Out of date code in vignette

[dg13]

Hi, Probably a minor issue, but I get the following error when trying to work through the example in the vignette:

exposures <- retrieve_pars(mcmc_samples_fit, par = "exposures", hpd_prob = 0.90)

Error in retrieve_pars(mcmc_samples_fit, par = "exposures", hpd_prob = 0.9) : unused argument (par = "exposures")

Looking at the retrieve_pars function, it looks like there's no par option:

function (mcmc_samples, feature, hpd_prob = 0.95, counts = NULL, signatures = NULL, opportunities = NULL, signature_names = NULL)

packageVersion("sigfit") [1] ‘1.0.0’ platform x86_64-apple-darwin15.6.0
arch x86_64
os darwin15.6.0
system x86_64, darwin15.6.0
status
major 3
minor 4.3
year 2017
month 11
day 30
svn rev 73796
language R
version.string R version 3.4.3 (2017-11-30) nickname Kite-Eating Tree

[baezortega]

I think it's because the vignette refers to the dev version and not to release 1.0. On 4 Apr 2018 20:33, "dg13" notifications@github.com wrote:

Hi, Probably a minor issue, but I get the following error when trying to work through the example in the vignette:

exposures <- retrieve_pars(mcmc_samples_fit, par = "exposures", hpd_prob = 0.90)

Error in retrieve_pars(mcmc_samples_fit, par = "exposures", hpd_prob = 0.9) : unused argument (par = "exposures")

Looking at the retrieve_pars function, it looks like there's no par option:

function (mcmc_samples, feature, hpd_prob = 0.95, counts = NULL, signatures = NULL, opportunities = NULL, signature_names = NULL)

packageVersion("sigfit") [1] ‘1.0.0’ platform x86_64-apple-darwin15.6.0 arch x86_64 os darwin15.6.0 system x86_64, darwin15.6.0 status major 3 minor 4.3 year 2017 month 11 day 30 svn rev 73796 language R version.string R version 3.4.3 (2017-11-30) nickname Kite-Eating Tree

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[dg13]

OK - do the installation instructions in the vignette install by default 1.0? Anyway, just a minor point, thought it would be useful to post here for reference

[baezortega]

I think the vignette installs master. It's just a matter of making a new release. On 4 Apr 2018 20:42, "dg13" notifications@github.com wrote:

OK - do the installation instructions in the vignette install by default 1.0? Anyway, just a minor point, thought it would be useful to post here for reference

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[dg13]

So is it useful to post these comments on the vignette? Or should I delete?

[kgori]

Thanks for letting us know about this. It looks like you have the vignette that goes with the dev branch of the code, but are running the master branch (1.0) version, so there is a mismatch in the function signature. Are you working from the locally-installed vignette that was built when you installed v1.0? If so, then our build script is producing the wrong vignette, which we need to fix. Otherwise, this vignette goes with v1.0.

[kgori]

Hi. The vignette link in README.md was pointing to the dev branch. I've changed it to point to the version 1.0 release vignette. Sorry for the confusion. The examples in this vignette will work with the release version of sigfit.

[baezortega]

Hi, Sorry for not replying properly before. Alternatively, you could try installing the dev version, which is more usable and has a more complete vignette than v1.0.0. You would have to repeat the devtools install command, adding the argument: ref="dev". Then you should be able to follow the vignette you were referring to. Cheers On 4 Apr 2018 21:05, "Kevin Gori" notifications@github.com wrote:

Thanks for letting us know about this. It looks like you have the vignette that goes with the dev branch of the code, but are running the master branch (1.0) version, so there is a mismatch in the function signature. Are you working from the locally-installed vignette that was built when you installed v1.0? If so, then our build script is producing the wrong vignette, which we need to fix. Otherwise, this vignette https://github.com/kgori/sigfit/blob/master/vignettes/sigfit_vignette.Rmd goes with v1.0.

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[dg13]

No problem, thanks for the help!