From 1266a53dae2b25cb715c3a4614ffbc80ffb39a9f Mon Sep 17 00:00:00 2001 From: wlandau Date: Fri, 31 May 2024 13:06:02 -0400 Subject: [PATCH] Fix fev1 vignette --- ...pes.Rmd.upstream => archetypes.Rmd.source} | 0 .../{bcva.Rmd.upstream => bcva.Rmd.source} | 2 +- vignettes/fev1.Rmd | 293 +++++++++--------- .../{fev1.Rmd.upstream => fev1.Rmd.source} | 10 +- ...ion.Rmd.upstream => simulation.Rmd.source} | 0 vignettes/subgroup.Rmd | 4 +- ...group.Rmd.upstream => subgroup.Rmd.source} | 0 .../{usage.Rmd.upstream => usage.Rmd.source} | 0 8 files changed, 152 insertions(+), 157 deletions(-) rename vignettes/{archetypes.Rmd.upstream => archetypes.Rmd.source} (100%) rename vignettes/{bcva.Rmd.upstream => bcva.Rmd.source} (99%) rename vignettes/{fev1.Rmd.upstream => fev1.Rmd.source} (98%) rename vignettes/{simulation.Rmd.upstream => simulation.Rmd.source} (100%) rename vignettes/{subgroup.Rmd.upstream => subgroup.Rmd.source} (100%) rename vignettes/{usage.Rmd.upstream => usage.Rmd.source} (100%) diff --git a/vignettes/archetypes.Rmd.upstream b/vignettes/archetypes.Rmd.source similarity index 100% rename from vignettes/archetypes.Rmd.upstream rename to vignettes/archetypes.Rmd.source diff --git a/vignettes/bcva.Rmd.upstream b/vignettes/bcva.Rmd.source similarity index 99% rename from vignettes/bcva.Rmd.upstream rename to vignettes/bcva.Rmd.source index 653950b5..aacc3abd 100644 --- a/vignettes/bcva.Rmd.upstream +++ b/vignettes/bcva.Rmd.source @@ -258,7 +258,7 @@ for (level in visit_levels) { b_mmrm_summary <- b_mmrm_draws |> summarize_draws() |> select(variable, mean, sd) |> - filter(!(variable %in% c("lprior", "lp__"))) |> + filter(!(variable %in% c("Intercept", "lprior", "lp__"))) |> rename(bayes_estimate = mean, bayes_se = sd) |> mutate( variable = variable |> diff --git a/vignettes/fev1.Rmd b/vignettes/fev1.Rmd index 35f201f9..fc5e5db9 100644 --- a/vignettes/fev1.Rmd +++ b/vignettes/fev1.Rmd @@ -44,7 +44,6 @@ This comparison workflow requires the following packages. + "parallel", + "brms.mmrm", + "mmrm", -+ "emmeans", + "posterior" + ) > invisible(lapply(packages, library, character.only = TRUE)) @@ -1746,48 +1745,48 @@ Here is a posterior summary of model parameters, including fixed effects and pai #> #> Correlation Structures: #> Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS -#> cortime(VIS1,VIS2) 0.80 0.04 0.72 0.86 1.00 29817 26486 -#> cortime(VIS1,VIS3) 0.58 0.06 0.45 0.69 1.00 29980 25992 -#> cortime(VIS2,VIS3) 0.79 0.04 0.70 0.85 1.00 37235 26736 -#> cortime(VIS1,VIS4) 0.17 0.07 0.02 0.31 1.00 39836 26523 -#> cortime(VIS2,VIS4) 0.35 0.07 0.20 0.49 1.00 43272 25958 -#> cortime(VIS3,VIS4) 0.51 0.07 0.36 0.64 1.00 43638 25600 +#> cortime(VIS1,VIS2) 0.36 0.08 0.19 0.51 1.00 51602 25934 +#> cortime(VIS1,VIS3) 