A tool to provide an easy, intuitive and consistent access to
information contained in various R models, like model formulas, model
terms, information about random effects, data that was used to fit the
model or data from response variables. 'insight' mainly revolves
around two types of functions: Functions that find (the names of)
information, starting with 'find_', and functions that get the
underlying data, starting with 'get_'. The package has a consistent
syntax and works with many different model objects, where otherwise
functions to access these information are missing.
29 February 2020:
* Replaced deprecated functions from testhat framework in unit tests (contributed by Avraham Adler).
26 February 2020:
* Fixed warnings (as requested by CRAN): R CMD config variables 'CPP' and 'CXXCPP' are deprecated.
20 October 2018:
* Exposed CCSAQ algorithm in R interface (contributed by Julien Chiquet).
03 October 2018:
* Build process was changed to solve issues on several OS (many thanks to the CRAN maintainers).
4.1-1 CRAN
4.1 svyquantile() has been COMPLETELY REWRITTEN. The old version is available
as oldsvyquantile() (for David Eduardo Jorquera Petersen)
svycontrast()'s improvements for statistics with replicates are now also there with
svyby(), for domain comparisons (Robert Baskin)
svyttest() now gives an error message if the binary group variable isn't binary
(for StackOverflow 60930323)
confint.svyglm Wald-type intervals now correctly label the columns (eg 2.5%, 97.5%)
(for Molly Petersen)
svyolr() using linearisation had the wrong standard errors for intercepts
other than the first, if extracted using vcov (it was correct in summary() output)
svyglm() gave deffs that were too large by a factor of nrow(design). (Adrianne Bradford)
svycoxph() now warns if you try to use frailty or other penalised terms, because they
just come from calling coxph and I have no reason to believe they work correctly
in complex samples (for Claudia Rivera)
coef.svyglm() now has a complete= argument to match coef.default(). (for Thomas Leeper)
summary.svyglm() now gives NA p-values and a warning, rather than Inf standard errors,
when the residual df are zero or negative (for Dan Simpson and Lauren Kennedy)
In the multigroup case, svyranktest() now documents which elements of the 'htest'
object have which parts of the result, because it's a bit weird (for Justin Allen)
svycontrast() gets a new argument add=TRUE to keep the old coefficients as well
twophase() can now take strata= arguments that are character, not just factor
or numeric. (for Pam Shaw)
add reference to Chen & Lumley on tail probabilities for quadratic forms.
add reference to Breslow et al for calibrate()
add svyqqplot and svyqqmath for quantile-quantile plots
SE.svyby would grab confidence interval limits instead of SEs if vartype=c("ci","se").
svylogrank(method="small") was wrong (though method="score" and method="large" are ok),
because of problems in obtaining the at-risk matrix from coxph.detail. (for Zhiwen Yao)
added as.svrepdesign.svyimputationList and withReplicates.svyimputationList
(for Ángel Rodríguez Laso)
logLik.svyglm used to return the deviance and now divides it by -2
svybys() to make multiple tables by separate variables rather than a joint table
(for Hannah Evans)
added predictat= option to svypredmeans for Steven Johnston.
Fixed bug in postStratify.svyrep.design, was reweighting all reps the same (Steven Johnston)
Fix date for Thomas & Rao (1987) (Neil Diamond)
Add svygofchisq() for one-sample chisquared goodness of fit (for Natalie Gallagher)
confint.svyglm(method="Wald") now uses t distribution with design df by default.
(for Ehsan Karim)
confint.svyglm() checks for zero/negative degrees of freedom
confint.svyglm() checks for zero/negative degrees of freedom
mrb bootstrap now doesn't throw an error when there's a single PSU in a stratum
(Steve White)
oldsvyquantile() bug with producing replicate-weight confidence intervals for
multiple quantiles (Ben Schneider)
regTermTest(,method="LRT") didn't work if the survey design object and model were
defined in a function (for Keiran Shao)
svyglm() has clearer error message when the subset= argument contains NAs (for Pam Shaw)
and when the weights contain NAs (for Paige Johnson)
regTermTest was dropping the first term for coxph() models (Adam Elder)
svydesign() is much faster for very large datasets with character ids or strata.
svyglm() now works with na.action=na.exclude (for Terry Therneau)
extractAIC.svylm does the design-based AIC for the two-parameter Gaussian model, so
estimating the variance parameter as well as the regression parameters.
(for Benmei Liu and Barry Graubard)
svydesign(, pps=poisson_sampling()) for Poisson sampling, and ppscov() for
specifying PPS design with weighted or unweighted covariance of sampling indicators
(for Claudia Rivera Rodriguez)
4.0 Some (and eventually nearly all) functions now return influence functions when
called with a survey.design2 object and the influence=TRUE option. These allow
svyby() to estimate covariances between domains, which could previously only be
done for replicate-weight designs, and so allow svycontrast() to do domain contrasts
- svymean, svytotal, svyratio, svymle, svyglm, svykappa
Nonlinear least squares with svynls() now available
Document that predict.svyglm() doesn't use a rescaled residual mean square
to estimate standard errors, and so disagrees with some textbooks. (for Trent Buskirk)
3.38 When given a statistic including replicates, svycontrast() now transforms the replicates
and calculates the variance, rather than calculating the variance then using the
delta method. Allows geometric means to exactly match SAS/SUDAAN (for Robert Baskin)
vcov.svyrep.design to simplify computing variances from replicates (for William Pelham)
svykm() no longer throws an error with single-observation domains (for Guy Cafri)
Documentation for svyglm() specifies that it has always returned
model-robust standard errors. (for various people wanting to fit relative risk
regression models).
3.37 RODBC database connections are no longer supported.
Use the DBI-compatible 'odbc' package
set scale<-1 if it is still NULL after processing, inside svrepdesign()
[https://stats.stackexchange.com/questions/409463]
Added withPV for replicate-weight designs [for Tomasz Żółtak]
svyquantile for replicate-weight designs now uses a supplied alpha to get
confidence intervals and estimates SE by dividing confidence interval length
by twice abs(qnorm(alpha/2)). [For Klaus Ignacio Lehmann Melendez]
All the svyquantile methods now take account of design degrees of freedom and
use t distributions for confidence intervals. Specify df=Inf to get a Normal.
[For Klaus Ignacio Lehmann Melendez]
svyivreg() for 2-stage least-squares (requires the AER package)
warn when rho= is used with type="BRR" in svrepdesign [for Tomasz Żółtak]
Add "ACS" and "successive-difference" to type= in svrepdesign(),
for the American Community Survey weights
Add "JK2" to type= in svrepdesign
Warn when scale, rscales are supplied unnecessarily to svyrepdesign
More explanation of 'symbolically nested' in anova.svyglm
Link to blog post about design df with replicate weights.
Chase 'Encyclopedia of Design Theory' link again.
# tibble 3.1.4
## Features
- `as.data.frame.tbl_df()` strips inner column names (#837).
- `new_tibble()` allows omitting the `nrow` argument again (#781).
## Documentation
- Move `vignette("digits")`, `vignette("numbers")`, `?num` and `?char`
from the pillar package here (#913).
- Replace `iris` by `trees` (#943).
- Various documentation improvements.
- New `?tibble_options` help page (#912).
## Performance
- `x[i, j] <- one_row_value` avoids explicit recycling of the
right-hand side, the recycling happens implicitly in
`vctrs::vec_assign()` for performance (#922).
## Internal
- Vignettes are now tested with a snapshot test (#919).
- `new_tibble()` uses `vctrs::new_data_frame()` internally (#726,
@DavisVaughan).
- Adapt to pillar 1.6.2.
- Fix tests for compatibility with pillar 1.6.2.
# tibble 3.1.3
## Bug fixes
- `tbl[row, col] <- rhs` treats an all-`NA` logical vector as a
missing value both for existing data (#773) and for the right-hand
side value (#868). This means that a column initialized with `NA`
(of type `logical`) will change its type when a row is updated to a
value of a different type.
- `[[<-()` supports symbols (#893).
## Features
- `as_tibble_row()` supports arbitrary vectors (#797).
- `enframe()` and `deframe()` support arbitrary vectors (#730).
- `tibble()` and `tibble_row()` ignore all columns that evaluate to
`NULL`, not only those where a verbatim `NULL` is passed (#895,
#900).
- `new_tibble()` is now faster (#901, @mgirlich).
## Internal
- Establish compatibility with rlang > 0.4.11 (#908).
- Use `pillar::dim_desc()` (#859).
- Establish compatibility with testthat > 3.0.3 (#896, @lionel-).
- Bump required versions of ellipsis and vctrs to avoid warning during
package load.
(R CMD Rdconv -t txt math/R-robustbase/work/robustbase/inst/NEWS.Rd)
CHANGES in robustbase VERSION 0.93-8 (2021-06-01, svn r879):
NEW FEATURES:
* 'scaleTau2()' gets new optional 'iter = 1' and 'tol.iter'
arguments; mostly experimentally to see if or when iteration
makes sense.
* 'Qn(x, *)' gets new optional 'k = .' to indicate the
"quantile" i.e., order statistic to be computed (with
default as previously hard-coded).
Experimentally to try for cases where more than n/2
observations coincide (with the median), i.e., 'x[i] == x0
== median(x[])', and hence 'Qn(x)' and 'mad(x)' are zero.
* 'adjOutlyingness()' gets new option 'IQRtype = 7'.
Tweaks:
* For tests: *again* differences found in the non-sensical
'adjOutlyingness()' example (with large p/n, hence many
"random" values in the order of 1e15). Disable the test for
now (and record the result in *.Rout).
BUG FIXES:
* The 'test()' utility in 'tests/lmrob-ex12.R' no longer calls
'matrix(x, n,4)' where the length of x does not match '4n'.
Similar change in 'tests/mc-strict.R'
CHANGES in robustbase VERSION 0.93-7 (2021-01-03, svn r865):
NEW FEATURES:
* Use '\CRANpkg{.}' in most places, providing web links to the
respective CRAN package page.
* 'adjOutlyingness()' now gains optional parameters to be
passed to 'mc()'.
