erikerhardt/erik_qmd_template_simple.qmd

## erik_qmd_template_simple.qmd
---
title:        Title
subtitle:     Subtitle
author:       Erik Erhardt
date:         last-modified # today, now, last-modified
date-format:  long          # full, long, medium, short, iso,   https://quarto.org/docs/reference/dates.html
format:
  html:
    theme:                  litera
    highlight-style:        atom-one
    page-layout:            full      # article, full   # https://quarto.org/docs/output-formats/page-layout.html
    toc:                    true
    toc-depth:              4
    toc-location:           body      # left, body, right
    number-sections:        true      # true, false
    number-depth:           3
    code-fold:              show      # true (initially hidden), false, show (initially shown)
    code-tools:                       # menu top-right to show/hide all code
      toggle:               true
      caption:              "Code"    # none
      source:               false
    code-overflow:          scroll    # scroll, wrap
    code-block-bg:          true
    code-block-border-left: "#30B0E0"
    df-print:               paged     # default, kable, tibble, paged   # https://quarto.org/docs/computations/r.html
  pdf:                                # Quarto uses KOMA Script document classes by default  https://ctan.org/pkg/koma-script
    keep-tex:               true      # keep .tex file that is produced
    documentclass:          scrartcl  # article, report, book, scrartcl, scrreprt, scrbook
    papersize:              letter
    classoption:            [oneside,11pt] # [twocolumn, landscape]
    geometry:
      - margin = 1in
      #- top  = 30mm
      #- left = 20mm
      #- heightrounded
    fontfamily:             libertinus
    cite-method:            biblatex
    #biblatexoptions List of options for biblatex
    #natbiboptions List of options for natbib
    #biblio-title  Title for bibliography
    #biblio-style  Style for bibliography
    toc:                    true
    toc-depth:              4
    toc-title:              Contents
    number-sections:        true
    number-depth:           5
    lof:                    true
    lot:                    true
    colorlinks:             true
    highlight-style:        atom-one  # a11y, arrow, atom-one, ayu, breeze, github, gruvbox; pygments, tango, espresso, zenburn, kate, monochrome, breezedark, haddock; dracula, mokokai, nord, oblivion, printing, radical, solarized, vim-dark
fig-width:                  6
fig-height:                 4
execute: # https://quarto.org/docs/computations/execution-options.html, https://quarto.org/docs/computations/r.html
  cache:    false   # false, true
  eval:     true    # true, false  Evaluate the code chunk (if false, just echos the code into the output).
  echo:     true    # true, false  Include the source code in output
---

<!---
# Erik's compile commands in R:
  setwd("D:/Dropbox/StatAcumen/consult/Rpackages/erikmisc/data-raw/qmd_template")
  fn_qmd <- "erik_qmd_template_simple.qmd"
  quarto::quarto_render(input = fn_qmd)
-->


{{< pagebreak >}}

# Executive summary {#sec-Executive_summary}

{{< pagebreak >}}

# Introduction {#sec-Introduction}

## Background/rationale

* Explain the scientific background and rationale for the investigation being reported

## Objectives

* State specific objectives, including any prespecified hypotheses

## Literature Review:

* Review of relevant prior research and theories.
* Identification of gaps in existing knowledge.

{{< pagebreak >}}

# Methods {#sec-Methods}

## Study design

* Present key elements of study design early in the paper

## Setting

* Describe the setting, locations, and relevant dates, including periods of recruitment, exposure, follow-up, and data collection

## Participants

* Cohort study --- Give the eligibility criteria, and the sources and methods of selection of participants. Describe methods of follow-up
* Case-control study --- Give the eligibility criteria, and the sources and methods of case ascertainment and control selection. Give the rationale for the choice of cases and controls
* Cross-sectional study --- Give the eligibility criteria, and the sources and methods of selection of participants
* Cohort study --- For matched studies, give matching criteria and number of exposed and unexposed
* Case-control study --- For matched studies, give matching criteria and the number of controls per case

