Skip to content

Load mlumr and ggplot2 once per vignette #114

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
choxos merged 1 commit into from
Sep 18, 2026
Merged

Load mlumr and ggplot2 once per vignette #114

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 0 additions & 3 deletions vignettes/binary-outcomes.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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")
Expand Down
3 changes: 0 additions & 3 deletions vignettes/binary-outcomes.Rmd.orig
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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")
Expand Down
1 change: 0 additions & 1 deletion vignettes/choosing-a-method.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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")

Expand Down
1 change: 0 additions & 1 deletion vignettes/choosing-a-method.Rmd.orig
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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")

Expand Down
3 changes: 0 additions & 3 deletions vignettes/continuous-outcomes.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down
3 changes: 0 additions & 3 deletions vignettes/continuous-outcomes.Rmd.orig
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down
3 changes: 0 additions & 3 deletions vignettes/count-outcomes.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down
3 changes: 0 additions & 3 deletions vignettes/count-outcomes.Rmd.orig
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down
1 change: 0 additions & 1 deletion vignettes/fitting-and-diagnostics.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,6 @@ in `vignette("binary-outcomes")`):


``` r
library(mlumr)
data("psoriasis_ipd") # bundled with mlumr (from multinma, GPL-3)
data("psoriasis_agd")

Expand Down
1 change: 0 additions & 1 deletion vignettes/fitting-and-diagnostics.Rmd.orig
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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")

Expand Down
3 changes: 0 additions & 3 deletions vignettes/survival-outcomes.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
3 changes: 0 additions & 3 deletions vignettes/survival-outcomes.Rmd.orig
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
Loading