BUG FIXES:
* update the internal man page, so new 'checkRdContents()' is
happy.
* fix several '\url{.}''s that now are diagnosed as 'moved'.
* 'adjOutlyingness()' finally works with 'p.samp > p'.
* 'scaleTau2()' now works with 'Inf' and very large values,
and obeys new 'na.rm = FALSE' argument.
* add 'check.environment=FALSE' to some of the 'all.equal()'
calls (for 'R-devel', i.e., future R 4.1.x).
* 'wgt.himedian(numeric())' now returns 'NA' instead of
occasionally seg.faulting or inf.looping. Ditto for a case
when called from 'Qn()'.
CHANGES in robustbase VERSION 0.93-6 (2020-03-20, svn r854):
NEW FEATURES:
* 'splitFrame()' now treats 'character' columns also as
categorical (the same as 'factor's).
Tweaks:
* Small updates, also in checks for newer compiler settings,
e.g., 'FCLEN' macro; also F77_*() etc, in order to fix 'LTO'
issues.
* More careful or _less_ calling 'intpr()': correct "Rank" of
array (for gfortran/gcc 10, when '-fallow-argument-mismatch'
is not set).
2021-07-26 Tomoaki NISHIYAMA <tomoakin@staff.kanazawa-u.ac.jp>
* Change LICENCE to GPL-3
* import new config.guess and config.sub
* Drop an unused variable RS_PostgreSQL_closeManager_t
* Use seq_along() instead of seq(along=)
* -Wno-stringop-truncation for libpq compilation on windows
* Change Description for new version and license.
* fix type as pointed out by PR #109
* http to https transition for URLs
Version 2.5-2, 2021-08-20
* Support hdf5 filters via multi-filter interface (netcdf>=4.8.0)
* Windows: update binary packages to netcdf 4.7.4 with OpenDAP
* Generate type conversions with m4 macros
* Reduce CPU time for utcal.nc example to pass CRAN checks
pbkrtest v0.5.1 (Release date: 2021-03-09)
============================================
Changes
* Improved documentation
pbkrtest v0.5-0.0 (Release date: 2020-08-04)
============================================
Changes
* Satterthwaite approximation added via the SATmodcomp function.
* Checks for models being nested is not performed for parametric
bootstrap any longer. Reason is that the simr package use parametric
bootstrap for testing variance components being zero.
* doi added to DESCRIPTION file
pbkrtest v0.4-8.6 (Release date: 2020-02-20)
============================================
Bug fixes:
* documentation fixed ddf_Lb is now exported
* mclapply issue for windows fixed
* vcovAdj.lmerMod is exported to make emmeans work. Contact Russ Lenth
to make emmeans used generic function vcovAdj.
pbkrtest v0.4-8 (Release date: 2020-02-20)
==========================================
Bug fixes:
* Issue related to class() versus inherits() fixed.
Changes:
* NEWS file added
* NAMESPACE file is now generated automatically
Summarizes key information about statistical objects in tidy tibbles.
This makes it easy to report results, create plots and consistently
work with large numbers of models at once. Broom provides three verbs
that each provide different types of information about a model. tidy()
summarizes information about model components such as coefficients of
a regression. glance() reports information about an entire model, such
as goodness of fit measures like AIC and BIC. augment() adds
information about individual observations to a dataset, such as fitted
values or influence measures.
# tidyr 1.1.3
* tidyr verbs no longer have "default" methods for lazyeval fallbacks. This
means that you'll get clearer error messages (#1036).
* `uncount()` error for non-integer weights and gives a clearer error message
for negative weights (@mgirlich, #1069).
* You can once again unnest dates (#1021, #1089).
* `pivot_wider()` works with data.table and empty key variables (@mgirlich, #1066).
* `separate_rows()` works for factor columns (@mgirlich, #1058).
# tidyr 1.1.2
* `separate_rows()` returns to 1.1.0 behaviour for empty strings
(@rjpatm, #1014).
# tidyr 1.1.1
* New tidyr logo!
* stringi dependency has been removed; this was a substantial dependency that
make tidyr hard to compile in resource constrained environments
(@rjpat, #936).
* Replace Rcpp with cpp11. See <https://cpp11.r-lib.org/articles/motivations.html>
for reasons why.
# tidyr 1.1.0
## General features
* `pivot_longer()`, `hoist()`, `unnest_wider()`, and `unnest_longer()` gain
new `transform` arguments; these allow you to transform values "in flight".
They are partly needed because vctrs coercion rules have become stricter,
but they give you greater flexibility than was available previously (#921).
* Arguments that use tidy selection syntax are now clearly documented and
have been updated to use tidyselect 1.1.0 (#872).
## Pivoting improvements
* Both `pivot_wider()` and `pivot_longer()` are considerably more performant,
thanks largely to improvements in the underlying vctrs code
(#790, @DavisVaughan).
* `pivot_longer()` now supports `names_to = character()` which prevents the
name column from being created (#961).
```{r}
df <- tibble(id = 1:3, x_1 = 1:3, x_2 = 4:6)
df %>% pivot_longer(-id, names_to = character())
```
* `pivot_longer()` no longer creates a `.copy` variable in the presence of
duplicate column names. This makes it more consistent with the handling
of non-unique specs.
* `pivot_longer()` automatically disambiguates non-unique ouputs, which can
occur when the input variables include some additional component that you
don't care about and want to discard (#792, #793).
```{r}
df <- tibble(id = 1:3, x_1 = 1:3, x_2 = 4:6)
df %>% pivot_longer(-id, names_pattern = "(.)_.")
df %>% pivot_longer(-id, names_sep = "_", names_to = c("name", NA))
df %>% pivot_longer(-id, names_sep = "_", names_to = c(".value", NA))
```
* `pivot_wider()` gains a `names_sort` argument which allows you to sort
column names in order. The default, `FALSE`, orders columms by their
first appearance (#839). In a future version, I'll consider changing the
default to `TRUE`.
* `pivot_wider()` gains a `names_glue` argument that allows you to construct
output column names with a glue specification.
* `pivot_wider()` arguments `values_fn` and `values_fill` can now be single
values; you now only need to use a named list if you want to use different
values for different value columns (#739, #746). They also get improved
errors if they're not of the expected type.
## Rectangling
* `hoist()` now automatically names pluckers that are a single string (#837).
It error if you use duplicated column names (@mgirlich, #834), and now uses
`rlang::list2()` behind the scenes (which means that you can now use `!!!`
and `:=`) (#801).
* `unnest_longer()`, `unnest_wider()`, and `hoist()` do a better job
simplifying list-cols. They no longer add unneeded `unspecified()` when
the result is still a list (#806), and work when the list contains
non-vectors (#810, #848).
* `unnest_wider(names_sep = "")` now provides default names for unnamed inputs,
suppressing the many previous name repair messages (#742).
## Nesting
* `pack()` and `nest()` gains a `.names_sep` argument allows you to strip outer
names from inner names, in symmetrical way to how the same argument to
`unpack()` and `unnest()` combines inner and outer names (#795, #797).
* `unnest_wider()` and `unnest_longer()` can now unnest `list_of` columns. This
is important for unnesting columns created from `nest()` and with
`pivot_wider()`, which will create `list_of` columns if the id columns are
non-unique (#741).
## Bug fixes and minor improvements
* `chop()` now creates list-columns of class `vctrs::list_of()`. This helps
keep track of the type in case the chopped data frame is empty, allowing
`unchop()` to reconstitute a data frame with the correct number and types
of column even when there are no observations.
* `drop_na()` now preserves attributes of unclassed vectors (#905).
* `expand()`, `expand_grid()`, `crossing()`, and `nesting()` once again
evaluate their inputs iteratively, so you can refer to freshly created
columns, e.g. `crossing(x = seq(-2, 2), y = x)` (#820).
* `expand()`, `expand_grid()`, `crossing()`, and `nesting()` gain a
`.name_repair` giving you control over their name repair strategy
(@jeffreypullin, #798).
* `extract()` lets you use `NA` in `into`, as documented (#793).
* `extract()`, `separate()`, `hoist()`, `unnest_longer()`, and `unnest_wider()`
give a better error message if `col` is missing (#805).
* `pack()`'s first argument is now `.data` instead of `data` (#759).
* `pivot_longer()` now errors if `values_to` is not a length-1 character vector
(#949).
* `pivot_longer()` and `pivot_wider()` are now generic so implementations
can be provided for objects other than data frames (#800).
* `pivot_wider()` can now pivot data frame columns (#926)
* `unite(na.rm = TRUE)` now works for all types of variable, not just character
vectors (#765).
* `unnest_wider()` gives a better error message if you attempt to unnest
multiple columns (#740).
* `unnest_auto()` works when the input data contains a column called `col`
(#959).
version 0.9.8
- Fixed some issues on C-level causing problems with the
CLANG compiler. (Thanks to Brian Ripley for not only
reporting this, but also sending updated code with
fixes).
version 0.9.7
- Fixes in use of INTEGER() and VECTOR_ELT() after updates in R's C API.
this affected 'afind' and 'max_length' (internally). (Thanks to Luke
Tierny and Kurt Hornik for the notification).
- Fix in 'amatch' causing utf-8 characters to be ignored in some
cases (thanks to Joan Mime for reporting #78).
- Fix: segfault when 'afind' was called with many search patterns or many
texts to be searched.
- Fix: stringsimmatrix was not normalized correctly (Thanks to Tamas Ferenci
for reporting GH).
version 0.9.6.3
- Resubmit. Fixed an URL redirect that was detected by CRAN.
version 0.9.6.2
- Resubmit. Fixed url issues detected by CRAN, added doi to description
as per CRAN request.
version 0.9.6.1
- Bugfix: afind/grab/grabl returned wrong results on MacOS only.
(thanks to Prof. Brian Ripley for the notification and for running tests
on his personal machine and to Tomas Kalibera for making the
ubuntu-rchk docker image available).
version 0.9.6
- New function 'afind': find approximate matches in text based on string distance.