## Variables

* Clearly define all outcomes, exposures, predictors, potential confounders, and effect modifiers. Give diagnostic criteria, if applicable

## Data sources/ measurement

* Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
* For each variable of interest, give sources of data and details of methods of assessment (measurement). Describe comparability of assessment methods if there is more than one group

## Bias

* Describe any efforts to address potential sources of bias

## Study size

* Explain how the study size was arrived at

## Quantitative variables

* Explain how quantitative variables were handled in the analyses. If applicable, describe which groupings were chosen and why

## Statistical methods

* Describe all statistical methods, including those used to control for confounding
* Describe any methods used to examine subgroups and interactions
* Explain how missing data were addressed
* Cohort study --- If applicable, explain how loss to follow-up was addressed
* Case-control study --- If applicable, explain how matching of cases and controls was addressed
* Cross-sectional study --- If applicable, describe analytical methods taking account of sampling strategy
* Describe any sensitivity analyses

{{< pagebreak >}}

# Results {#sec-Results}

```{r init}
#| output:  false
#| warning: false
#| error:   false

options(
  dplyr.print_min         = 6
, dplyr.print_max         = 6
, pillar.max_footer_lines = 2
, pillar.min_chars        = 15
, stringr.view_n          = 6
, cli.num_colors          = 0       # Temporarily deactivate cli output for quarto
, cli.hyperlink           = FALSE
, pillar.bold             = TRUE
, width                   = 77      # 80 - 3 for #> comment
, readr.show_col_types    = FALSE   # readr::read_csv(), do not show column types
, str                     = strOptions(list.len = 1e3)
, knitr.kable.NA          = ''      # Display NAs as blanks
)

my_seed <- 76543
set.seed(my_seed)
library(erikmisc)
library(tidyverse)

ggplot2::theme_set(ggplot2::theme_bw(base_size = 12))

# Parallel processing
library(parallel)
options(rf.cores = parallel::detectCores() - 2) # OpenMP Parallel Processing
options(mc.cores = parallel::detectCores() - 2) # R-side Parallel Processing
```

Read data

```{r}
dat_sheet <-
  readr::read_csv(
    file = "../data/.csv"
  ) |>
  #dplyr::select(
  #) |>
  dplyr::filter(
  ) |>
  dplyr::mutate(
  )

dat_sheet |> str()
dat_sheet |> summary()
```

```{r}
#| fig-width:  8
#| fig-height: 8

dat_sheet |>
  erikmisc::e_plot_missing(
  , var_group           = NULL
  , sw_group_sort       = FALSE
  , var2_sort           = NULL
  , sw_title_data_name  = TRUE
  , sw_text_pct_miss    = FALSE
  )
```

```{r}
#| fig-width:  12
#| fig-height: 12

## Scatterplot matrix
p <-
  GGally::ggpairs(
    dat_sheet %>% select()
  , title = "Title"
  #, mapping = ggplot2::aes(colour = , alpha = 0.5)
  , diag  = list(
              continuous =
                GGally::wrap(
                  c("densityDiag", "barDiag", "blankDiag")[1]
                , alpha = 1/2
                )
            , discrete =
                c("barDiag", "blankDiag")[1]
            )
  # scatterplots on top so response as first variable has y on vertical axis
  , upper = list(
              continuous =
                GGally::wrap(
                  c("points", "smooth", "smooth_loess", "density", "cor", "blank")[2]
                , se = FALSE
                , alpha = 1/2
                , size = 1
                )
            , discrete =
                c("ratio", "facetbar", "blank")[2]
            , combo =
                wrap(
                  c("box", "box_no_facet", "dot", "dot_no_facet", "facethist", "facetdensity", "denstrip", "blank")[2]
                #, bins = 10  # for facethist
                )
            )
  , lower = list(
              continuous =
                GGally::wrap(
                  c("points", "smooth", "smooth_loess", "density", "cor", "blank")[5]
                #, se = FALSE
                #, alpha = 1/2
                #, size = 1
                )
            , discrete =
                c("ratio", "facetbar", "blank")[2]
            , combo =
                wrap(
                  c("box", "box_no_facet", "dot", "dot_no_facet", "facethist", "facetdensity", "denstrip", "blank")[5]
                , bins = 10  # for facethist
                )
            )
  , progress = FALSE
  , legend = 1        # create legend
  )
p <- p + theme_bw()
p <- p + labs(
                title     = "title"
              , subtitle  = "subtitle"
              , x         = "x"
              , y         = "y"
              , caption = paste0(  "Caption 1"
                                , "\nCaption 2"
                                )
              , colour    = "Class"
              #, shape     = "Class"
              #, linetype  = "General Health"  #"Diagnosis"
              #, fill      = "Diagnosis"
              #, tag = "A"
              )
p <- p + theme(legend.position = "bottom")
print(p)
```


