with error message "Internal error: Final residual
  not 0" are now running.
  
## Simulations

* When drawing from the prior, the intercept is always set to 0. Terms
  with SVD or Known priors are not touched. All other terms are
  centered.


# bage 0.4.0

## Changes to back-end for SVD priors

* Move most functions for creating 'bage_ssvd' objects to package
  'bssvd'.
* Allowed number of components of a 'bage_ssvd' object to differ from
  10.
  
## Bug fixes

* Corrected error in calculation of logit in `ssvd_comp()`.


# bage 0.3.2

## New functions

* `forecast.bage_mod()` Forecasting. Interface not yet finalised.

## Bug fixes

* Corrected error in C++ template for Lin and ELin priors (due to use
  of integer arithmetic.)

# bage 0.2.2

## New functions

* `generate.bage_ssvd()` Generate random age-sex profiles from SVD.

## Bug fixes

* Internal function `draw_vals_effect_mod()` was malfunctioning on models that contained SVD priors.