- New functions 'grab', 'grabl': fuzzy matching equivalent to 'grep' and 'grepl'.
- New function 'extract': fuzzy matching equivalent of stringr::str_extract.
- New algorithm 'running_cosine': fast fuzzy text search using cosine distance.
- New function 'stringsimmatrix' (Thanks to Johannes Gruber).
- Number of threads used is now reported when loading 'stringdist'.
- Internal fixes (in some cases class() == 'class' was used).
25 Aug 2020: Statmod 1.4.35
- Fix Bug in tweedie(link.power=0) so that the resulting functions
$linkinv() and $mu.eta() preserve the attributes of their
arguments.
16 Feb 2020: statmod 1.4.34
- Improve the model description provided in the remlscoregamma() help
page.
- tweedie() now checks whether `var.power` or `link.power` are
character strings instead of numeric. If `var.power` is one of the
standard family names ("gaussian", "poisson", "gamma" or
"inverse.gaussian") or `link.power` is one of the standard link
functions ("identity","log","inverse") then the argument is reset
to the corresponding numerical value with a message, otherwise an
informative error message is given.
- Cleaning up of internal code to avoid partial matching of function
arguments, attributes or list component names. The automatic package
tests are now run with the warnPartialMatchArgs,
warnPartialMatchAttr and warnPartialMatchDollar options all set to
TRUE.
4 Jan 2020: statmod 1.4.33
- The components returned by mixedModel2Fit() relating to fixed
coefficients are now documented explicitly. The help page has been
corrected to refer to the argument `only.varcomp` instead of
`fixed.estimates`. The vector of `reml.residuals` is no longer
part of the output.
- The test file has been slightly revised using zapsmall() so ensure
that the test output file remains correct for R with ATLAS BLAS.
# sandwich 3.0-1
* Extended the "Getting started" page with information on how to use _sandwich_ in
combination with the _modelsummary_ package (Arel-Bundock) based on _broom_
infrastructure (Robinson, Hayes, Couch). (Based on ideas from Grant McDermott.)
<https://sandwich.R-Forge.R-project.org/articles/sandwich.html>
* Catch `NA` observations in `cluster` and/or `order.by` indexes for `vcovCL()`,
`vcovBS()`, `vcovPL()`, and `vcovPC()`. Such missing observations cannot be
handled in the covariance extractor functions but need to be addressed prior
to fitting the model object, either by omitting these observations or by
imputing the missing values. (Raised by Alexander Fischer on StackOverflow
<https://stackoverflow.com/questions/64849935/clustered-standard-errors-and-missing-values>.)
* In `vcovHC()` if there are `estfun()` rows that are all zero and `type = "const"`,
then the working residuals for `lm` and `glm` objects are obtained via
`residuals()` rather than `estfun()`. (Prompted by an issue raised by
Alex Torgovitsky.)
# sandwich 3.0-0
* Release of version 3.0-0 accompanying the publication of the paper
"Various Versatile Variances: An Object-Oriented Implementation of
Clustered Covariances in R." together with Susanne Koell and Nathaniel Graham
in the _Journal of Statistcal Software_ at <https://doi.org/10.18637/jss.v095.i01>.
The paper is also provided as a vignette in the package as
`vignette("sandwich-CL", package = "sandwich")`.
* Improved or clarified notation in Equations 6, 9, 21, and 22 (based on
feedback from Bettina Gruen).
* The documentation of the HC1 bias correction for clustered covariances
in `vignette("sandwich-CL", package = "sandwich")` has been corrected (Equation 15).
While both the code in `vcovCL()` and the corresponding documentation `?vcovCL`
always correctly used (n-1)/(n-k), the vignette had incorrectly stated it as
n/(n-k). (Reported by Yves Croissant.)
* The package is also accompanied by a `pkgdown` website on R-Forge now:
<https://sandwich.R-Forge.R-project.org/>
This essentially uses the previous content of the package (documentation,
vignettes, NEWS) and just formatting was enhanced. But a few new features
were also added:
- A "Get started" vignette for the `pkgdown` page (but not shipped in the
package) providing an introduction to the package and listing all
variance-covariance functions provided with links to further details.
- R/Markdown overview vignettes for the `pkgdown` page (but also not shipped
in the package) linking the `Sweave`-based PDF vignettes so that they are
easily accessible online.
- A `README` with very brief overview for the `pkgdown` title page.
- A nice logo, kindly provided by Reto Stauffer.
* All kernel weights functions in `kweights()` are made symmetric around zero now
(suggested by Christoph Hanck). The quadratic spectral kernal is approximated
by `exp(-c * x^2)` rather than `1` for very small `x`.
* In case the `Formula` namespace is loaded, warnings are suppressed now for
processing formula specifications like `cluster = ~ id` in `expand.model.frame()`.
Otherwise warnings may occur with the `|` separator in multi-part formulas with
factors. (Reported by David Hugh-Jones.)
* The `bread()` method for `mlm` objects has been improved to also handle
_weighted_ `mlm` objects. (Suggested by James Pustejovsky.)
# rstudioapi 0.13
* Fixed an issue where `rstudioapi::insertText()` would fail. (#208)
# rstudioapi 0.12
* Fixed an issue where remote `rstudioapi` calls would erroneously use
a previous response in some cases.
* Allow `navigateToFile` to accept an empty file. This file will
default to the file currently in view in the active column.
* Added `registerChunkExecCallback` and `unregisterChunkExecCallback`,
used to execute a callback after a chunk is ran.
# NLopt Release Notes
## NLopt 2.6.2
15 April 2020
* Fixed forced stop exception with dimension elimination ([#317])
* Fixed `get_initial_step` wrapping ([#319])
* Various build fixes ([#314], [#308], [#303], [#278])
## NLopt 2.6.1
13 April 2019
* Fix `nlopt_version` result for 2.6.x and update soname.
## NLopt 2.6
12 April 2019
* New `nlopt_set_upper_bound` and `nlopt_set_lower_bound` functions in the low-level C API to set one bound at a time ([#257]).
* There is no longer a separate `libnlopt_cxx` library: C++ algorithms (STOGO and AGS) are compiled and included by default ([#198]).
* Various build fixes ([#197], [#216], [#245], [#250], [#230], [#261], etc.), other fixes ([#242], [#258]).
## NLopt 2.5
26 July 2018
* New AGS global solver ([#194]), thanks to Vladislav Sovrasov.
* New `nlopt_get_numevals` function providing a built-in evaluation counter ([#160]).
* New `nlopt_get_errmsg` function for more descriptive error messages.
* Build system is converted to `cmake` ([#49]), thanks to Julien Schueller
* Plugins updated for recent Octave and Guile versions.
* Various other build fixes and minor bug fixes.
(from: inst/NEWS)
CHANGES IN VERSION 0.11.1 (May 2021)
USER LEVEL CHANGES
-- Add information about categorical sampler and univariate version of ESS
sampler to `help(samplers)`.
BUG FIXES
-- Fix to the `posterior_predictive_branch` MCMC sampler, to update
the log-probabilities of the sampled posterior predictive nodes (PR #1127).
CHANGES IN VERSION 0.11.0 (April 2021)
USER LEVEL CHANGES
-- Add new `posterior_predictive_branch` MCMC sampler, which is
automatically assigned to trailing dependency node networks of entirely
non-data nodes (jointly posterior predictive branches). This sampler
simulates jointly from the predictive distribtion of these posterior
predictive node branches, and is designed to improve MCMC mixing of the
branch, and consequently of the entire model (PR #1086).
-- Allow use of elliptical slice sampler for univariate nodes, which can be
useful in multimodal problems (PR #1109).
-- Add a `getParents` method to the model API, allowing one to determine parent
nodes, analogous to use of `getDependencies` to determine child nodes
(PR #1094).
-- Add `getConditionallyIndependentSets` method (not yet documented) to the model
API, allowing one to determine nodes that are conditionally independent of
each other given parent nodes (PR #1094).
-- Improve efficiency of conjugate samplers by avoiding unneeded calculations
when a conjugate relationship does not involve shifting or scaling (PR #1087).
-- Allow use of `nimNumeric`, `nimMatrix`, `nimArray` in model code (PR #1096).
-- Add progress bar to `getSamplesDPmeasure` (NCT issue 110).
-- Allow model definition using `if` without `else`, fixing a longstanding
oversight (PR #1104).
-- Improve warning when multiple nodes provided to `getParam` (PR #1118).
-- Check during model building for unnamed elements of `data` and `inits`
(PR #1117).
-- Remove error trapping to prevent use of variables in defining node names,
such as `getDependencies('y[idx]')` as this is hard to check robustly and
efficiently (PR #1122).
-- Improve error messages when reporting `getParam` cannot calculate a parameter
when checking a model (PR #1112).
-- Error trap cases where model nodes are defined in two different declarations,
adding check for overlapping multivariate nodes (PR #1110).
-- Improve error trapping of mis-formed stochastic declarations in models
(PR #1106).
-- Increase maximum length of compiler output when using
`compileNimble(..., showCompilerOutput = TRUE)` (NCT issue 205).
-- Point to parallelization example on r-nimble.org in relevant places of manual.
BUG FIXES
-- Fix a bug (issue #1091) causing incorrect node names when having more than
100,000 elements in a vector node or in a dimension of a multi-dimensional
node (PR #1092).
-- Fix `getNodeNames` to return no nodes when `latentOnly` is `TRUE` and model
contains no latent nodes (PR #1116).
-- Fix checking for unknown nimbleFunction methods and improve related error
trapping (PRs #1107, #1105).
DEVELOPER LEVEL CHANGES
-- Update our testing code/infrastructure to use latest testthat API (PR #1090).
-- Shift internal code to use `model$calculate(...)` style rather than
`calculate(model, ...)` style for various node functions (PR #1114).
-- Clean up commented out code (PR #1098) and remove unused test files
(PR #1097).
-- Update to a newer (but not latest) version of Eigen to suppress some compiler
warnings (PR #1093).
CHANGES IN VERSION 0.10.1 (November 2020)
USER LEVEL CHANGES
-- Add `round` argument to `samplesSummary` (PR #1077).