## Participants

* *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
* Report numbers of individuals at each stage of study --- eg numbers potentially eligible, examined for eligibility, confirmed eligible, included in the study, completing follow-up, and analysed
* Give reasons for non-participation at each stage
* Consider use of a flow diagram

## Descriptive data

* *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
* (a) Give characteristics of study participants (eg demographic, clinical, social) and information on exposures and potential confounders
* (b) Indicate number of participants with missing data for each variable of interest
* (c) Cohort study --- Summarise follow-up time (eg, average and total amount)

## Outcome data

* *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
* Cohort study --- Report numbers of outcome events or summary measures over time
* Case-control study --- Report numbers in each exposure category, or summary measures of exposure
* Cross-sectional study --- Report numbers of outcome events or summary measures

## Main results

* Give unadjusted estimates and, if applicable, confounder-adjusted estimates and their precision (eg, 95% confidence interval). Make clear which confounders were adjusted for and why they were included
* Report category boundaries when continuous variables were categorized
* If relevant, consider translating estimates of relative risk into absolute risk for a meaningful time period

## Other analyses

* Report other analyses done --- eg analyses of subgroups and interactions, and sensitivity analyses

{{< pagebreak >}}

# Discussion {#sec-Discussion}

## Key results

* Summarise key results with reference to study objectives

## Limitations

* Discuss limitations of the study, taking into account sources of potential bias or imprecision. Discuss both direction and magnitude of any potential bias

## Interpretation

* Give a cautious overall interpretation of results considering objectives, limitations, multiplicity of analyses, results from similar studies, and other relevant evidence

## Generalisability

* Discuss the generalisability (external validity) of the study results

{{< pagebreak >}}

# Conclusion {#sec-Conclusion}

## Summary of the main findings.

## Implications of the study.

## Suggestions for future research.

{{< pagebreak >}}

# References {#sec-References}

## List of all sources cited in the report, following a specific citation style (e.g., APA, MLA, Chicago).

{{< pagebreak >}}

# Appendices {#sec-Appendices}

## Supplementary materials such as raw data, additional tables or figures, questionnaires, etc.

{{< pagebreak >}}

# Other information {#sec-Other_information}

## Funding

* Give the source of funding and the role of the funders for the present study and, if applicable, for the original study on which the present article is based

Note: An Explanation and Elaboration article discusses each checklist item and gives methodological background and published examples of transparent reporting. The STROBE checklist is best used in conjunction with this article (freely available on the Web sites of PLoS Medicine at http://www.plosmedicine.org/, Annals of Internal Medicine at http://www.annals.org/, and Epidemiology at http://www.epidem.com/). Information on the STROBE Initiative is available at www.strobe-statement.org.


--------------------------------------------------------------------------------

{{< pagebreak >}}

# Report sections

STROBE <https://www.strobe-statement.org/index.php?id=available-checklists>

STROBE Statement --- checklist of items that should be included in reports of observational studies

Added some additional items.

