pkgdown
stuff - not much more needs to be said here.pkgdown
website.data(cjs)
object.get_p()
became get_params()
match_p()
became match_params()
base_p()
became drop_index()
p
argument now accept a params
argument (match_params()
, diag_plots()
post_subset()
, post_summ()
, post_remove()
, vcov_decomp()
, etc.) (#14)p_summ
has been replaced with probs
in post_summ()
(#25)match_params
and get_params
now both take a type
argument, and both accept only values of "base_only"
or "base_index"
(#20 - some other function and arguments changed here as well).density_plot()
and trace_plot()
previously accepted a p_one
argument – this is now param
(distinction between multiple parameters and one parameter); but most users won’t notice this as these are non-exported functions.ins_regex_bracket()
, rm_regex_bracket()
, ins_regex_lock()
, and rm_regex_lock()
now take the params
argument rather than the string
argument, but most users won’t notice this.matrix2mcmclist()
was deleted and now post_convert()
does its job (#23).par()
after completing diag_plots()
(#17)StatonMisc
dependencies (#16)post_thin()
thin_percent
is not a perfect multiple of the number of iterations per chain - this causes the thinning to be “quasi-evenly” spaced. As this function is only ever used in code development and not final products, this should not be an issue (#13).thin_percent
to be keep_percent
, and implemented throughout.keep_iters
argument – now users can choose to keep either a fixed number of samples (again, may be quasi-equal to keep_iters
, due to rounding errors) or a fixed percent of samples.by_chain
argument to post_summ()
(#10)
post_summ(..., by_chain = TRUE)
. For now, Rhat, ess, and mcse will be ignored if by_chain = TRUE
.post_convert()
functionpostpack
requires (for the most part) that MCMC samples be stored in mcmc.list
objects. But not all R packages that perform MCMC return samples immediately in this format. This new function may help users get their samples into mcmc.list
format, potentially broadening the accessibility of the functions in this package.density_plot()
and trace_plot()
from exported listpost_remove
functionpost_subset
, except that it prompts the user to verify that they wish to exclude the match nodes and returns everything that does not match the p
argument.post_summ
(#11)auto_escape
option (#5)mcmc.lists
(#7, #9)
post_subset()
and post_thin()
previously used coda::as.mcmc.list()
to convert matrices to mcmc.list objects, however, if the matrix contained only one node, this would result in the mcmc.list no longer having a name for that node. Because most of the postpack functions rely on node names, this caused issues (e.g., diag_plots()
, post_bind()
).matrix2mcmclist
to perform this task, which should fix these issues.Bug fix when calculating Rhat
When calculating Rhat using post_summ(..., Rhat = T)
(which wraps coda::gelman.diag
) on an object containing only one node, an error would be thrown:
Error in data[1:nobs, , drop = FALSE] : incorrect number of dimensions
Which I tracked down to be a result of the autoburnin
argument being true by default. Being able to perform the calculations for only one node was required for the diag_plots(..., show_diags = T)
update. So I have forced this argument to be FALSE
in its usage within post_summ()
.
ins_regex_bracket()
rm_regex_bracket()
id_mat()
vcov_decomp()
: it now internally uses id_mat()
post_bind()
now allows one of the objects to be a matrix of derived quantities, but still requires that it has the same number of samples as the object it is being binded to.diags_plots(..., show_diags)
argument to display Rhat and ESS on the density plotmatch_p
now uses StatonMisc::list_out
to print the unique node names, which makes its printing much cleaner (#2)warn
argument from all functions that call match_p
prettify
argument to post_summ()
was removedpost_dim(..., kind)
was included in other functions including:
post_bind
post_thin
vcov_decomp
vcov_decomp
has improved error messages and relies on StatonMisc::progress_updater
to print the progress of the calculationpost_dim
improved to rely on StatonMisc::list_out
id_mat
functionbuild_vignettes = T
when installing from GitHub and several other simplifications to the readme since there is now a vignettepost_dim()
now accepts a kind
argument, which represents certain element(s) from the returned vector.vcov_decomp()
function
mcmc.list
object with these nodesdiag_plots
(#6)
diag_plots(..., layout = "2x1")
and diag_plots(..., layout = "4x2")
added, and the "auto"
option will now consider these when selecting the best option.write_model()
: I essentially duplicated R2OpenBUGS::write.model
because it was the only function I ever used from that package now all my BUGS models are fitted with JAGS.
post_dim
was counting the chain and iters columns as nodes (#1){codaTools}
to {postpack}
. This is a better name, because it is not just used for convergence diagnostics.get_nodes
and filter_post
: better error messagesformat = "matrix"
to matrix = T/F
argumentmatch_p
function - now all subsetting is handled by this one functionfilter_post
became post_subset
ins_regex_lock
, rm_regex_lock
, and base_p
- all intended to improve the behavior of diag_plots
StatonMisc
functions, they are now imported rather than requiring the whole package at the start of a function that needs themsumm_post
became post_summ
native_format
became array_format
get_nodes
became get_p
bind_post
became post_bind
thin_post
became post_thin
post_dim
diag_plots
through the my_title
functionthin_post
, native_format
bind_post
: combines two mcmc.list
objectsthin_post
: thins an mcmc.list
object at regularly-spaced intervals from each chain