-- `samplesSummary` function (and also `runMCMC(..., summary = TRUE)`) was made
to be robust against non-valid values in posterior samples array (PR #1075).
BUG FIXES
-- Fix `makeParamInfo` when there is only one declID involved to address a bug
affecting usage of `getParam`. This bug was introduced in version 0.10.0 when
reducing memory use of `getParam` (PR #1016). This fixes incorrect behavior
of conjugate samplers (because of incorrect inputs from `getParam`) under
certain model structures, in particular state-space style models (PR #1080).
-- Prevent usage of marginal version of WAIC (i.e., when not monitoring all
direct stochastic parents of data nodes); use of marginal version of WAIC in
previous versions gave incorrect results (PR #1083).
DEVELOPER LEVEL CHANGES
-- Deprecate `samplerAssignmnentRules` system (PR #1078).
-- Deprecate `autoBlock` MCMC option (PR #1079).
CHANGES IN VERSION 0.10.0 (October 2020)
USER LEVEL CHANGES
-- Greatly extend BNP functionality with the CRP (Chinese restaurant process)
distribution by allowing multiple observations to be grouped together (e.g.,
for longitudinal or time series data) without requiring they be specified
as a multivariate node (PR #1033).
-- Add a variety of conjugate cases to BNP conjugate samplers (PR #1033).
-- Greatly improve efficiency of model and MCMC building and configuration for
BNP-based models with CRP components (PR #1033).
-- Move all sequential Monte Carlo (SMC; aka particle filtering) methods to
new package `nimbleSMC`, including various particle-filter-based MCMC
samplers.
-- Prevent use of variables in indexes of nodes, such as `y[idx]`, which was
incorrectly being evaluated based on R scoping rules (PR #1064).
-- Allow use of `logdet` in model code (Issue #1018).
-- New `resetMV` argument available to `mcmc$run` method. In combination
with `reset = FALSE`, specifying `resetMV = TRUE` will continue the current
run of the MCMC, but discard any previously-collected samples
(PR #1051; thanks to 'DJRP').
-- New methods `setMonitors` and `setMonitors2` added for MCMC configuration
objects. These methods replace the current set of monitors (or monitors2)
with the specified variables (PR #1061).
-- Add `as.list` method for modelValues objects (PR #1060).
-- Update `getSamplesDPmeasure` function to improve efficiency and reduce
output size; output is now a list of matrices (PR #1059).
-- Add `dimensions` argument to `nimbleMCMC` (PR #1058).
-- Add method `getWidthHistory` to slice sampler to retrieve sampling history
information (PR #1057; thanks to 'rpatin').
-- Various improvements to the manual.
BUG FIXES
-- Fix a bug in k-fold cross-validation routine (`runCrossValidate`), where
the merging of MCMC sampler configurations was done incorrectly and causing
incorrect results (PR #1068).
-- Fix bug giving incorrect `dwish` density when using non-default S
parameterization (PR #1017).
-- Fix incorrect NaN eigenvalues in singular normalized adjacency matrices
under `dcar_normal` (PR #1019).
-- Update all MCMC sampler functions to use a new syntax for control list
element extraction, which prevents a possible bug caused by R's partial
matching of list names (PR #1065).
-- Define auto-generated simulation ('r') functions for user-defined
distributions in the global environment to avoid scoping issues (PR #1063).
-- Update user-defined distribution processing so user-defined distributions
can be defined inside functions (PR #1063).
-- Fix bug preventing use of `dirName` argument to `compileNimble` (PR #1062).
-- Fix a bug preventing model building when there are overly long names of
model variables resulting from long deterministic expressions in model code
(PR #1069).
-- Fix `buildMCEM` so it works with a compiled model as argument (PR #1028).
-- Fix `dmvt` so default unnamed parameters work (PR #1027).
-- Fix error in model building in corner case where
`makeVertexNamesFromIndexArray2` made a simplifying assumption to conclude
a block of nodes was contiguous (PR #1026).
-- Fix bug in `nimbleRcall` causing run-time warnings when `returnType` is void
(PR #1013).
DEVELOPER LEVEL CHANGES
-- Improve efficiency of `getParam` implementation, which improves speed for
MCMC compilation (PR #1016).
-- Improve MCMC sampling efficiency by not copying data nodes, only data node
logProbs, during sampler execution for various samplers (PR #1040).
-- Update Travis testing to use R 4.0.
-- Remove `GID_map` internal to modelValues (PR #1032).
-- Remove deprecated function `getLoadingNamespace` and (deprecated) use of
`where=getLoadingNamespace`. Also improve handling of environments set up
by `nimbleFunction` to make it easier to write packages depending on NIMBLE
(PRs #1029, 1011).
-- Force intermediates of index range expressions to be of type 'int' for use
in AD (PR #1024).
CHANGES IN VERSION 0.9.1 (May 2020)
USER LEVEL CHANGES
-- Switched from use of `system` to `system2` to avoid problems with installation
under R 4.0 on Windows (PR #1003).
-- Modify various adaptive MCMC samplers so the exponent controlling the scale
decay of the adaptation is adjustable by user (rather than hard-coded at 0.8
(PR #981).
-- Allow `pmin` and `pmax` to be used in models (PR #982).
-- Add documentation for `is.na`,`is.nan`,`any`,`all` (PR #988)
-- Add system option `MCMCuseConugacy` to control whether conjugate samplers are
used (PR #998).
-- Adds checks for `niter`, `nburnin` in the `mcmc$run` method (PR #980).
-- Modify print handling in `addSampler` and `configureMCMC` (PRs #986, 989).
-- Improve handling of NA values in `dCRP` to avoid error messages when building
models (PR #994).
-- Avoid monitoring top-level data nodes in models (PR #1006).
BUG FIXES
-- Modify MCMC `autoBlock` routine to only group Wishart, Inverse-Wishart, and
Dirichlet nodes with themselves, to avoid violating the constraints of those
nodes (PR #999).
-- Fix incorrect error message from `warnRHSonlyDynIdx` when variable appears
multiple times on right-hand side of a model expression (PR #997).
-- Fix `checkDistributionFunctions` to respect default `nDim=0` when extracting
first argument, to avoid error when dimension not specified in user-defined
distributions (PR #992).
-- Fix `print` option of `addSampler` (PR #986).
-- Improve handling of cases where indexing goes beyond extent of variable in
`expandNodeNames` and related queries of model structure (PR #977).
DEVELOPER LEVEL CHANGES
-- Use `inherits` rather than testing for equality of `class(object)` (PR #988).
Provides a high-level R interface to data files written using
Unidata's netCDF library (version 4 or earlier), which are binary data
files that are portable across platforms and include metadata
information in addition to the data sets. Using this package, netCDF
files (either version 4 or "classic" version 3) can be opened and data
sets read in easily. It is also easy to create new netCDF dimensions,
variables, and files, in either version 3 or 4 format, and manipulate
existing netCDF files. This package replaces the former ncdf package,
which only worked with netcdf version 3 files. For various reasons
the names of the functions have had to be changed from the names in
the ncdf package. The old ncdf package is still available at the URL
given below, if you need to have backward compatibility. It should be
possible to have both the ncdf and ncdf4 packages installed
simultaneously without a problem. However, the ncdf package does not
provide an interface for netcdf version 4 files.
2020-06-24: 2.0.1
R version requirement is reduced from 4.0.0 to 2.2.0
2020-06-24: 2.0.1
fixed a bug which effectively prevented using dmtruncnorm and dmtrunct with
an argument 'x' of vector type; various improvements in the documentation of
recintab and mom2cum.
2020-06-02: 2.0.0
support for the truncated versions of the multivariate normal and the t
distributions is introduced; for the truncated normal distribution,
functions recintab and mom2cum allow computation of corresponding moments
and cumulants; the latter function can also be used for obtaining the
cumulants of other distributions of which the moments are known.
2020-04-29: 1.5-7
improved R coding of sadmvn and sadmvt, with increased use of biv.nt.prob;
fixed a bug of pmnorm affecting a peculiar input set; a new function is
introduced: sample_Mardia_measures.
Importance sampling from the truncated multivariate normal using the
GHK (Geweke-Hajivassiliou-Keane) simulator. Unlike Gibbs sampling
which can get stuck in one truncation sub-region depending on initial
values, this package allows truncation based on disjoint regions that
are created by truncation of absolute values. The GHK algorithm uses
simple Cholesky transformation followed by recursive simulation of
univariate truncated normals hence there are also no convergence
issues. Importance sample is returned along with sampling weights,
based on which, one can calculate integrals over truncated regions for
multivariate normals.
HANGES IN VERSION 1.1-27.1:
USER-VISIBLE CHANGES:
* 'influence.merMod' allows user-specified starting parameters
* cleaned up performance vignette
BUG FIXES:
* 'cooks.distance' now works with objects computed by
'influence' method
* 'influence.merMod' now works with 'glmer' models using
'nAGQ=0'
* 'predict' (with new data) and 'simulate' methods now work
for models with >100 levels in a random effect grouping
variable (GH #631)
CHANGES IN VERSION 1.1-27 (2021-05-15):
USER-VISIBLE CHANGES:
* improvements from Lionel Henry (via
https://github.com/lme4/lme4/pull/587) to fix corner cases
in data checking; also resolves GH #601 (allFit scoping)
* 'getME(., "lower")' now has names (request of GH #609)
* improved detection of 'NaN' in internal calculations
(typically due to underflow/overflow or out-of-bounds linear
predictors from non-constraining link functions such as
identity-link Gamma models)
* 'influence.merMod' allows parallel computation
* the 'statmod' package is no longer required unless
attempting to simulate results from a model with an inverse
Gaussian response
BUG FIXES:
* long formulas work better in 'anova' headings (GH #611)
CHANGES IN VERSION 1.1-26 (2020-11-30):
BUG FIXES:
* 'predict', 'model.frame(.,fixed.only=TRUE)' work with
variable names containing spaces (GH #605)
* 'simulate' works when original response variable was logical
* 'densityplot' handles partly broken profiles more robustly
NEW FEATURES:
* 'thpr' method for 'densityplot()' (for plotting profiles
scaled as densities) gets new arguments
CHANGES IN VERSION 1.1-25 (2020-10-23):
* Set more tests to run only if environment variable
'LME4_TEST_LEVEL'>1
CHANGES IN VERSION 1.1-24 (never on CRAN):
USER-VISIBLE CHANGES:
* 'anova()' now returns a p-value of 'NA' if the df difference
between two models is 0 (implying they are equivalent
models) (GH#583, @MetaEntropy)
* speedup in 'coef()' for large models, by skipping
conditional variance calculation (Alexander Bauer)
* 'simulate.formula' machinery has changed slightly, for
compatibility with the 'ergm' package (Pavel Krivitsky)
* informational messages about (non-)convergence improved (GH
#599)
* improved error messages for 0 non-NA cases in data (GH #533)
NEW FEATURES:
* 'getME(.,"devfun")' now works for 'glmer' objects.