1. Title Page:
    1. Title of the Report
    1. Author(s) Name(s)
    1. Affiliation(s)
    1. Date
1. Title and abstract/Executive summary
    1. Indicate the study's design with a commonly used term in the title or the abstract
    1. Provide in the abstract an informative and balanced summary of what was done and what was found
1. Abstract:
    1. A brief summary of the report, typically around 150-250 words, highlighting the purpose, methods, results, and conclusions.
1. Table of Contents (optional):
    1. List of sections and subsections with page numbers for easy navigation.
1. List of Figures and Tables (optional):
    1. If your report contains numerous figures and tables, provide a list with their titles and page numbers.
1. List of Abbreviations (optional):
    1. Define any acronyms or abbreviations used in the report.
1. Introduction
    1. Background/rationale
    1. Explain the scientific background and rationale for the investigation being reported
    1. Objectives
    1. State specific objectives, including any prespecified hypotheses
    1. Literature Review:
        1. Review of relevant prior research and theories.
        1. Identification of gaps in existing knowledge.
1. Methods
    1. Study design
        1. Present key elements of study design early in the paper
    1. Setting
        1. Describe the setting, locations, and relevant dates, including periods of recruitment, exposure, follow-up, and data collection
    1. Participants
        1. Cohort study --- Give the eligibility criteria, and the sources and methods of selection of participants. Describe methods of follow-up
        1. Case-control study --- Give the eligibility criteria, and the sources and methods of case ascertainment and control selection. Give the rationale for the choice of cases and controls
        1. Cross-sectional study --- Give the eligibility criteria, and the sources and methods of selection of participants
        1. Cohort study --- For matched studies, give matching criteria and number of exposed and unexposed
        1. Case-control study --- For matched studies, give matching criteria and the number of controls per case
    1. Variables
        1. Clearly define all outcomes, exposures, predictors, potential confounders, and effect modifiers. Give diagnostic criteria, if applicable
    1. Data sources/ measurement
        1. *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
        1. For each variable of interest, give sources of data and details of methods of assessment (measurement). Describe comparability of assessment methods if there is more than one group
    1. Bias
        1. Describe any efforts to address potential sources of bias
    1. Study size
        1. Explain how the study size was arrived at
    1. Quantitative variables
        1. Explain how quantitative variables were handled in the analyses. If applicable, describe which groupings were chosen and why
    1. Statistical methods
        1. Describe all statistical methods, including those used to control for confounding
        1. Describe any methods used to examine subgroups and interactions
        1. Explain how missing data were addressed
        1. Cohort study --- If applicable, explain how loss to follow-up was addressed
        1. Case-control study --- If applicable, explain how matching of cases and controls was addressed
        1. Cross-sectional study --- If applicable, describe analytical methods taking account of sampling strategy
        1. Describe any sensitivity analyses
1. Results
    1. Participants
        1. *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
        1. Report numbers of individuals at each stage of study --- eg numbers potentially eligible, examined for eligibility, confirmed eligible, included in the study, completing follow-up, and analysed
        1. Give reasons for non-participation at each stage
        1. Consider use of a flow diagram
    1. Descriptive data
        1. *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
        1. (a) Give characteristics of study participants (eg demographic, clinical, social) and information on exposures and potential confounders
        1. (b) Indicate number of participants with missing data for each variable of interest
        1. (c) Cohort study --- Summarise follow-up time (eg, average and total amount)
    1. Outcome data
        1. *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
        1. Cohort study --- Report numbers of outcome events or summary measures over time
        1. Case-control study --- Report numbers in each exposure category, or summary measures of exposure
        1. Cross-sectional study --- Report numbers of outcome events or summary measures
    1. Main results
        1. Give unadjusted estimates and, if applicable, confounder-adjusted estimates and their precision (eg, 95% confidence interval). Make clear which confounders were adjusted for and why they were included
        1. Report category boundaries when continuous variables were categorized
        1. If relevant, consider translating estimates of relative risk into absolute risk for a meaningful time period
    1. Other analyses
        1. Report other analyses done --- eg analyses of subgroups and interactions, and sensitivity analyses
1. Discussion
    1. Key results
        1. Summarise key results with reference to study objectives
    1. Limitations
        1. Discuss limitations of the study, taking into account sources of potential bias or imprecision. Discuss both direction and magnitude of any potential bias
    1. Interpretation
        1. Give a cautious overall interpretation of results considering objectives, limitations, multiplicity of analyses, results from similar studies, and other relevant evidence
    1. Generalisability
        1. Discuss the generalisability (external validity) of the study results
1. Conclusion:
    1. Summary of the main findings.
    1. Implications of the study.
    1. Suggestions for future research.
1. References:
    1. List of all sources cited in the report, following a specific citation style (e.g., APA, MLA, Chicago).
1. Appendices (if applicable):
    1. Supplementary materials such as raw data, additional tables or figures, questionnaires, etc.
1. Other information
    1. Funding
        1. Give the source of funding and the role of the funders for the present study and, if applicable, for the original study on which the present article is based

