mcmc | R package mcmc | Development Tools library

by cjgeyer R Version: Current License: No License

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kandi X-RAY | mcmc Summary

mcmc is a R library typically used in Utilities, Development Tools applications. mcmc has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

The main branch is morph (not master). We will probably never go back to master being the main branch. This is the source tree for the R contributed package mcmc. The version for users is at CRAN (This package suggests packages Iso and xtable. So if don't have need to add to R. In R do. Since one of the vignettes takes a long time, probably want. (instead of without --no-vignettes) except for one last check before commit.

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Support

mcmc has a low active ecosystem.

It has 15 star(s) with 4 fork(s). There are 3 watchers for this library.

It had no major release in the last 6 months.

There are 2 open issues and 0 have been closed. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of mcmc is current.

Quality

mcmc has no bugs reported.

Security

mcmc has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

mcmc does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

mcmc releases are not available. You will need to build from source code and install.

Installation instructions are not available. Examples and code snippets are available.

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mcmc Key Features

No Key Features are available at this moment for mcmc.

mcmc Examples and Code Snippets

No Code Snippets are available at this moment for mcmc.

Community Discussions

Trending Discussions on mcmc

Complex function that iterates mvrnorm over rows of a data frame

PyMC3 Minibatch ADVI

Gelman-Rubin statistic for MCMCglmm model in R

A JAX custom VJP function for multiple input variable does not work for NumPyro/HMC-NUTS

Change title: mcmc_trace function with ggplot

jags: coda package, how to select multiple parameters

issue running valued exponential random graph model (ergm) with block diagonal constraint

Select the same name with different [number]

understanding the output of str function in R

How to decompose a mixed distribution using MCMC

QUESTION

Complex function that iterates mvrnorm over rows of a data frame

Asked 2021-Jun-01 at 22:07

I have data that looks like this:

...

ANSWER

Answered 2021-Jun-01 at 22:07

We can use lapply

Source https://stackoverflow.com/questions/67796552

QUESTION

PyMC3 Minibatch ADVI

Asked 2021-May-31 at 17:36

I’m trying to use PyMC3 Minibatch ADVI for Bayesian Regression. The pm.fit function throws the following error and I’m not sure how to fix it.

It says that the ‘str’ object has no attribute ‘type’. What is any ‘str’ object from the error message here? I’ve mapped float tensors for more_replacements to the best of what I know.

...

ANSWER

Answered 2021-May-31 at 17:34

The blog post you are working from shows

Source https://stackoverflow.com/questions/67738634

QUESTION

Gelman-Rubin statistic for MCMCglmm model in R

Asked 2021-May-21 at 01:31

I have a multivariate model with this (approximate) form:

...

ANSWER

Answered 2021-May-21 at 01:08

The gelman.diag requires a mcmc.list. If we are running models with different set of parameters, extract the 'Sol' and place it in a list (Below, it is the same model)

Source https://stackoverflow.com/questions/67629517

QUESTION

A JAX custom VJP function for multiple input variable does not work for NumPyro/HMC-NUTS

Asked 2021-Apr-07 at 16:08

I am trying to use a custom VJP (vector-Jacobian product) function as a model for a HMC-NUTS in numpyro. I was able to make a single variable function that works for HMC-NUTS as follows:

...

ANSWER

Answered 2021-Feb-11 at 03:08

def model(x,y):
sigma = numpyro.sample('sigma', dist.Exponential(1.))
x0 = numpyro.sample('x0', dist.Uniform(-1.,1.))
A = numpyro.sample('A', dist.Exponential(1.))
hv=vmap(h,(0,None),0)
mu=hv(x-x0,A)
numpyro.sample('y', dist.Normal(mu, sigma), obs=y)

Source https://stackoverflow.com/questions/65684271

QUESTION

Change title: mcmc_trace function with ggplot

Asked 2021-Apr-02 at 20:00

I used mcmc_trace function from the bayesplot package to plot traceplot with mcmc list, which is a ggplot item so it can be further edited by ggplot function.

Follows is the plot that produced by the function. I needed to change the title k1...k[20] to subject 1... subject 20. Are there any approaches I can achieve this with ggplot function?

Follows is a simple reproducible model.

...

ANSWER

Answered 2021-Apr-02 at 20:00

Use colnames<- to modify the column names. Since the object is a 1-element list containing a matrix-like object, you need to use [[1]]; if you have multiple chains you'll need to lapply() (or use a for loop) to apply the solution to every chain (i.e., every element in the list).

Source https://stackoverflow.com/questions/66920925

QUESTION

jags: coda package, how to select multiple parameters

Asked 2021-Mar-31 at 20:03

I used r2jags to run jags and do the sampling. Then, I used coda package to check convergence. As I have many subjects and many parameters, I would need to manually type them as the codes below. Are there any easier approaches that I can for example, choose gamma for every subject? Or, just select gamma from subject 1 to 10 without typing them manually?

...

ANSWER

Answered 2021-Mar-31 at 20:03

A reproducible example would be nice but presumably

Source https://stackoverflow.com/questions/66894425

QUESTION

issue running valued exponential random graph model (ergm) with block diagonal constraint

Asked 2021-Mar-24 at 02:10

I am trying to run an exponential random graph model (ergm) on a weighted network (network_ex). This network shows the interactions between individuals in four different groups. Interactions between groups cannot occur so a blockdiagonal constraint needs to be included in the model. However when I include the blockdiagonal constraint the ergm function (that runs otherwise) returns an error (see below) and my R session either runs indefinitely or abort directly.

Is there a way to run an ergm based on a weighted block diagonal matrix?

...

ANSWER

Answered 2021-Mar-24 at 02:10

That does appear to be a bug. I've fixed it in the latest development version. These can be obtained by going to https://github.com/statnet/ergm and https://github.com/statnet/ergm.count and either using install_github() or downloading the binaries found in the README. Note, also that, the blockdiag() constraint has been provisionally moved to https://github.com/statnet/tergm .

Source https://stackoverflow.com/questions/66750371

QUESTION

Select the same name with different [number]

Asked 2021-Mar-14 at 11:09

I have column names like the following plot

Can I select all alpha one time instead of typing alpha[1], alpha[2]...alpha[9]?

How can I put in the following codes to let R know I need results of all alpha?

...

ANSWER

Answered 2021-Mar-14 at 11:09

Something like this perhaps?

Source https://stackoverflow.com/questions/66623676

QUESTION

understanding the output of str function in R

Asked 2021-Mar-07 at 18:00

I use the str to print out information for a calculate variable

...

ANSWER

Answered 2021-Mar-07 at 18:00

The attr implies there is an attribute named 'mcpar' which is a numeric vector

Source https://stackoverflow.com/questions/66519587

QUESTION

How to decompose a mixed distribution using MCMC

Asked 2021-Mar-07 at 03:45

I have data that is a 50:50 mix of a normal distribution and a constant value:

...

ANSWER

Answered 2021-Mar-07 at 03:45

Incommensurability of Probability Density and Mass

The issue here is that the likelihood of coming from each model involves probability density for the Gaussian and mass for the discrete, which are not commensurate. Specifically, the computation for comparing where a zero observation came from, will involve likelihoods

Source https://stackoverflow.com/questions/66407576

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install mcmc

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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