Additionally, 'profile'/'confint' for GLMMs no longer depend
on objects in the fitting environment remaining unchanged
(GH #589). This change also affects likelihood profiling
machinery; results of 'glmer' profiling/CIs may not match
results from previous versions exactly.
BUG FIXES:
* improved handling/documentation of 'glmer.nb' controls (GH
#556)
* 'predict' works better for 'gamm4' objects (GH #575)
* resolved some long-standing UBSAN issues (GH #561)
CHANGES IN VERSION 1.1-23 (2020-03-06):
This is primarily for CRAN compliance (previous submission was
retracted to allow time for downstream package adjustments).
* Some PROTECT/UNPROTECT fixes
CHANGES IN VERSION 1.1-22 (never on CRAN):
USER-VISIBLE CHANGES:
* prediction now works better for factors with many levels
(GH#467, solution by @sihoward)
* minor changes to argument order in '[g]lmerControl'; default
tolerance for convergence checks increased from 0.001 to
0.002 for 'glmerControl' (now consistent with 'lmerControl')
* 'lmer(*, family="<fam>")' is no longer valid; it had been
deprecated since 2013-06.
* 'lmer()', 'glmer()', and 'nlmer()' no longer have a formal
'...' argument. This defunctifies the use of a 'sparseX =
.' argument and will reveal some user errors, where
extraneous arguments were previously disregarded.
* In 'isSingular(x, tol)', the default tolerance ('tol') has
been increased from '1e-5' to '1e-4', the default of
'check.conv.singular' in 'g?lmerControl()'.
* for clarity and consistency with base R methods, some column
names of 'anova()' output are changed: "Df" becomes "npar",
"Chi Df" becomes "Df" (GH #528)
* 'simulate()' now works with inverse-Gaussian models (GH #284
revisited, @nahorp/Florian Hartig)
* single-model mode of 'anova()' now warns about unused
arguments in ... (e.g. 'type="III"')
* default tolerances for 'nloptwrap'/BOBYQA optimizer
tightened ('xtol_abs' and 'ftol_abs' were 1e-6, now 1e-8).
(To revert to former tolerances, use
'control=lmerControl(optimizer="nloptwrap",
optCtrl=list(xtol_abs=1e-6, ftol_abs=1e-6))'.)
BUG FIXES:
* improved checking for missing data (@lionel-)
* internal 'checkZrank()' should be able to deal with
('Matrix' package) 'rankMatrix()' returning 'NA'.
* 'allFit(fm)' now works for a model that had an explicit
'control = lmerControl(..)' call.
* internal 'getStart()' now works when model's 'start' was
specified as a list, and when called from 'drop1()' on a
submodel, fixing GH #521.
* internal function 'mkdevfun' now works even if there is an
extraneous 'getCall' function defined in the global
environment (GH #535)
* 'allFit()' works even if a variable with symbol 'i' is used
somewhere in the original model call (GH #538, reported by
Don Cohen); generally more robust
* 'glmer.nb' works even if an alternative version of
'negative.binomial' (other than the one from 'MASS') is
loaded in the workspace (e.g. by the 'GLMMadaptive' package)
(GH#516)
* 'level' argument is now honoured by 'confint(...,
type="boot", level=...)' (GH #543)
gtools 3.9.2 - 2021-06-03
-------------------------
Bug fixes:
- Fix missing man page and export for `combinations` and `permutations`.
Behind the scenes:
- Fixed more spelling/typographical errors, mostly in `NEWS.md`.
- Speed up `checkRversion` by removing checks for versions 2.x and 3.x.
gtools 3.9.1 - 2021-06-01
-------------------------
Bug fixes:
- Use valid HTTP request for example in `setTCPNoDelay` to prevent
errors when running tests.
Behind the scenes:
- Fixed numerous spelling/typographical errors.
- Update obsolete http URLs to https
gtools 3.9.0 - 2021-05-31
-------------------------
New functions:
- New `script_file` and `script_path` functions to obtain the
directory or full path to the currently executing script.
- New 'stat_mode` function to calculate the statistical mode (most
frequently occurring value).
- New `capwords` function to apply title capitalization rules to a
character vector.
- Move `baseOf` from `gplots` as requested by Steffen Möller. #2
New parameters:
- Add `scientific` parameter to `mixedsort` and `mixedorder` to
control whether numbers in scientific notation are recognized.
Resolved#7.
- Enhance `invalid` to detect `try-error` objects. #6
Bug fixes:
- Add support for R version 4 to `checkRVersion`. Resolved#5.
- Correct bug in `lastAdd` by explicitly checking for a `.Last` of
mode function.
Behind the scenes:
- Modernize package code by using `roxygen2` for documentation and
managing the NAMESPACE.
- Modernize C function registration.
- Replace http URLs with `https` and resolve broken links.
- Add github actions to automated testing
- Use pkgdown to generate HTML documentation.
- Use `styler` package to standardize R code formatting.
gtools 3.8.2 - 2020-03-23
-------------------------
Minor changes to support R 4.0
# version 2.0-7
* return `NA` as estimate when prediction/simulation fails; #80
# version 2.0-6
* fixes `object 'ret' not found` bug introduced by #63; #65#66#70
# version 2.0-5
* use multiple cores in `variogramST`, using pkg future; #63 by
@sigmafelix
* fix bug with conditional simulation using `stars` target grid and
nsim=1, #58
# version 2.0-4
* fix CRAN warning issue
# version 2.0-3
* fix bug in support for `sf` objects; #46
* fix `krigeTg` for the case when data or newdata are of class `sf` or
`sfc`; #51
(from inst/doc/CHANGES)
=====================================
CHANGES IN geoR VERSION 1.8-1
=====================================
Changes
o Removed the example in subarea() using geoRglm:::rongelap
ultil the package gets back to CRAN
o added reference to Diggle & Ribeiro (2007) on the description
file
Fixes
o no longer using attach() to address NOTE in CRAN checks
(it mostly affects image() persp() and countour() functions)
o no longer writing/assigning objects to the global environment
to address NOTE in CRAN checks
o Brain's changes in C code to address valgrind issues
=====================================
CHANGES IN geoR VERSION 1.7-5
=====================================
BUGS/Fixes
o call to sp::overlay changed to sp::over()
o changes to fix issues on CRAN reported errors/warnings
regarding namespaces and foreign calls
# energy 1.7-8
* User level changes:
- Poisson goodness-of-fit tests
- EVnormal (data) issue fixed
- gsl package required
* Internal changes
- mvnorm.e: use gsl::hyperg_1F1
- poisMstat in energy.c moved to Rcpp poisMstat.cpp
# energy 1.7-7
* User level changes:
- dcorT.test replaces dcor.ttest, now deprecated.
- dcorT replaces dcor.t, now deprecated.
- edist method "discoF" removed
* Internal changes
- BCDCOR function (used in the high dim. dcorT test) has been revised.
- edist method "discoB" correction
- changes for compatibility with R 4.0.0
(by R CMD Rdconv -t txt math/R-e1071/work/e1071/inst/NEWS.Rd)
Changes in version 1.7-8:
* Bugfixes in 'gknn()': wrong behavior in case of tied
k-nearest neighbors (for 'use_all=TRUE'), and also in case of
an overall class tie.
Changes in version 1.7-7:
* Bugfix in examples of 'cshell()'
Changes in version 1.7-6:
* Bugfix in 'scale_data_frame()' - now calls 'scale()' if x is
not a data frame.
Changes in version 1.7-5:
* NaiveBayes: better handling od character and logical features
* Added: 'gknn()' for generalized k-Nearest Neighbours (using
arbitrary proximity measures)
* Added: 'scale_data_frame()' for scaling the numeric columns
of a data frame.
Changes in version 1.7-4:
* Bug fix: "inverse" argument for class.weights argument in
'svm.default()' did not work
## Version 3.1.3 (September 2, 2021)
Patch release with miscellaneous fixes
* Fix undefined access of a vector when empty
* Require sphinx 4.0.3
* Build sphinx/doxygen docs with CMake
* Use PYIMATH_OVERRIDE_PYTHON_INSTALL_DIR to specify destination python modules
* Guard `__has_attribute` for compilers that don't support it
* Cuda safety fixes
* Replace stray Imath:: with IMATH_INTERNAL_NAMESPACE::
# dplyr 1.0.7
* `across()` uses the formula environment when inlining them (#5886).
* `summarise.rowwise_df()` is quiet when the result is ungrouped (#5875).
* `c_across()` and `across()` key deparsing not confused by long calls (#5883).
* `across()` handles named selections (#5207).
Changes in version 1.1-2 (2021-06-07)
o Miwa(n) now also works for non-zero mean|delta; n <= 4097, not 4098 (from C code);
optional 'checkCorr=' argument; documentation, one NOTE less.
Minimal C code cleanup.
mvt() <-> probval() simplification.
Handles +/-Inf as +/-maxval for non-orthrant probabilities (with a warning).
o TVPACK() now also works when some (but not all) bounds are (-Inf, Inf).
o mvtnorm() and mvt() now also return an attribute "algorithm" and gain optional
argument 'keepAttr' to allow returning bare numbers.