Note: An Explanation and Elaboration article discusses each checklist item and gives methodological background and published examples of transparent reporting. The STROBE checklist is best used in conjunction with this article (freely available on the Web sites of PLoS Medicine at http://www.plosmedicine.org/, Annals of Internal Medicine at http://www.annals.org/, and Epidemiology at http://www.epidem.com/). Information on the STROBE Initiative is available at www.strobe-statement.org.
	---
	title: Title
	subtitle: Subtitle
	author: Erik Erhardt
	date: last-modified # today, now, last-modified
	date-format: long # full, long, medium, short, iso, https://quarto.org/docs/reference/dates.html
	format:
	html:
	theme: litera
	highlight-style: atom-one
	page-layout: full # article, full # https://quarto.org/docs/output-formats/page-layout.html
	toc: true
	toc-depth: 4
	toc-location: body # left, body, right
	number-sections: true # true, false
	number-depth: 3
	code-fold: show # true (initially hidden), false, show (initially shown)
	code-tools: # menu top-right to show/hide all code
	toggle: true
	caption: "Code" # none
	source: false
	code-overflow: scroll # scroll, wrap
	code-block-bg: true
	code-block-border-left: "#30B0E0"
	df-print: paged # default, kable, tibble, paged # https://quarto.org/docs/computations/r.html
	pdf: # Quarto uses KOMA Script document classes by default https://ctan.org/pkg/koma-script
	keep-tex: true # keep .tex file that is produced
	documentclass: scrartcl # article, report, book, scrartcl, scrreprt, scrbook
	papersize: letter
	classoption: [oneside,11pt] # [twocolumn, landscape]
	geometry:
	- margin = 1in
	#- top = 30mm
	#- left = 20mm
	#- heightrounded
	fontfamily: libertinus
	cite-method: biblatex
	#biblatexoptions List of options for biblatex
	#natbiboptions List of options for natbib
	#biblio-title Title for bibliography
	#biblio-style Style for bibliography
	toc: true
	toc-depth: 4
	toc-title: Contents
	number-sections: true
	number-depth: 5
	lof: true
	lot: true
	colorlinks: true
	highlight-style: atom-one # a11y, arrow, atom-one, ayu, breeze, github, gruvbox; pygments, tango, espresso, zenburn, kate, monochrome, breezedark, haddock; dracula, mokokai, nord, oblivion, printing, radical, solarized, vim-dark
	fig-width: 6
	fig-height: 4
	execute: # https://quarto.org/docs/computations/execution-options.html, https://quarto.org/docs/computations/r.html
	cache: false # false, true
	eval: true # true, false Evaluate the code chunk (if false, just echos the code into the output).
	echo: true # true, false Include the source code in output
	---

	<!---
	# Erik's compile commands in R:
	setwd("D:/Dropbox/StatAcumen/consult/Rpackages/erikmisc/data-raw/qmd_template")
	fn_qmd <- "erik_qmd_template_simple.qmd"
	quarto::quarto_render(input = fn_qmd)
	-->


	{{< pagebreak >}}

	# Executive summary {#sec-Executive_summary}

	{{< pagebreak >}}

	# Introduction {#sec-Introduction}

	## Background/rationale

	* Explain the scientific background and rationale for the investigation being reported

	## Objectives

	* State specific objectives, including any prespecified hypotheses

	## Literature Review:

	* Review of relevant prior research and theories.
	* Identification of gaps in existing knowledge.

