dformula |
[dynamiteformula ] The model formula.
See dynamiteformula() and 'Details'.
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data |
[data.frame , tibble::tibble , or data.table::data.table ]
The data that contains the variables in the model in long format.
Supported column types are integer , logical , double , and
factor . Columns of type character will be converted to factors.
Unused factor levels will be dropped. The data can contain missing
values which will simply be ignored in the estimation in a case-wise
fashion (per time-point and per channel). Input data is converted to
channel specific matrix representations via stats::model.matrix.lm() .
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time |
[character(1) ] A column name of data that denotes the
time index of observations. If this variable is a factor, the integer
representation of its levels are used internally for defining the time
indexing.
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group |
[character(1) ] A column name of data that denotes the
unique groups or NULL corresponding to a scenario without any groups.
If group is NULL , a new column .group is created with constant
value 1L is created indicating that all observations belong to the same
group. In case of name conflicts with data , see the group_var element
of the return object to get the column name of the new variable.
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priors |
[data.frame ] An optional data frame with prior
definitions. See get_priors() and 'Details'.
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backend |
[character(1) ] Defines the backend interface to Stan,
should be either "rstan" (the default) or "cmdstanr" . Note that
cmdstanr needs to be installed separately as it is not on CRAN. It also
needs the actual CmdStan software. See https://mc-stan.org/cmdstanr/ for
details.
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verbose |
[logical(1) ] All warnings and messages are suppressed
if set to FALSE . Defaults to TRUE . Setting this to FALSE will also
disable checks for perfect collinearity in the model matrix.
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verbose_stan |
[logical(1) ] This is the verbose argument for
rstan::sampling() . Defaults to FALSE .
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stanc_options |
[list() ] This is the stanc_options argument
passed to the compile method of a CmdStanModel object via
cmdstanr::cmdstan_model() when backend = "cmdstanr" .
Defaults to list("O0") . To enable level one compiler optimizations,
use list("O1") .
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threads_per_chain |
[integer(1) ] A Positive integer defining the
number of parallel threads to use within each chain. Default is 1 . See
rstan::rstan_options() and cmdstanr::sample() for details.
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grainsize |
[integer(1) ] A positive integer defining the
suggested size of the partial sums when using within-chain parallelization.
Default is number of time points divided by threads_per_chain .
Setting this to 1 leads the workload division entirely to the internal
scheduler. The performance of the within-chain parallelization can be
sensitive to the choice of grainsize , see Stan manual on reduce-sum for
details.
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custom_stan_model |
[character(1) ] An optional character string
that either contains a customized Stan model code or a path to a .stan
file that contains the code. Using this will override the generated model
code. For expert users only.
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debug |
[list() ] A named list of form name = TRUE indicating
additional objects in the environment of the dynamite function which are
added to the return object. Additionally, values no_compile = TRUE and
no_sampling = TRUE can be used to skip the compilation of the Stan code
and sampling steps respectively. This can be useful for debugging when
combined with model_code = TRUE , which adds the Stan model code to the
return object.
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mice_args |
[list() ]
Arguments passed to mice::mice() excluding data .
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impute_format |
[character(1) ] Format of the data that will be
passed to the imputation method. Should be either "wide" (the default)
or "long" corresponding to wide format and long format imputation.
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keep_imputed |
[logical(1) ] Should the imputed datasets be
kept in the return object? The default is FALSE . If TRUE , the
imputations will be included in the imputed field in the return object
that is otherwise NULL .
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stan_csv_dir |
[character(1) ] A directory path to output the
Stan .csv files when backend is "cmdstanr" . The files are saved here
via $save_output_files() to avoid garbage collection between sampling
runs with different imputed datasets.
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... |
For dynamite() , additional arguments to rstan::sampling() or
cmdstanr::sample() , such as chains and cores (chains and
parallel_chains in cmdstanr ). For summary() , additional arguments to
as.data.frame.dynamitefit() . For print() , further arguments
to the print method for tibbles (see tibble::formatting). Not used for
formula() .
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