Changes in version 1.1-1 (2020-06-09)
o allow to turn-off symmetry checks (patch contributed by Feng Li <feng.li_at_cufe.edu.cn>
Changes in version 1.1-0 (2020-02-24)
o replace MVPHI and MVPHNV by calls to R's {p,q}norm5, following
a suggestion by Benjamin Christoffersen <boennecd_at_gmail.com>
Changes in version 1.0-12 (2020-01-06)
o fix Rdiff issues
Changes in version 1.0-11 (2019-06-19)
o improve documentation and error messages
Changes in version 1.0-10 (2019-03-04)
o eliminate warning when calling qmvt with arg sigma = 1
Changes in version 1.0-9 (2019-02-28)
o adapt to recent changes in r-devel
Changes in version 1.0-8 (2018-05-31)
o pmvt(..., sigma = ) was ignored in the univariate case
(reported by Alec Stephenson)
o documentation updates
Changes in version 1.0-7 (2018-01-25)
o pmvt(..., df = ) is scalar only
Changes in version 1.0-6 (2017-03-01)
o use registered C routines
Changes in version 1.0-5 (2016-02-02)
o improvements in quantile estimation
Changes in version 1.0-4 (2016-01-19)
o a new algorithm for quantile estimation, again. Quantiles are
now computed by a stochastic root finding algorithm. Note
that f.quantile in the output of qmv{t,norm} is now (again)
the squared difference between the cdf evaluated at the
quantile and the level. The \code{interval} argument to the
quantile functions is used as a starting value for the
root finder when available.
o clean-ups in C and R code and documentation
Changes in version 1.0-3 (2015-07-21)
o new algorithm for quantile estimation. Quantiles are
now computed by minimising the squared distance between the
distribution function and the probability whereas previous versions
used uniroot(). The procedure is now performed multiple times with
difference random seeds in order to stabilise the results. The
\code{interval} argument to the quantile functions is IGNORED now.
Changes in version 1.0-2 (2014-12-16)
o start providing C interfaces to the underlying algorithms.
mvtnorm_C_mvtdst() directly calls Alan's FORTRAN code and
can be used in other packages via LinkingTo. See
mvtnorm/inst/C_API_Example for an example very much inspired
by the example provided in package xts.
o provide .C interfaces to the FORTRAN routines and allow switching
on/off of R' RNG.
Changes in version 1.0-1 (2014-11-11)
o replace internal MVCHNV FORTRAN FUNCTION with
R's sqrt(qchisq(p, n, FALSE, FALSE). This fixes a
problem where NaN was returned as reported by
David Charles Airey <airey_david_charles_at_lilly.com>
Changes in version 1.0-0 (2014-07-08)
o After 14 years, we now feel safe enough to publish mvtnorm 1.0-0.
Many packages depend, import, or suggest mvtnorm, so this version
change also indicates that the package is now stable and, to a very
large extent, the API is frozen. We will of course continue to fix
bugs or other problems but new features are unlikely to go into this
package.
o use Authors@R in DESCRIPTION
o switch to standard NEWS format
Changes in version 0.9-99992 (2014-05-03)
o cleanups by MM
Changes in version 0.9-99991 (2014-04-25)
o version 0.9-9999 introduced new bug in dmvnorm
Changes in version 0.9-9999 (2014-04-17)
o dmvnorm (again) returns NaN in case sigma is not decomposable
Changes in version 0.9-9998 (2014-03-21)
o faster code for dmvnorm by Matteo Fasiolo <mf364 at bath.ac.uk>
Changes in version 0.9-9997 (2014-01-17)
o T. Miwa fixed a runtime error in miwa.c reported by UB sanitizer
Changes in version 0.9-9996 (2013-09-16)
o documentation updates/corrections/examples by Marius Hofert
o df = Inf
o rmvt(): argument 'mean' not allowed anymore (prone to misuse)
o pmvnorm(lower=c(-Inf, 0, 0), upper=c(0, Inf, Inf),
mean=c(0, 0, 0), sigma=S, algorithm = Miwa())
returned NaN, fixed by Xuefei Mi
Changes in version 0.9-9995 (2013-05-29)
o update to version 2013-06-29 of mvtdst.f from Alan's website
(fixed a bug for 2-dim pmvt)
Changes in version 0.9-9994 (2012-12-06)
o set.seed(29)
rmvnorm(10, ...)
produces the same first ten rows as
set.seed(29)
rmvnorm(100, ...)
o as suggested by Paul Johnson <pauljohn_at_ku.edu>. There is a new
argument pre0.9_9993 for changing back to the `old' output. This
_DOES NOT_ apply to rmvt.
Changes in version 0.9-9993 (2012-10-22)
o sigma is called `scale' matrix of {dpq}mvt, thanks to
Richard Boys <Richard.Boys_at_ncl.ac.uk> for the hint
Changes in version 0.9-9992 (2012-01-19)
o qmvt(..., df = 0, ...) gave NaN
o R CMD check works on x64 with GCC 4.6.2 (Debian 4.6.2-11)
Changes in version 0.9-9991 (2011-06-10)
o tvpack wasn't working on 64bit machines. The reason
was that the wrapper SUBROUTINEs around the original
FUNCTIONs didn't return the appropriate double precision
for unknown reasons. Redefining TVTL and BVTL as FUNCTIONs
fixed the problem.
Changes in version 0.9-999 (2011-04-26)
o still problems in fix approx_interval (when !is.null(sigma));
disable for the time being
Changes in version 0.9-99 (2011-04-21)
o fix bug in approx_interval spotted by Ravi Varadhan
<rvaradhan_at_jhmi.edu>
Changes in version 0.9-98 (2011-04-19)
o allow ... to pass arguments to rmvnorm in rmvt
Changes in version 0.9-97 (2011-01-31)
o use check.attributes = FALSE in isSymmetric calls
(requested by Nick Sabbe <nick.sabbe_at_ugent.be>)
Changes in version 0.9-96 (2011-01-28)
o use fixed interval when sigma is specified in qmvt
Changes in version 0.9-95 (2010-11-18)
o q{mvt,mvnorm} shall always return a list, not a vector
checks for correlation matrices are less picky now
Changes in version 0.9-94 (2010-11-16)
o allow for two different noncentral t distributions (via type
argument)
o add support for one-dimensional quantiles (requested by Jerry Lewis
<jerry.lewis_at_biogenidec.com>)
o documentation fixes for problems spotted by
Jerry Lewis <jerry.lewis_at_biogenidec.com>
o interface to Alan's TVPACK algorithms for 2- and 3-d
probabilities by Bjoern Bornkamp added.
Changes in version 0.9-92 (2010-07-06)
o update to new mvtdstpack.f (7/10) by Alan. Fixes
potential bias problem in higher dimension.
Changes in version 0.9-91 (2010-04-13)
o better search interval for uniroot in qmv{t,norm} speeds up
quantile estimation; suggestion by Björn Bornkamp
<bornkamp_at_statistik.tu-dortmund.de>
Changes in version 0.9-9 (2010-01-27)
o document ... in pmvt.Rd
Changes in version 0.9-8 (2009-10-27)
o add citation entry
Changes in version 0.9-7 (2009-05-22)
o make sure `error' is not NA
Changes in version 0.9-6 (2009-03-25)
o update Alan's FORTRAN code
Changes in version 0.9-5 (2009-03-17)
o fix FORTRAN bug spotted by Alex Lenkoski
<lenkoski_at_stat.washington.edu>
Changes in version 0.9-3 (2008-12-22)
o update meta data
Changes in version 0.9-2 (2008-07-08)
o be a little more liberal (tol = sqrt(.Machine$double.eps))
when testing for symmetry of covariance matrices
(and make R CMD CHECK monomvn happy again)
Changes in version 0.9-1 (2008-07-02)
o better check for covariance matrices, suggested by
James Rogers <James.A.Rogers_at_pfizer.com>
Changes in version 0.9-0 (2008-04-01)
o add support for the multivariate normal distributions in small
dimensions by Miwa's method thanks to Tetsuhisa Miwa and Xuefei Mi;
both have been added as `authors'.
o new argument `algorithm' defaulting to `GenzBretz()' with
`Miwa()' being the alternative. Those two functions are now used
to specify hyper parameters such as `abseps'.
o internal function `mvt' is no longer exported.
Changes in version 0.8-3 (2008-02-19)
o make sure rmvnorm(1, sigma = matrix(0.5, 1, 1)) works
(reported by Kurt Hornik)
Changes in version 0.8-2 (2008-02-10)
o rmvnorm() now issues a warning for non-symmetric sigma and uses
the eigenvalue decomposition as default.
o make gfortran 4.3 happy
Changes in version 0.8-1 (2007-07-24)
o Orion Poplawski <orion_at_cora.nwra.com> spotted a meaningless check in
the regression tests
Changes in version 0.8-0 (2007-07-23)
o upgrade to 7/7 version of MVTDST (includes better support for
dimensions > 100). Thanks to Karen Conneely <conneely_at_umich.edu>
for motivating the update and for checking the new version.
o rmvnorm() now can also use a Cholesky decomposition to compute
the root of sigma (thanks to Fabian Scheipl)
Changes in version 0.7-5 (2006-09-15)
o fix problem reported by valgrind
Changes in version 0.7-4 (2006-09-08)
o add long requested `dmvt'
o call RNG functions only one time
o make sure unifrnd is double precision
Changes in version 0.7-3 (2006-08-23)
o make sure pmvnorm(lo=c(-Inf,-Inf), up=c(Inf,Inf), mean=c(0,0) == 0
Changes in version 0.7-2 (2005-08-29)
o make gfortran happy (a warning about unused variable NF remains)
Changes in version 0.7-1 (2004-11-18)
o use #!/bin/sh
Changes in version 0.7-0 (2004-10-14)
o a coding session with Frank produced `qmv{t,norm}'.
try to check if the support specified by `lower' and `upper' is
empty (problem spotted by Peter Thomson <peter_at_statsresearch.co.nz>)
Alan's fix prevents negative values to be returned.
o some cosmetics
Changes in version 0.6-8 (2004-06-03)
o EXIT statements are not supported by `f2c', Alan added GOTO
statements to `MVCHNC'
Changes in version 0.6-7 (2004-05-27)
o Alan's fix to MVCHNC solves problems with large degree of freedom
Changes in version 0.6-6 (2004-01-22)
o `La.eigen' is deprecated and `eigen' replaces it in R-1.9.0
Changes in version 0.6-5 (2003-11-14)
o check if covariance matrix is pd in rmvnorm (by Fritz Leisch)
Changes in version 0.6-4 (2003-10-06)
o use new base function `cov2cor'
Changes in version 0.6-3 (2003-07-21)
o Alans changes were restricted to N <= 100, now N <= 1000
are possible again
Changes in version 0.6-2 (2003-06-25)
o Alan's recent changes to `mvt.f' make `g77 -pedantic -Wall'
happy
Changes in version 0.6-1 (2003-06-18)
o pmvt(..., df = 0, ...) will return normal probabilities for both
the univariate and multvariate problem
Changes in version 0.6-0 (2003-06-17)
o Fortran code in `mvt.f' updated to recent version by Alan and Frank.