	{{< pagebreak >}}

	# Methods {#sec-Methods}

	## Study design

	* Present key elements of study design early in the paper

	## Setting

	* Describe the setting, locations, and relevant dates, including periods of recruitment, exposure, follow-up, and data collection

	## Participants

	* Cohort study --- Give the eligibility criteria, and the sources and methods of selection of participants. Describe methods of follow-up
	* Case-control study --- Give the eligibility criteria, and the sources and methods of case ascertainment and control selection. Give the rationale for the choice of cases and controls
	* Cross-sectional study --- Give the eligibility criteria, and the sources and methods of selection of participants
	* Cohort study --- For matched studies, give matching criteria and number of exposed and unexposed
	* Case-control study --- For matched studies, give matching criteria and the number of controls per case

	## Variables

	* Clearly define all outcomes, exposures, predictors, potential confounders, and effect modifiers. Give diagnostic criteria, if applicable

	## Data sources/ measurement

	* Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
	* For each variable of interest, give sources of data and details of methods of assessment (measurement). Describe comparability of assessment methods if there is more than one group

	## Bias

	* Describe any efforts to address potential sources of bias

	## Study size

	* Explain how the study size was arrived at

	## Quantitative variables

	* Explain how quantitative variables were handled in the analyses. If applicable, describe which groupings were chosen and why

	## Statistical methods

	* Describe all statistical methods, including those used to control for confounding
	* Describe any methods used to examine subgroups and interactions
	* Explain how missing data were addressed
	* Cohort study --- If applicable, explain how loss to follow-up was addressed
	* Case-control study --- If applicable, explain how matching of cases and controls was addressed
	* Cross-sectional study --- If applicable, describe analytical methods taking account of sampling strategy
	* Describe any sensitivity analyses

	{{< pagebreak >}}

	# Results {#sec-Results}

	```{r init}
	#\| output: false
	#\| warning: false
	#\| error: false

	options(
	dplyr.print_min = 6
	, dplyr.print_max = 6
	, pillar.max_footer_lines = 2
	, pillar.min_chars = 15
	, stringr.view_n = 6
	, cli.num_colors = 0 # Temporarily deactivate cli output for quarto
	, cli.hyperlink = FALSE
	, pillar.bold = TRUE
	, width = 77 # 80 - 3 for #> comment
	, readr.show_col_types = FALSE # readr::read_csv(), do not show column types
	, str = strOptions(list.len = 1e3)
	, knitr.kable.NA = '' # Display NAs as blanks
	)

	my_seed <- 76543
	set.seed(my_seed)
	library(erikmisc)
	library(tidyverse)

	ggplot2::theme_set(ggplot2::theme_bw(base_size = 12))

	# Parallel processing
	library(parallel)
	options(rf.cores = parallel::detectCores() - 2) # OpenMP Parallel Processing
	options(mc.cores = parallel::detectCores() - 2) # R-side Parallel Processing
	```

