You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: NEWS.md
+75-5Lines changed: 75 additions & 5 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -1,23 +1,93 @@
1
1
# cmdstanr (development version)
2
2
3
+
* Chain IDs in generated filenames are now zero-padded to at least two digits,
4
+
for example `01` instead of `1`. (#1244)
5
+
* When using CmdStan through WSL, paths for output, diagnostic, profile, config,
6
+
and metric files now remain accessible to Windows R when an explicit output
7
+
directory is supplied. (#1110; related: #1113)
8
+
* Lists of matrices/vectors and data frames can now be supplied for variables
9
+
declared as `int` in the Stan program. Previously these worked only for `real`
10
+
variables and errored for `int` ones. (#817)
11
+
* Data frame columns that are not numeric, integer, logical, or
12
+
factor are now an error. Previously `data.matrix()` silently coerced them, so a
13
+
character column reached Stan as alphabetically ordered integer codes. Convert
14
+
the column explicitly, e.g. with `as.integer()`, if integer codes are what you
15
+
want. (#1225)
16
+
* Lists of logical vectors/matrices are now converted to integers like logical
17
+
variables are, instead of erroring. (#1225)
18
+
* Supplying a factor for a variable not declared as `int` is now an error. (#1225)
19
+
* Factors are now accepted for length-1 `int` arrays (e.g. `array[1] int x`),
20
+
which previously errored. (#1225)
21
+
* The `CMDSTANR_NO_VER_CHECK` R option and environment variable are deprecated
22
+
as of CmdStanR 1.0.0; use the lowercase `cmdstanr_no_ver_check` forms instead.
23
+
*`check_cmdstan_toolchain()` now locates Windows toolchains using `R_TOOLS_SOFT` and falls back to `PATH`, improving support for alternate R distributions and future Rtools releases. (#1211)
24
+
*`$compile()` now works with named `stanc_options` values such as
25
+
`canonicalize`. The values were shell-quoted for Make and the same quoted
26
+
strings were also passed to `stanc` directly, which rejected them. (#1227)
27
+
*`$compile()` now enables `allow-undefined` for user headers supplied through
28
+
`cpp_options`, not just through the `user_header` argument. (#1227)
29
+
*`stanc` failures during `$compile()` are now reported immediately, with the
30
+
`stanc` error message. Previously they surfaced several steps later. (#1227)
31
+
* Errors for include paths that do not exist now report the resolved absolute
32
+
path. (#1227)
33
+
* Numeric `stanc_options` values such as `list("max-line-length" = 78)` are no
34
+
longer dropped. (#1233)
35
+
* CmdStanModel methods now correctly handle `#include` directories with spaces
36
+
in their paths. (#820)
37
+
*`$include_paths()` now returns absolute paths, and relative include paths are
38
+
resolved when the model object is created or `$compile()` is called rather than
39
+
on each `stanc` call. Previously a model created from a relative path could
40
+
resolve `#include` directives against the wrong directory if the working
41
+
directory changed. (#1229)
42
+
*`$cpp_options()` no longer includes a `STAN_VERSION` entry read from the model
43
+
executable's metadata. It was never a C++ option; use `$cmdstan_version()` instead. (#1215)
44
+
* CmdStanModel methods now use executable metadata regardless of the
45
+
capitalization of C++ option names. Any executable reporting threading enabled
46
+
requires the corresponding `threads` or `threads_per_chain` argument. (#765, #1100)
47
+
* Pathfinder fits used as initial values now use uniform weights when CmdStan
48
+
already PSIS-resampled their draws, avoiding a second application of importance weights. (#1206)
49
+
* Pathfinder fits used as initial values now correctly treat draws with different
50
+
initialization parameter values as distinct even when their log weights are equal,
51
+
and collapse duplicate resampled draws while retaining their selection frequency. (#1207)
52
+
*`pathfinder()` now passes separately supplied initial values to every path
53
+
instead of using only the first path's initial values. (#1206)
3
54
*`pathfinder()` now respects `save_single_paths = TRUE` instead of always
4
55
passing `0` to CmdStan.
5
56
*`pathfinder()` now uses `threads` argument (`num_threads` is deprecated),
6
57
to be consistent with other methods.
58
+
* The `num_paths` documentation for `pathfinder()` now notes that running
59
+
multiple paths in parallel requires compiling with
60
+
`cpp_options = list(stan_threads = TRUE)` and setting `threads`. (#896)
61
+
* The `save_latent_dynamics` argument is now limited to `$sample()`,
62
+
`$sample_mpi()`, and `$variational()`, matching the CmdStan algorithms
63
+
that support diagnostic CSV output.
7
64
* Informative error when exposing functions using names that are reserved
8
65
keywords (@VisruthSK, #1154)
9
-
*`save_cmdstan_config` and `save_metric` default to `FALSE` but can be
66
+
*`save_cmdstan_config` and `save_metric` default to `FALSE` but can be
10
67
set to `TRUE` for an entire R session via new global options. (#1159)
11
-
*`cmdstan_model()` no longer fails when `MAKEFLAGS` enables directory-printing
68
+
* The compilation spinner can now be disabled for an entire R session by setting
69
+
the new `cmdstanr_spinner` global option to `FALSE`. The spinner shown while
70
+
installing or rebuilding CmdStan and while checking syntax also respects this
71
+
option, and is no longer shown when knitting. (#486)
72
+
*`save_metric_files()` now gives an informative error when metric files were
73
+
not created and keeps saved metric files after the fitted model is garbage-collected. (#1021)
74
+
*`cmdstan_model()` no longer fails when `MAKEFLAGS` enables directory-printing
12
75
output while reading `STANCFLAGS` from `make`. (#1163)
76
+
*`cmdstan_model()` now retains include paths when initialized with both a Stan file
77
+
and a precompiled executable (#1094).
78
+
*`$generate_quantities()` now also accepts `CmdStanMLE`, `CmdStanLaplace`,
79
+
and `CmdStanPathfinder` fitted model objects as `fitted_params`. (#1203)
80
+
*`$generate_quantities()` now reports per-process execution times with
81
+
CmdStan 2.39 or newer, and `read_cmdstan_csv()` returns these times from
0 commit comments