0.14 0.10 -0.06 0.33 1.00 52857 23880 +#> cortime(VIS2,VIS3) 0.04 0.10 -0.16 0.23 1.00 49144 24017 +#> cortime(VIS1,VIS4) 0.17 0.11 -0.06 0.38 1.00 49267 24904 +#> cortime(VIS2,VIS4) 0.11 0.09 -0.06 0.28 1.00 51841 24385 +#> cortime(VIS3,VIS4) 0.01 0.10 -0.18 0.21 1.00 49136 24852 #> #> Regression Coefficients: #> Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS -#> Intercept 1.13 2.70 -4.21 6.41 1.00 44625 -#> FEV1_BL 0.07 0.05 -0.04 0.17 1.00 60027 -#> AVISITVIS2 -0.08 1.26 -2.58 2.40 1.00 38274 -#> AVISITVIS3 0.27 1.20 -2.07 2.62 1.00 36317 -#> AVISITVIS4 -1.26 1.14 -3.49 0.95 1.00 37383 -#> RACEBlackorAfricanAmerican -0.08 1.08 -2.21 2.03 1.00 49597 -#> RACEWhite 0.58 1.22 -1.80 2.98 1.00 48740 -#> SEXFemale -0.01 0.95 -1.88 1.84 1.00 57317 -#> AVISITVIS1:ARMCDTRT -1.75 1.90 -5.48 1.99 1.00 26028 -#> AVISITVIS2:ARMCDTRT -2.46 1.92 -6.20 1.36 1.00 30977 -#> AVISITVIS3:ARMCDTRT -2.66 1.90 -6.43 1.05 1.00 30450 -#> AVISITVIS4:ARMCDTRT -1.98 1.63 -5.18 1.23 1.00 30861 -#> sigma_AVISITVIS1 2.55 0.06 2.43 2.67 1.00 40244 -#> sigma_AVISITVIS2 2.58 0.06 2.47 2.70 1.00 38175 -#> sigma_AVISITVIS3 2.55 0.06 2.44 2.68 1.00 41255 -#> sigma_AVISITVIS4 2.41 0.06 2.29 2.53 1.00 41086 +#> Intercept 24.34 1.42 21.59 27.12 1.00 45329 +#> FEV1_BL -0.84 0.03 -0.89 -0.79 1.00 55921 +#> AVISITVIS2 4.79 0.82 3.18 6.39 1.00 34165 +#> AVISITVIS3 10.38 0.83 8.75 12.01 1.00 31754 +#> AVISITVIS4 15.19 1.34 12.57 17.85 1.00 34809 +#> RACEBlackorAfricanAmerican 1.41 0.59 0.26 2.57 1.00 47354 +#> RACEWhite 5.45 0.62 4.24 6.66 1.00 49043 +#> SEXFemale 0.34 0.51 -0.66 1.34 1.00 52998 +#> AVISITVIS1:ARMCDTRT 3.99 1.06 1.89 6.08 1.00 33842 +#> AVISITVIS2:ARMCDTRT 3.94 0.83 2.29 5.58 1.00 50214 +#> AVISITVIS3:ARMCDTRT 2.98 0.67 1.67 4.31 1.00 52318 +#> AVISITVIS4:ARMCDTRT 4.42 1.69 1.11 7.78 1.00 44517 +#> sigma_AVISITVIS1 1.83 0.06 1.71 1.95 1.00 50151 +#> sigma_AVISITVIS2 1.59 0.06 1.47 1.71 1.00 53871 +#> sigma_AVISITVIS3 1.33 0.06 1.20 1.46 1.00 50428 +#> sigma_AVISITVIS4 2.28 0.06 2.16 2.40 1.00 49571 #> Tail_ESS -#> Intercept 24929 -#> FEV1_BL 24110 -#> AVISITVIS2 26022 -#> AVISITVIS3 26067 -#> AVISITVIS4 26450 -#> RACEBlackorAfricanAmerican 25697 -#> RACEWhite 27147 -#> SEXFemale 24672 -#> AVISITVIS1:ARMCDTRT 25266 -#> AVISITVIS2:ARMCDTRT 26108 -#> AVISITVIS3:ARMCDTRT 27137 -#> AVISITVIS4:ARMCDTRT 25421 -#> sigma_AVISITVIS1 25694 -#> sigma_AVISITVIS2 26294 -#> sigma_AVISITVIS3 26185 -#> sigma_AVISITVIS4 26887 +#> Intercept 23313 +#> FEV1_BL 24977 +#> AVISITVIS2 24844 +#> AVISITVIS3 23618 +#> AVISITVIS4 23548 +#> RACEBlackorAfricanAmerican 25483 +#> RACEWhite 25692 +#> SEXFemale 24210 +#> AVISITVIS1:ARMCDTRT 26085 +#> AVISITVIS2:ARMCDTRT 24388 +#> AVISITVIS3:ARMCDTRT 24805 +#> AVISITVIS4:ARMCDTRT 24757 +#> sigma_AVISITVIS1 24768 +#> sigma_AVISITVIS2 25617 +#> sigma_AVISITVIS3 23158 +#> sigma_AVISITVIS4 24658 #> #> Draws were sampled using sampling(NUTS). For each parameter, Bulk_ESS #> and Tail_ESS are effective sample size measures, and Rhat is the potential @@ -1886,7 +1885,7 @@ We extract and standardize the Bayesian estimates. > b_mmrm_summary <- b_mmrm_draws |> + summarize_draws() |> + select(variable, mean, sd) |> -+ filter(!(variable %in% c("lprior", "lp__"))) |> ++ filter(!(variable %in% c("Intercept", "lprior", "lp__"))) |> + rename(bayes_estimate = mean, bayes_se = sd) |> + mutate( + variable = variable |> @@ -2454,120 +2453,115 @@ Because of the different statistical paradigms and estimation procedures, especi intercept -1.1350 +24.3429 24.3537 -−23.2188 -−0.9534 +−0.0108 +−0.0004 fev1_bl -0.0664 +−0.8401 −0.8402 -0.9066 -−1.0790 +0.0001 +−0.0001 avisitvis2 -−0.0843 +4.7948 4.7904 -−4.8746 -−1.0176 +0.0044 +0.0009 avisitvis3 -0.2691 +10.3809 10.3660 -−10.0969 -−0.9740 +0.0149 +0.0014 avisitvis4 -−1.2615 +15.1908 15.1923 -−16.4538 -−1.0830 +−0.0015 +−0.0001 raceblackorafricanamerican -−0.0829 +1.4123 1.4192 -−1.5021 -−1.0584 +−0.0069 +−0.0048 racewhite -0.5806 +5.4537 5.4568 -−4.8762 -−0.8936 +−0.0031 +−0.0006 sexfemale -−0.0052 +0.3417 0.3381 -−0.3433 -−1.0155 +0.0035 +0.0104 avisitvis1:armcdtrt -−1.7519 +3.9860 3.9833 -−5.7352 -−1.4398 +0.0027 +0.0007 avisitvis2:armcdtrt -−2.4582 +3.9393 3.9308 -−6.3890 -−1.6254 +0.0086 +0.0022 avisitvis3:armcdtrt -−2.6578 +2.9830 2.9837 -−5.6415 -−1.8908 +−0.0007 +−0.0002 avisitvis4:armcdtrt -−1.9767 +4.4177 4.4040 -−6.3807 -−1.4488 +0.0137 +0.0031 sigma_avisitvis1 -12.7967 +6.2310 6.1506 -6.6461 -1.0806 +0.0804 +0.0131 sigma_avisitvis2 -13.2657 +4.9122 4.8526 -8.4131 -1.7337 +0.0596 +0.0123 sigma_avisitvis3 -12.8917 +3.7752 3.7153 -9.1764 -2.4699 +0.0599 +0.0161 sigma_avisitvis4 -11.1114 +9.7952 9.6417 -1.4697 -0.1524 +0.1535 +0.0159 correlation_vis1_vis2 -0.7963 +0.3608 0.3795 -0.4169 -1.0986 +−0.0187 +−0.0492 correlation_vis1_vis3 -0.5833 +0.1410 0.1523 -0.4310 -2.8307 +−0.0113 +−0.0740 correlation_vis2_vis3 -0.7873 +0.0385 0.0430 -0.7443 -17.2927 +−0.0045 +−0.1053 correlation_vis1_vis4 -0.1711 +0.1680 0.1802 -−0.0091 -−0.0504 +−0.0122 +−0.0676 correlation_vis2_vis4 -0.3523 +0.1114 0.1178 -0.2345 -1.9915 +−0.0063 +−0.0539 correlation_vis3_vis4 -0.5132 +0.0139 0.0159 -0.4973 -31.3491 - intercept -2.5788 -24.3537 -−21.7750 -−0.8941 +−0.0020 +−0.1255 @@ -3051,70 +3045,65 @@ Because of the different statistical paradigms and estimation procedures, especi intercept -2.6963 +1.4172 1.4075 -1.2888 -0.9156 +0.0097 +0.0069 fev1_bl -0.0524 +0.0278 0.0278 -0.0246 -0.8874 +0.0000 +0.0016 avisitvis2 -1.2625 +0.8172 0.7985 -0.4640 -0.5811 +0.0188 +0.0235 avisitvis3 -1.2014 +0.8288 0.8132 -0.3882 -0.4774 +0.0156 +0.0192 avisitvis4 -1.1357 +1.3385 1.3086 -−0.1728 -−0.1321 +0.0299 +0.0229 raceblackorafricanamerican -1.0832 +0.5869 0.5787 -0.5044 -0.8716 +0.0081 +0.0140 racewhite -1.2188 +0.6204 0.6163 -0.6025 -0.9778 +0.0041 +0.0067 sexfemale -0.9479 +0.5108 0.4927 -0.4552 -0.9237 +0.0180 +0.0366 avisitvis1:armcdtrt -1.9039 +1.0615 1.0454 -0.8585 -0.8212 +0.0161 +0.0154 avisitvis2:armcdtrt -1.9189 +0.8333 0.8135 -1.1054 -1.3588 +0.0197 +0.0243 avisitvis3:armcdtrt -1.9023 +0.6745 0.6657 -1.2367 -1.8578 +0.0089 +0.0133 avisitvis4:armcdtrt -1.6255 +1.6873 1.6605 -−0.0350 -−0.0211 - intercept -0.7521 -1.4075 -−0.6554 -−0.4657 +0.0268 +0.0161 diff --git a/vignettes/fev1.Rmd.upstream b/vignettes/fev1.Rmd.source similarity index 98% rename from vignettes/fev1.Rmd.upstream rename to vignettes/fev1.Rmd.source index 1e19ca47..905f0ec0 100644 --- a/vignettes/fev1.Rmd.upstream +++ b/vignettes/fev1.Rmd.source @@ -1,6 +1,6 @@ --- title: FEV1 data comparison between Bayesian and frequentist MMRMs -date: "`r format(Sys.time(), '%d/%m/%Y')`" +date: "`r format(Sys.time(), '%Y-%d-%m')`" output: rmarkdown::html_document: theme: spacelab @@ -269,7 +269,7 @@ for (level in visit_levels) { b_mmrm_summary <- b_mmrm_draws |> summarize_draws() |> select(variable, mean, sd) |> - filter(!(variable %in% c("lprior", "lp__"))) |> + filter(!(variable %in% c("Intercept", "lprior", "lp__"))) |> rename(bayes_estimate = mean, bayes_se = sd) |> mutate( variable = variable |> @@ -399,3 +399,9 @@ gt(table_se) |> diff_relative_se = "Relative" ) ``` + +## Session info {#session} + +```{r} +sessionInfo() +``` \ No newline at end of file diff --git a/vignettes/simulation.Rmd.upstream b/vignettes/simulation.Rmd.source similarity index 100% rename from vignettes/simulation.Rmd.upstream rename to vignettes/simulation.Rmd.source diff --git a/vignettes/subgroup.Rmd b/vignettes/subgroup.Rmd index 34a75ff2..9409f0b6 100644 --- a/vignettes/subgroup.Rmd +++ b/vignettes/subgroup.Rmd @@ -1,7 +1,7 @@ --- title: "Subgroup analysis" -bibliography: '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/brms.mmrm/bibliography.bib' -csl: '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/brms.mmrm/asa.csl' +bibliography: '`r system.file("bibliography.bib", package = "brms.mmrm")`' +csl: '`r system.file("asa.csl", package = "brms.mmrm")`' output: rmarkdown::html_vignette: toc: true diff --git a/vignettes/subgroup.Rmd.upstream b/vignettes/subgroup.Rmd.source similarity index 100% rename from vignettes/subgroup.Rmd.upstream rename to vignettes/subgroup.Rmd.source diff --git a/vignettes/usage.Rmd.upstream b/vignettes/usage.Rmd.source similarity index 100% rename from vignettes/usage.Rmd.upstream rename to vignettes/usage.Rmd.source