diff --git a/vignettes/binary-outcomes.Rmd b/vignettes/binary-outcomes.Rmd index 4b0a17b3..1ec163a4 100644 --- a/vignettes/binary-outcomes.Rmd +++ b/vignettes/binary-outcomes.Rmd @@ -95,9 +95,6 @@ informs the comparator intercept, whereas STC regresses on the IPD alone.) ``` r -library(mlumr) -library(ggplot2) - # IPD + AgD bundled with mlumr (copied from multinma's plaque_psoriasis, GPL-3). data("psoriasis_ipd") data("psoriasis_agd") diff --git a/vignettes/binary-outcomes.Rmd.orig b/vignettes/binary-outcomes.Rmd.orig index f52427d1..a2974fb5 100644 --- a/vignettes/binary-outcomes.Rmd.orig +++ b/vignettes/binary-outcomes.Rmd.orig @@ -116,9 +116,6 @@ still differ: ML-UMR fits a joint likelihood in which the aggregate outcome informs the comparator intercept, whereas STC regresses on the IPD alone.) ```{r data} -library(mlumr) -library(ggplot2) - # IPD + AgD bundled with mlumr (copied from multinma's plaque_psoriasis, GPL-3). data("psoriasis_ipd") data("psoriasis_agd") diff --git a/vignettes/choosing-a-method.Rmd b/vignettes/choosing-a-method.Rmd index 7fcfc684..6c884fdd 100644 --- a/vignettes/choosing-a-method.Rmd +++ b/vignettes/choosing-a-method.Rmd @@ -48,7 +48,6 @@ secukinumab) with three prognostic covariates: ``` r -library(mlumr) data("psoriasis_ipd") # bundled with mlumr (from multinma, GPL-3) data("psoriasis_agd") diff --git a/vignettes/choosing-a-method.Rmd.orig b/vignettes/choosing-a-method.Rmd.orig index 6d6dd95f..21d2b760 100644 --- a/vignettes/choosing-a-method.Rmd.orig +++ b/vignettes/choosing-a-method.Rmd.orig @@ -69,7 +69,6 @@ the plaque-psoriasis PASI 75 endpoint (UNCOVER-2 ixekizumab vs FIXTURE secukinumab) with three prognostic covariates: ```{r data} -library(mlumr) data("psoriasis_ipd") # bundled with mlumr (from multinma, GPL-3) data("psoriasis_agd") diff --git a/vignettes/continuous-outcomes.Rmd b/vignettes/continuous-outcomes.Rmd index da4a831b..0423603a 100644 --- a/vignettes/continuous-outcomes.Rmd +++ b/vignettes/continuous-outcomes.Rmd @@ -79,9 +79,6 @@ mlumr precisely because no aggregation bias arises from a nonlinear link ``` r -library(mlumr) -library(ggplot2) - data("shoulder_ipd") # index IPD (ASD), bundled with mlumr data("shoulder_agd") # comparator AgD (ET) diff --git a/vignettes/continuous-outcomes.Rmd.orig b/vignettes/continuous-outcomes.Rmd.orig index a631d73a..c578e09d 100644 --- a/vignettes/continuous-outcomes.Rmd.orig +++ b/vignettes/continuous-outcomes.Rmd.orig @@ -100,9 +100,6 @@ mlumr precisely because no aggregation bias arises from a nonlinear link (contrast the log odds ratio in `vignette("binary-outcomes")`). ```{r data} -library(mlumr) -library(ggplot2) - data("shoulder_ipd") # index IPD (ASD), bundled with mlumr data("shoulder_agd") # comparator AgD (ET) diff --git a/vignettes/count-outcomes.Rmd b/vignettes/count-outcomes.Rmd index df2f517c..dd222f6c 100644 --- a/vignettes/count-outcomes.Rmd +++ b/vignettes/count-outcomes.Rmd @@ -77,9 +77,6 @@ $\mathrm{RR}=\bar\lambda_{\text{index}}/\bar\lambda_{\text{comparator}}$ ``` r -library(mlumr) -library(ggplot2) - data("caries_ipd") # index IPD (SDF), bundled with mlumr data("caries_agd") # comparator AgD (NSF) diff --git a/vignettes/count-outcomes.Rmd.orig b/vignettes/count-outcomes.Rmd.orig index bf63cd78..b4a97a09 100644 --- a/vignettes/count-outcomes.Rmd.orig +++ b/vignettes/count-outcomes.Rmd.orig @@ -98,9 +98,6 @@ $\mathrm{RR}=\bar\lambda_{\text{index}}/\bar\lambda_{\text{comparator}}$ (null = 1), reported in both populations. ```{r data} -library(mlumr) -library(ggplot2) - data("caries_ipd") # index IPD (SDF), bundled with mlumr data("caries_agd") # comparator AgD (NSF) diff --git a/vignettes/fitting-and-diagnostics.Rmd b/vignettes/fitting-and-diagnostics.Rmd index c42c6438..db0220da 100644 --- a/vignettes/fitting-and-diagnostics.Rmd +++ b/vignettes/fitting-and-diagnostics.Rmd @@ -37,7 +37,6 @@ in `vignette("binary-outcomes")`): ``` r -library(mlumr) data("psoriasis_ipd") # bundled with mlumr (from multinma, GPL-3) data("psoriasis_agd") diff --git a/vignettes/fitting-and-diagnostics.Rmd.orig b/vignettes/fitting-and-diagnostics.Rmd.orig index e5718986..48e79d5e 100644 --- a/vignettes/fitting-and-diagnostics.Rmd.orig +++ b/vignettes/fitting-and-diagnostics.Rmd.orig @@ -58,7 +58,6 @@ of this vignette inspects, tunes, and diagnoses (the data preparation is covered in `vignette("binary-outcomes")`): ```{r data} -library(mlumr) data("psoriasis_ipd") # bundled with mlumr (from multinma, GPL-3) data("psoriasis_agd") diff --git a/vignettes/survival-outcomes.Rmd b/vignettes/survival-outcomes.Rmd index dd03bcef..554eb17c 100644 --- a/vignettes/survival-outcomes.Rmd +++ b/vignettes/survival-outcomes.Rmd @@ -131,9 +131,6 @@ We adjust for age, ISS stage III, complete/very-good-partial response, and sex. ``` r -library(mlumr) -library(ggplot2) - data("ndmm_ipd") # bundled with mlumr (copied from multinma, GPL-3) data("ndmm_agd") # reconstructed pseudo-IPD (KM) data("ndmm_agd_covs") # covariate moments for the AgD arm diff --git a/vignettes/survival-outcomes.Rmd.orig b/vignettes/survival-outcomes.Rmd.orig index f41fb08a..c9b10f9a 100644 --- a/vignettes/survival-outcomes.Rmd.orig +++ b/vignettes/survival-outcomes.Rmd.orig @@ -151,9 +151,6 @@ Surv(lower, upper, type = "interval2") # interval censoring We adjust for age, ISS stage III, complete/very-good-partial response, and sex. ```{r data} -library(mlumr) -library(ggplot2) - data("ndmm_ipd") # bundled with mlumr (copied from multinma, GPL-3) data("ndmm_agd") # reconstructed pseudo-IPD (KM) data("ndmm_agd_covs") # covariate moments for the AgD arm