All flavors markdown
Gerko Vink 
Methodology & Statistics @ UU University
Hanne Oberman
Methodology & Statistics @ UU
27 Sep 2023
RStudio
Figures
The above figure is left-aligned
The caption is also left-aligned
The above figure is centered
The caption is still left-aligned
The code for the figures is
Columns, Sizing, Equations and proper centering
\(e^{i\pi} + 1 = 0\)
The above figure is left-aligned
The caption is also left-aligned
The equation is left-aligned too
\[e^{i\pi} + 1 = 0\]
The above figure is centered
The caption is also centered
The equation is centered
The code for the slide is
## Columns, Sizing, Equations and proper centering
::: columns
::: {.column width="50%"}
{fig-align="left" width="80%"}
$e^{i\pi} + 1 = 0$
The above figure is left-aligned <br>
The caption is also left-aligned <br>
The equation is left-aligned too
:::
::: {.column width="50%"}
<center>
{fig-align="center" width="80%"}
</center>
$$e^{i\pi} + 1 = 0$$
The above figure is centered <br>
The caption is also centered <br>
The equation is centered
:::
:::
The code for the slide is
``` markdown
## Columns, Sizing, Equations and proper centering
::: columns
::: {.column width="50%"}
{fig-align="left" width="80%"}
$e^{i\pi} + 1 = 0$
The above figure is left-aligned <br>
The caption is also left-aligned <br>
The equation is left-aligned too
:::
::: {.column width="50%"}
<center>
{fig-align="center" width="80%"}
</center>
$$e^{i\pi} + 1 = 0$$
The above figure is centered <br>
The caption is also centered <br>
The equation is centered
:::
:::F-ing it all up
\(e^{i\pi} + 1 = 0\)
The above figure is left-aligned
The caption is also left-aligned
The equation is left-aligned too
\[e^{i\pi} + 1 = 0\]
The above figure is centered
The caption is also centered
The equation is centered
Math-ing it all up
\(e^{i\pi} + 1 = 0\)
\[e^{i\pi} + 1 = 0\]
## Math-ing it all up
::: columns
::: {.column width="70%"}
{fig-align="left" width="30%"}
$e^{i\pi} + 1 = 0$
:::
::: {.column width="30%"}
<center>
{fig-align="center" width="70%"}
</center>
$$e^{i\pi} + 1 = 0$$
:::
:::
```markdown
END OF EXAMPLER figures
Code chunks
We already saw some markdown code chunks. We can run inline code to calculate that 12 * 234 is 2808 by using `r ` and code chunks to evaluate larger blocks of code, such as:
Code
How Does Explicit Caching Work?
In RMarkdown and Quarto, you can use cache directives to specify which code chunks should be cached and which should not.
- Cached chunks are identified by a unique hash based on their code content, ensuring consistency.
The following code block
#| cache: true
#| code-line-numbers: true
#| label: imputation
library(mice)
library(magrittr)
library(purrr)
imp <- nhanes %>% mice(print = FALSE)
imp |>
complete("all") %>%
map(~.x %$% lm(bmi ~ chl + hyp)) |>
pool()would result in this output
library(mice)
library(magrittr)
library(purrr)
imp <- nhanes %>% mice(print = FALSE)
imp |>
complete("all") %>%
map(~.x %$% lm(bmi ~ chl + hyp)) |>
pool()Class: mipo m = 5
term m estimate ubar b t dfcom
1 (Intercept) 5 22.74349586 1.466782e+01 5.5748962726 2.135770e+01 22
2 chl 5 0.02798109 4.276476e-04 0.0001721876 6.342727e-04 22
3 hyp 5 -1.13102073 4.505032e+00 0.3052774523 4.871365e+00 22
df riv lambda fmi
1 10.36596 0.45609201 0.31323021 0.4159942
2 10.01903 0.48316686 0.32576703 0.4293435
3 18.23535 0.08131639 0.07520129 0.1623012with corresponding cache structure relative to the root and format of the output file: 
Scientific publishing with rticles and Quarto
To use rticles from RStudio, you can access the templates through File -> New File -> R Markdown. This will open the dialog box where you can select from one of the available templates:
Quarto
The quarto use template command can be used to create an article from one the below formats.
Citations
Oberman and Vink (2023) and Cai, Van Buuren and Vink (2023) are some of our team’s most recent publications. Some references - such as some work by Reinder Banning and Gerko Vink are much older (2010) or contain simple and contemporary solutions by Volker and Vink (2022, 2–4) or cool but potentially confusing images (Schouten and Vink 2021, 1255).
Banning, Reinder, and Gerko Vink. 2010. “Methoden En Indicatoren Voor Het Evalueren En Beschrijven van Controle- En Correctieprocessen.” CBS nota DMV-2010- 06-08-RBNG-GVNK. Centraal Bureau voor de Statistiek.
Cai, Mingyang, Stef van Buuren, and Gerko Vink. 2023. “Graphical and Numerical Diagnostic Tools to Assess Multiple Imputation Models by Posterior Predictive Checking.” Heliyon.
Oberman, Hanne I., and Gerko Vink. 2023. “Toward a Standardized Evaluation of Imputation Methodology.” Biometrical Journal, 2200107. https://doi.org/https://doi.org/10.1002/bimj.202200107.
Schouten, Rianne Margaretha, and Gerko Vink. 2021. “The Dance of the Mechanisms: How Observed Information Influences the Validity of Missingness Assumptions.” Sociological Methods & Research 50 (3): 1243–58.
Volker, Thom, and Gerko Vink. 2022. “Synthetic Data in r: Generating Synthetic Data with High Utility Using Mice.” Https://Www.gerkovink.com/miceVignettes/Synthetic/Synthetic.html.
## Citations
@eval and Cai, Van Buuren and Vink [-@cai2023graphical] are some of our team's most recent publications. Some references - such as some work by Reinder Banning and Gerko Vink are much older [-@banningvink] or contain simple and contemporary solutions by @vigntg [p. 2-4] or cool but potentially confusing images [@schouten2021dance, 1255].
::: footer
But you can also refer to @eval here
:::
::: {#refs}
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