mmrm() models #229
mmrm() models #229
Conversation
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Hey hey! I am getting an error trying to run # this version is from the mmrm branch ("refs/heads/mmrm")
packageVersion("broom.helpers")
#> [1] '1.13.1'
fit <-
mmrm::mmrm(
formula = FEV1 ~ RACE + SEX + ARMCD * AVISIT + us(AVISIT | USUBJID),
data = mmrm::fev_data
)
summary(fit)
#> mmrm fit
#>
#> Formula: FEV1 ~ RACE + SEX + ARMCD * AVISIT + us(AVISIT | USUBJID)
#> Data: mmrm::fev_data (used 537 observations from 197
#> subjects with maximum 4 timepoints)
#> Covariance: unstructured (10 variance parameters)
#> Method: Satterthwaite
#> Vcov Method: Asymptotic
#> Inference: REML
#>
#> Model selection criteria:
#> AIC BIC logLik deviance
#> 3406.4 3439.3 -1693.2 3386.4
#>
#> Coefficients:
#> Estimate Std. Error df t value Pr(>|t|)
#> (Intercept) 30.77748 0.88656 218.80000 34.715 < 2e-16
#> RACEBlack or African American 1.53050 0.62448 168.67000 2.451 0.015272
#> RACEWhite 5.64357 0.66561 157.14000 8.479 1.56e-14
#> SEXFemale 0.32606 0.53195 166.13000 0.613 0.540744
#> ARMCDTRT 3.77423 1.07415 145.55000 3.514 0.000589
#> AVISITVIS2 4.83959 0.80172 143.88000 6.037 1.27e-08
#> AVISITVIS3 10.34211 0.82269 155.56000 12.571 < 2e-16
#> AVISITVIS4 15.05390 1.31281 138.47000 11.467 < 2e-16
#> ARMCDTRT:AVISITVIS2 -0.04193 1.12932 138.56000 -0.037 0.970439
#> ARMCDTRT:AVISITVIS3 -0.69369 1.18765 158.17000 -0.584 0.559996
#> ARMCDTRT:AVISITVIS4 0.62423 1.85085 129.72000 0.337 0.736463
#>
#> (Intercept) ***
#> RACEBlack or African American *
#> RACEWhite ***
#> SEXFemale
#> ARMCDTRT ***
#> AVISITVIS2 ***
#> AVISITVIS3 ***
#> AVISITVIS4 ***
#> ARMCDTRT:AVISITVIS2
#> ARMCDTRT:AVISITVIS3
#> ARMCDTRT:AVISITVIS4
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Covariance estimate:
#> VIS1 VIS2 VIS3 VIS4
#> VIS1 40.5537 14.3960 4.9747 13.3867
#> VIS2 14.3960 26.5715 2.7855 7.4745
#> VIS3 4.9747 2.7855 14.8979 0.9082
#> VIS4 13.3867 7.4745 0.9082 95.5568
broom.helpers::tidy_plus_plus(fit)
#> ! `broom::tidy()` failed to tidy the model.
#> mmrm() registered as emmeans extension
#> Warning: The `full` argument of `model.frame.mmrm_tmb()` is deprecated as of mmrm 0.3.
#> ℹ The deprecated feature was likely used in the insight package.
#> Please report the issue at <https://github.com/easystats/insight/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> ✔ `tidy_parameters()` used instead.
#> ℹ Add `tidy_fun = broom.helpers::tidy_parameters` to quiet these messages.
#> Error in stats::model.matrix.default(model %>% model_get_terms(), data = stats::model.frame(model)): model frame and formula mismatch in model.matrix()Created on 2023-08-04 with reprex v2.0.2 I'll try to look into it further this weekend 🍁 |
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Just for you information, #228 has not been merged into the main branch yet. |
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Ok. I do not have an issue on my side, but I'm using It seems that there is some change with the dev version. Should we wait for the stabilisation and the release of version 0.3.0 before updating that PR? Regards |
Great suggestion. The author is back from leave this coming week. Perhaps we can update mmrm to have all the needed methods and correct the |
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Perfect. Let's wait for the release of 0.3.0 then |
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hey hey @larmarange ! hope you're well! mmrm made their release to CRAN, and i bumped the min version requirement to the CRAN version. Would you like me to try and take it from here, or you prefer to do it? |
Hey I'm currently traveling for work. Don't hesitate to look / test the PR if you have time. I could myself look at it next week Best |
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We have to check but with the new version of the package, some dedicated methods in broom.helpers won't be needed anymore |
There was a problem hiding this comment.
Hi @larmarange !
I did some testing, and we were able to remove the custom methods (as you suggested), since I updated the methods in the mmrm package.
I added some unit tests (modeled after the betareg unit tests). Do you think we should add more?
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@larmarange the tests that are failing are related to lme4, rather than mmrm FYI |
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This is strange. I just deleted all caches and I'm trying to re run all jobs |
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Everything seems OK for me. Test failures are related to https://stackoverflow.com/questions/77481539/error-in-initializeptr-function-cholmod-factor-ldeta-not-provided-by-pack and not to the PR So, for me, not a problem to merge this PR. However, we will have to fix all checks before next release |
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #229 +/- ##
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Coverage 95.48% 95.48%
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Files 43 43
Lines 2680 2680
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Hits 2559 2559
Misses 121 121
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fix #228