Nothing
In the code:
sample_from()
(when error.draws
was > 1, a mistake in the way sampled sizes and proportions were joined together resulted in too many rows in the returned table).stanfit_to_named_mcmclist()
which was causing problems when running MCMC sampling with thinning.quick_sankey()
.traceplot()
.In the documentation:
(This error message was related to the NEWS for R-devel: "Calling && or || with either argument of length greater than one now gives a warning (which it is intended will become an error)".)
method
argument to run_mcmc()
to choose between matrix_exp
(the default) and euler
solvers.*()
to *_p()
to avoid collision with other R functions.params()
to a tibble, for consistency with priors()
.euler_control
argument to run_mcmc()
to be able to tune the fixed time step parameter of the Euler solver.stanfit_to_named_mcmclist()
for easier manipulation of the output of run_mcmc()
when a stanfit object is returned with stanfit = TRUE
.set_priors()
as a synonym for set_prior()
.set_priors()
now also accepts a tibble an as input to make copying priors across models easier.available_priors()
function to list all the priors implemented in
the package.prop_family()
and add size_family()
(to easily check the meaning of eta
and zeta
parameters).lalaja
dataset to the package so that the Trinidadian case study based on Collins et al. (2016) can be reproduced more easily.dt
or grid_size
arguments were used for the Euler method.\value
tags and removing examples using :::
.dontrun{}
vs donttest{}
, examples for unexported functions).@return
roxygen tags for all exported functions..Random.seed
directly anymore.options(mc.cores = 4)
._R_CHECK_LIMIT_CORES_
environmental variable to limit the number of cores to 2 when running on CRAN servers.vignettes/
when building the tarballRmd
files to avoid issues with long run times and with the usage of multiple cores when performing R CMD checks.First version submitted to CRAN.
trini_mod
dataset.select
generic so that it can be used without having to load dplyr
first.networkModelStanfit
objects.prep-data/
scripts.ggtopo()
function to plot topologies.ggflows()
function to visualize flows.zeta
(the parameter for variation in predicted compartment sizes).c()
method for mcmc.list
objects.tidy_trajectories()
, tidy_flows()
and predict.networkModel()
.furrr::future_map()
.tidy_data()
, tidy_posterior_predict()
and tidy_dpp()
for easier posterior predictions.mcmc_heatmap()
.filter()
methods for isotracer S3 classes are correctly exported and do not depend on dplyr
being attached first.set_topo()
related to dependencies update.select()
method for mcmc.list
objects.tests/
folder and re-write tests from scratch.R CMD check
.mcmc_heatmap()
.derived.mcmc.list
class to objects returned by Math generics for MCMC
output (to automatically use isotracer
plot method for derived parameters).devtools::install_gitlab()
.tidyOutput()
function to the core interface.run()
method only
working for flow input for now).run()
method in pure R first for use as a reference when
optimizing speed with C++.datasetTopo()
,
datasetAddition()
and datasetObs()
.tidyChain()
function to get the MCMC run of a network model in a tidy
format, including columns with parameter values and network trajectories.tidyFluxes()
function to get run-averaged fluxes and
compartment sizes for each iteration.$renderMovie()
method to SingleNetwork
object to make an animation of
tracer enrichment in a network.plot.topology()
method output.plotEstimatedProp()
, plotEstimatedSize()
and
plotSankey()
compatible with the new implementation.No major changes to the package, but a lot of small fixes, minor improvements and documentation additions.
Proposal
to be used as a parent for all proposal
classes.txtplot
package and
using the crayon
package for colored output in the terminal.mcmcssm
, is renamed isotracer
.isotracer
(this older package was not submitted to CRAN
though - it was living on the maintainer computer and on GitLab). To
distinguish between them, this other package has been renamed
isotracerPrototype
. This older package never reached above version 0.0.2
under the isotracer
name, so there is no possible confusion between the two
packages when version number is taken into account.FoodwebModel
MCMC run, in particular for models with
split compartments.Any scripts or data that you put into this service are public.
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