This fixes problems with `pmvt' and large degrees of freedom.
Changes in version 0.5-15 (2003-06-16)
o a note on one-sided probabilities in `pmvt'
correlation matrices in cats example a little bit nicer
Changes in version 0.5-14 (2003-05-06)
o the package owns a vignette based on the paper in RNews 1(2)
Changes in version 0.5-12 (2003-05-08)
o allow df=0 for pmvt
Changes in version 0.5-11 (2003-04-29)
o package npmc trys to use 'mvt' which is internal: export it anyway
Changes in version 0.5-10 (2003-04-23)
o mvtnorm is now in a NAMESPACE
Changes in version 0.5-9 (2003-02-13)
o log argument added to dmvnorm, thanks to
Jerome Asselin <jerome_at_hivnet.ubc.ca>
Changes in version 0.5-8 (2003-01-21)
o fixed bugreport PR#2478: sigma for univariate probabilities
Changes in version 0.5-7 (2002-11-27)
o use R's random number generator in the FORTRAN code:
set.seed has now has the desired impact.
Changes in version 0.5-6 (2002-10-07)
o rmvt added
Changes in version 0.5-5 (2002-07-03)
o use .Fortran(..., PACKAGE="mvtnorm")
Changes in version 0.5-4 (2002-04-09)
o correlation matrices for sigma with unequal variances incorrectly
computed, added `sig2corr' for that propose, tol argument removed,
fix by Alan to mvt.f
Changes in version 0.5-2 (2002-03-22)
o Frank added `tol' argument to MVTDST, now in mvtnorm
Changes in version 0.5-1 (2002-01-24)
o pmvt(0,1) works now
Changes in version 0.5-0 (2001-12-10)
o release for R-1.4.0
Changes in version 0.4-4 (2001-12-06)
o bugfix
Changes in version 0.4-3 (2001-12-05)
o the length of lower, upper and mean (delta) is now recycled to the
length of the largest, i.e. it is possible to say
pmvnorm(lower=-Inf, upper=1, mean=rep(1,10), corr=diag(10))
Changes in version 0.4-2 (2001-12-04)
o several typos, man-pages improved
Changes in version 0.4-1 (2001-12-04)
o interface changed: sigma (covariance matrix) can be specified as
well
o {rd}mvnorm added from package e1071 (thanks to Fritz!)
Changes to Version 3.0-11
o boxCox() function now allows the use of any of the usual graphics
parameters in the plot() function. If particuar boxCox(model,
main="my title") will add a title to the plot, and boxCox(model,
main="") will suppress it.
o car::Boot(object, method="residual") will work for
method="residual" only if the car package has been previously
attached via either library(car) or require(car).
o Added error checking with vcov. argument. Changed vcov.boot to
print a warning of bootstrap replicates that returned NA
o Introduced brief.tbl(), which simply calls print(), to cope with
changes to tibbles.
o qqPlot() fills (shades) confidence envelopes by default, and
smoothers for scatterplots fill variance (spread) envelopes by
default (suggestions of Michael Friendly).
o Fixed problem in infIndexPlot.influence.lme() (reported by Francis
L. Huang).
o New "polr" and "svyolr" methods for vif() (following report by
Abra Jeffers).
o Make linearHypothesis() and Anova() work with "svyolr" objects via
their default methods.
o Regularize handling of vcov. argument in Anova() and
linearHypothesis().
o vcov. argument now works with Anova() for models produced by
lme4::lmer() and glmer(), (fixing a bug reported by Amy MacDougall).
o New linearHypothesis.lmList() method.
o New "lm" method for symbox().
o New cex and pt.wts arguments for avPlot() "lm" and "glm" methods,
and for mcPlot.lm().
o Fix handling of imatrix argument to Anova.mlm() (suggestion of
Benedikt Langenberg).
o Remove influence.merMod() and related methods in favor of versions
of these methods in the lme4 package.
o Rewrite "embedding" vignette.
o Small fixes and improvements.
Added math/R-hexbin version 1.28.2
Added devel/R-R.methodsS3 version 1.8.1
Added devel/R-R.utils version 2.10.1
Updated graphics/R-latex2exp to 0.5.0
Updated math/R-compositions to 2.0.2
Added devel/R-R.oo version 1.24.0
Added math/R-sets version 1.0.18
Added math/R-stat.extend version 0.1.4
Updated graphics/R-ggplot2 to 3.3.5
Updated graphics/R-ggtern to 3.3.5
Highest Density Regions are the smallest set in the support of a
probability distribution with the specified coverage probability.
'HDRs' may contain disjoint intervals, but can be calculated
efficiently using iterative methods. One can similarly construct
optimal (i.e., shortest) confidence intervals for some basic
inferential problems, including for population means, variances, or
proportion parameters.
Data structures and basic operations for ordinary sets,
generalizations such as fuzzy sets, multisets, and fuzzy multisets,
customizable sets, and intervals.
Version 2.0-1.9001
Minor changes / Bugfixes:
* functions that do not work with sticky classes are now wrapped
(e.g. `anova()`)
Version 2.0-1.9000
Major change: sticky classes!
Now objects of compositional classes do not miss their class
when subsetting. For example, if `x` is an "acomp" object,
x[1:2,] will also be an "acomp" object. Selection of columns work
as well, but it is a bit more tricky. Check ?`[.acomp` for
details. You can get skip this behaviour by setting
setStickyClassOption(FALSE). The dollar notation `$` also works!
Added:
* Limited support for using compositions classes as formal S4
classes, for instance in slots of S4 classes expecting a
"data.frame" or a "structure" (matrix or array).
* self-invertibility: now "rmult" objects created by any
transformation (cdt, clr, cpt, idt, ilr, ipt, iit, ilt, alr,
apt) remember the original data and the transformation between
them, and can be back-transformed with `backtransform`.
* added cdt and idt methods for objects of class "factor" (returning
the contrasts and their ipt transformation), and for "data.frame"
objects (exploiting the attribute "origClass" if they have it).
* `pwlr()`: pairwise logratio transformation (and inverse: `pwlrInv()`)
* `pwlrPlot()`: pairwise logratio plots vs covariables, both as explained
and as explanatory variables. This makes use of the ability of plot(x~y)
to react to the nature of `x` and `y` to create scatterplots, boxplots
and spineplots.
* transformation functions between variation and clrvar: variation2clrvar
and clrvar2variation
* `split()` methods for compositional classes
* new panels for filling `pairs()` plots with boxplots, densities,
kde2d-densities, etc...: check ?vp.kde2dplot
Minor Changes:
* the function to fit linear models of coregionalisation is now called
`fit.lmc()`; use full name specification with it! `compositions::fit.lmc()`
Bugfixes:
* bug in subsetting of one-column rmult object corected
## Version 3.1.2 (July 31, 2021)
Patch release that fixes a Windows header issue.
* Improve handling of ``#include <*intrin.h>``
## Version 3.1.1 (July 20, 2021)
Patch release that fixes a build failure on ARM64 macOS
## Version 3.1.0 (July 13, 2021)
Minor release with new features:
* Optimized half-to-float and float-to-half conversion, using F16C SSE
instruction set if available. Non-SSE conversion eliminates the
float-to-half exponent lookup table, and half-to-float conversion
provides a compile-time-optional bit shifting that is slower but
eliminates the need for the lookup table, for applications where
memory is limited.
Half-to-float and float-to-half conversion is also available as
C-language functions ``imath_half_to_float()`` and
``imath_float_to_half()``.
All new conversions produced identical results, and new options are
off by default to ensure backwards compatibility. See
https://imath.readthedocs.io for more info.
* NOEXCEPT specifier can be eliminated at compile-time via the
``IMATH_USE_NOEXCEPT`` CMake option.
* Python bindings:
* FixedArray objects support a "read only" state.
* FixedArray objects support python buffer protocol.
* Optimized 4x4 matrix multiplication.
Upstream changes:
CHANGES IN R 4.1.1:
NEW FEATURES:
* require(pkg, quietly = TRUE) is quieter and in particular does
not warn if the package is not found.
DEPRECATED AND DEFUNCT:
* Use of ftp:// URIs should be regarded as deprecated, with
on-going support confined to method = "libcurl" and not routinely
tested. (Nowadays no major browser supports them.)
* The non-default method = "internal" is deprecated for http:// and
ftp:// URIs for both download.file and url.
* On Windows, method = "wininet" is deprecated for http://,
https:// and ftp:// URIs for both download.file and url. (A
warning is only given for ftp://.)
For ftp:// URIs the default method is now "libcurl" if available
(which it is on CRAN builds).
method = "wininet" remains the default for http:// and https://
URIs but if libcurl is available, using method = "libcurl" is
preferred.
INSTALLATION:
* make check now works also without a LaTeX installation. (Thanks
to Sebastian Meyer's PR#18103.)
