Feedstock license: BSD-3-Clause
Home: http://github.com/mclements/rstpm2
Package license: GPL-2.0-or-later
Summary: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth doi:10.1177/0962280216664760. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects doi:10.1002/sim.7451. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0(t)=exp(-exp(eta_0(t))) is modelled for natural splines for eta_0, and the time-dependent cumulative acceleration factor eta(t,x)=\int_0^t exp(eta_1(u,x)) du for log acceleration factor eta_1(u,x). The Markov multi-state models allow for a range of models with smooth transitions to predict transition probabilities, length of stay, utilities and costs, with differences, ratios and standardisation.
Home: http://github.com/mclements/rstpm2
Package license: GPL-2.0-or-later
Summary: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth doi:10.1177/0962280216664760. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects doi:10.1002/sim.7451. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0(t)=exp(-exp(eta_0(t))) is modelled for natural splines for eta_0, and the time-dependent cumulative acceleration factor eta(t,x)=\int_0^t exp(eta_1(u,x)) du for log acceleration factor eta_1(u,x). The Markov multi-state models allow for a range of models with smooth transitions to predict transition probabilities, length of stay, utilities and costs, with differences, ratios and standardisation.
Azure |
Name | Downloads | Version | Platforms |
---|---|---|---|
Installing r-rstpm2
from the conda-forge
channel can be achieved by adding conda-forge
to your channels with:
conda config --add channels conda-forge
conda config --set channel_priority strict
Once the conda-forge
channel has been enabled, r-rstpm2
can be installed with conda
:
conda install r-rstpm2
or with mamba
:
mamba install r-rstpm2
It is possible to list all of the versions of r-rstpm2
available on your platform with conda
:
conda search r-rstpm2 --channel conda-forge
or with mamba
:
mamba search r-rstpm2 --channel conda-forge
Alternatively, mamba repoquery
may provide more information:
# Search all versions available on your platform:
mamba repoquery search r-rstpm2 --channel conda-forge
# List packages depending on `r-rstpm2`:
mamba repoquery whoneeds r-rstpm2 --channel conda-forge
# List dependencies of `r-rstpm2`:
mamba repoquery depends r-rstpm2 --channel conda-forge
conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.
A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.
To manage the continuous integration and simplify feedstock maintenance
conda-smithy has been developed.
Using the conda-forge.yml
within this repository, it is possible to re-render all of
this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender
.
For more information please check the conda-forge documentation.
feedstock - the conda recipe (raw material), supporting scripts and CI configuration.
conda-smithy - the tool which helps orchestrate the feedstock.
Its primary use is in the construction of the CI .yml
files
and simplify the management of many feedstocks.
conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)
If you would like to improve the r-rstpm2 recipe or build a new
package version, please fork this repository and submit a PR. Upon submission,
your changes will be run on the appropriate platforms to give the reviewer an
opportunity to confirm that the changes result in a successful build. Once
merged, the recipe will be re-built and uploaded automatically to the
conda-forge
channel, whereupon the built conda packages will be available for
everybody to install and use from the conda-forge
channel.
Note that all branches in the conda-forge/r-rstpm2-feedstock are
immediately built and any created packages are uploaded, so PRs should be based
on branches in forks and branches in the main repository should only be used to
build distinct package versions.
In order to produce a uniquely identifiable distribution:
- If the version of a package is not being increased, please add or increase
the
build/number
. - If the version of a package is being increased, please remember to return
the
build/number
back to 0.