BUG FIXES:
* make check-devel works again in an R build configured with
--without-recommended-packages.
* qnbinom(p, size, mu) for large size/mu is correct now in a range
of cases (PR#18095); similarly for the (size, prob)
parametrization of the negative binomial. Also qpois() and
qbinom() are better and or faster for extreme cases. The
underlying C code has been modularized and is common to all four
cases of discrete distributions.
* gap.axis is now part of the axis() arguments which are passed
from bxp(), and hence boxplot(). (Thanks to Martin Smith's
report and suggestions in PR#18109.)
* .First and .Last can again be set from the site profile.
* seq.int(from, to, *) and seq.default(..) now work better in large
range cases where from-to is infinite where the two boundaries
are finite.
* all.equal(x,y) now returns TRUE correctly also when several
entries of abs(x) and abs(y) are close to .Machine$double.xmax,
the largest finite numeric.
* model.frame() now clears the object bit when removing the class
attribute of a value via na.action (PR#18100).
* charClass() now works with multi-character strings on Windows
(PR#18104, fixed by Bill Dunlap).
* encodeString() on Solaris now works again in Latin-1 encoding on
characters represented differently in UTF-8. Support for
surrogate pairs on Solaris has been improved.
* file.show() on Windows now works with non-ASCII path names
representable in the current native encoding (PR#18132).
* Embedded R on Windows can now find R home directory via the
registry even when installed only for the current user
(PR#18135).
* pretty(x) with finite x now returns finite values also in the
case where the extreme x values are close in size to the maximal
representable number .Machine$double.xmax.
Also, it's been tweaked for very small ranges and when a boundary
is close (or equal) to zero; e.g., pretty(c(0,1e-317)) no longer
has negative numbers, currently still warning about a very small
range, and pretty(2^-(1024 - 2^-1/(c(24,10)))) is more accurate.
* The error message for not finding vignette files when weaving has
correct file sizes now. (Thanks to Sebastian Meyer's PR#18154.)
* dnbinom(20, <large>, 1) now correctly gives 0, and similar cases
are more accurate with underflow precaution. (Reported by
Francisco Vera Alcivar in PR#18072.)
0.8.2
Changes
- Improved yank and undo alloc'ing. Malloc as much we need from start
in a long batch and avoid small mallocs.
- Changed the way lua scripts are referenced in formulas. Now they are
input as any other string formula, like this:
\"@lua("script_name.lua", 1) being 1 if the reference should be added
to the depgraph or not, making it evaluated just once or every time
the depgraph is evaluated.
NOTE that if set to 0 and the cell is referenced by another cell, it
will be executed nonetheless.
- Added new exec_lua configuration variable.
- Rows now can have height higher than one LINE. See fj and fk in
normal mode or :formatrow in command mode.
- Wrap cell content. new autowrap config value. works when nooverlap
and notruncate are set.
- Open URL or file specified on cell (PR 401)
- Import mkd files
- Multiple frozen rows/columns (fr / fc in normal mode)
- Added mapping_timeout configuration variable with a default value of
1500ms (used to be a fixed value of 800ms).
- Added mouse support in insert and command mode. The selection of a
cell gets copied to inputbar.
- Added command_timeout configuration variable.
- handle hidden rows/cols in undo/redo of ir/ic/dr/dc
- Added backwards search with '?'
- Restore \\* from old SC. \\{char} fills the cell with n occurrences
of {char} to complete its width
- Store frozen rows and cols when saving file
- Added :formatcol command (handling its undo as well)
- Added :formatrow command (handling its undo as well)
- Added undo of freeze row and col
- Handle \n in cell input, and with autowrap
- Handle undoing changes in row height produced by string input
- Changed input bar from window to pad: permits entering string longer
than COLS.
- @count counts cells with strings as well, and not just with numbers.
- Handle entering a label after :datefmt for datetime value edition.
- New dracula / papercolor themes.
- Added EvalRange() so that the graph is not evaluated entirely all the
time.
- Replaced 'EvalAll' with 'EvalRange'.
- Removed unneeded parameters on EvalJustVertex"
- Added eval_order in EvalRange and rebuild_graph.
- Added @evaluate / @sevaluate functions
- Handle @nval dependencies.
- Handle @mycol/@myrow calls during startup when no EvalJustOneVertex
is yet called
- Added @getent (FR issue #451)
- The saving format for :w command would be according to current file
format. #493
- modified savefile() of file.c to check current file format before
saving a file.
- Keep consistent with other format such as csv and save the file with
the same format as current file.
- Added HELP_HIGHLIGHT definition color for help page.
- Renamed GRID_PAIR to GRID_EVEN in color.c.
- UNDO of :fsum is handled by let.
- calc_offscr_rows/cols rewriten and renamed to calc_mobile_rows/cols
Fixes
- Fix old sc bug - issue #371
- Fix when saving sc files of cells that has some string expressions -
issue #541
- Fix leak in nval.
- Fix Issue #372.
- Free lua memory at exit.
- Fix when saving marks in file after importing xlsx file and saving it
in sc format.
- EXPR and NUMBER colors were overloaded by STRING color #546
- Fix markdown export when empty col was added left to data
- Fix in :showrows command.
- :fsum added to command mode commands. It was missing.
- Added :showcols command that was missing.
- Handled issue #429
- handled issue #374
- Ignore SIGWINCH outside ncurses.
- triggers: Avoid segfault when not being able to load module. Issue
#325
0.8.1
New features
- Braille support
- Added latex export - issue #394
- Added mappings for command mode
- Work on issues #225 and #247: support mapping of ñ and other special
chars
- Basic ODS file import
- Paste to a range of selected cells - (actually added on v0.8 - issue
438 - PR 445)
- Added txtdelim | for csv files import - issue 409
- Added macros to --version (show version)
- Support higher versions of lua.
- Handle ESC key in mappings. related to issue #492.
- Added freeze to visual mode - issue #459
Changes
- Recognise SPACE in mappings rather than simple ' '
- Visual change: Moved cmd multiplier to the left of mode
- Changed default headings colors
- many improvements to the config facility and usage - PR 519
- improved sort for 65k rows
Fixes
- Fix issues on CIRCULAR REFERENCES: #473#201#475#321. these were as
hard.
- Fix issue 417 and added a date type in xlsx import.
- Fix Engformat overlap text y número. Mostraba * (actually fixed
on v0.8)
- Fix column header display - overflow with column width 2 and column
with two letters - PR 517
- Fix isnumeric test to recognise floats: affects copy/paste - PR 450
- Fix issue setting conf variables like nonumeric
- Fix when showing empty text - 944844505d7cdb7d3d392a5c1d2b3ffde40a1fff
- Fix issue #227 - this was hard. used to segfault and keep wrong
reference after deleting row that is last in range of expr. ex.
@avg(B1:B4) and deleting row 4
- Fix issue #433: large memory use with multiple linked cells.
- Fix issue #287 - valueize didnt update depgraph
- Solved issue #399. 'g' command of NORMAL_MODE changed to 'gt'"
- Fixed vmaps in get_mappings function.
- Fixed bug on 'error' in gram.y - comment on issue #482
- Fix issue #457: cursor position could add empty rows or columns when
exporting csv files
- Fix issue #288: ^ misbehaving when having fixed rows
- Fix in mouse clicks
- Fix possible memory leak in add freeze
- XLSX: Free memory leak when looking for specified sheet.
- XLSX: Avoid segfault when using shared formulas. issue #218.
Imath is a basic, light-weight, and efficient C++ representation of 2D
and 3D vectors and matrices and other simple but useful mathematical
objects, functions, and data types common in computer graphics
applications.
While the license allows to re-distribute the source tarball
unchanged, an automatic download fails, so it will have to be
downloaded in a browser.
From the upstream description:
SMath Studio is a tiny, powerful, free mathematical program with
WYSIWYG editor and complete units of measurements support.
It provides numerous computing features and rich user interface
translated into about 40 different languages. The application also
contains an integrated mathematical reference book.
It can be easily extended based on your needs. A built-in Extensions
Manager tool allows to get access to hundreds official and third-party
resources of the following types: usage examples, plug-ins, SMath
Viewer based applications, snippets, interface translations,
interactive books, handbooks and tutorials.
* What is new in gsl-2.7:
** fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
** fixed bug #60335 (spmatrix test failure, J. Lamb)
** fixed bug #36577
** clarified documentation on interpolation accelerators (V. Krishnan)
** fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M. Sitte)
** fixed doc bug #59758
** fixed bug #58202 (rstat median for n=5)
** added support for native C complex number types in gsl_complex
when using a C11 compiler
** upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6
** updated exponential fitting example for nonlinear least squares
** added banded LU decomposition and solver (gsl_linalg_LU_band)
** New functions added to the library:
- gsl_matrix_norm1
- gsl_spmatrix_norm1
- gsl_matrix_complex_conjtrans_memcpy
- gsl_linalg_QL: decomp, unpack
- gsl_linalg_complex_QR_* (thanks to Christian Krueger)
- gsl_vector_sum
- gsl_matrix_scale_rows
- gsl_matrix_scale_columns
- gsl_multilarge_linear_matrix_ptr
- gsl_multilarge_linear_rhs_ptr
- gsl_spmatrix_dense_add (renamed from gsl_spmatrix_add_to_dense)
- gsl_spmatrix_dense_sub
- gsl_linalg_cholesky_band: solvem, svxm, scale, scale_apply
- gsl_linalg_QR_UD: decomp, lssolve
- gsl_linalg_QR_UU: decomp, lssolve, QTvec
- gsl_linalg_QR_UZ: decomp
- gsl_multifit_linear_lcurvature
- gsl_spline2d_eval_extrap
** bug fix in checking vector lengths in gsl_vector_memcpy (dieggsy@pm.me)
** made gsl_sf_legendre_array_index() inline and documented
gsl_sf_legendre_nlm()
The omppool file is both in PLIST and PLIST.Linux. One needs to go. This hotfix
just removes the typo. Do we remove PLIST.Linux and assume every platform
of interest has working OpenMP? Add Darwin dep for parallel/openmp?