	Read data

	```{r}
	dat_sheet <-
	readr::read_csv(
	file = "../data/.csv"
	) \|>
	#dplyr::select(
	#) \|>
	dplyr::filter(
	) \|>
	dplyr::mutate(
	)

	dat_sheet \|> str()
	dat_sheet \|> summary()
	```

	```{r}
	#\| fig-width: 8
	#\| fig-height: 8

	dat_sheet \|>
	erikmisc::e_plot_missing(
	, var_group = NULL
	, sw_group_sort = FALSE
	, var2_sort = NULL
	, sw_title_data_name = TRUE
	, sw_text_pct_miss = FALSE
	)
	```

	```{r}
	#\| fig-width: 12
	#\| fig-height: 12

	## Scatterplot matrix
	p <-
	GGally::ggpairs(
	dat_sheet %>% select()
	, title = "Title"
	#, mapping = ggplot2::aes(colour = , alpha = 0.5)
	, diag = list(
	continuous =
	GGally::wrap(
	c("densityDiag", "barDiag", "blankDiag")[1]
	, alpha = 1/2
	)
	, discrete =
	c("barDiag", "blankDiag")[1]
	)
	# scatterplots on top so response as first variable has y on vertical axis
	, upper = list(
	continuous =
	GGally::wrap(
	c("points", "smooth", "smooth_loess", "density", "cor", "blank")[2]
	, se = FALSE
	, alpha = 1/2
	, size = 1
	)
	, discrete =
	c("ratio", "facetbar", "blank")[2]
	, combo =
	wrap(
	c("box", "box_no_facet", "dot", "dot_no_facet", "facethist", "facetdensity", "denstrip", "blank")[2]
	#, bins = 10 # for facethist
	)
	)
	, lower = list(
	continuous =
	GGally::wrap(
	c("points", "smooth", "smooth_loess", "density", "cor", "blank")[5]
	#, se = FALSE
	#, alpha = 1/2
	#, size = 1
	)
	, discrete =
	c("ratio", "facetbar", "blank")[2]
	, combo =
	wrap(
	c("box", "box_no_facet", "dot", "dot_no_facet", "facethist", "facetdensity", "denstrip", "blank")[5]
	, bins = 10 # for facethist
	)
	)
	, progress = FALSE
	, legend = 1 # create legend
	)
	p <- p + theme_bw()
	p <- p + labs(
	title = "title"
	, subtitle = "subtitle"
	, x = "x"
	, y = "y"
	, caption = paste0( "Caption 1"
	, "\nCaption 2"
	)
	, colour = "Class"
	#, shape = "Class"
	#, linetype = "General Health" #"Diagnosis"
	#, fill = "Diagnosis"
	#, tag = "A"
	)
	p <- p + theme(legend.position = "bottom")
	print(p)
	```


	## Participants

	* *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
	* Report numbers of individuals at each stage of study --- eg numbers potentially eligible, examined for eligibility, confirmed eligible, included in the study, completing follow-up, and analysed
	* Give reasons for non-participation at each stage
	* Consider use of a flow diagram

	## Descriptive data

	* *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
	* (a) Give characteristics of study participants (eg demographic, clinical, social) and information on exposures and potential confounders
	* (b) Indicate number of participants with missing data for each variable of interest
	* (c) Cohort study --- Summarise follow-up time (eg, average and total amount)

	## Outcome data

	* *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
	* Cohort study --- Report numbers of outcome events or summary measures over time
	* Case-control study --- Report numbers in each exposure category, or summary measures of exposure
	* Cross-sectional study --- Report numbers of outcome events or summary measures

	## Main results

	* Give unadjusted estimates and, if applicable, confounder-adjusted estimates and their precision (eg, 95% confidence interval). Make clear which confounders were adjusted for and why they were included
	* Report category boundaries when continuous variables were categorized
	* If relevant, consider translating estimates of relative risk into absolute risk for a meaningful time period

	## Other analyses

	* Report other analyses done --- eg analyses of subgroups and interactions, and sensitivity analyses

	{{< pagebreak >}}

	# Discussion {#sec-Discussion}

	## Key results

	* Summarise key results with reference to study objectives

	## Limitations

	* Discuss limitations of the study, taking into account sources of potential bias or imprecision. Discuss both direction and magnitude of any potential bias

	## Interpretation

	* Give a cautious overall interpretation of results considering objectives, limitations, multiplicity of analyses, results from similar studies, and other relevant evidence

	## Generalisability

	* Discuss the generalisability (external validity) of the study results

	{{< pagebreak >}}

	# Conclusion {#sec-Conclusion}

	## Summary of the main findings.

	## Implications of the study.

	## Suggestions for future research.

	{{< pagebreak >}}

	# References {#sec-References}

	## List of all sources cited in the report, following a specific citation style (e.g., APA, MLA, Chicago).

	{{< pagebreak >}}

	# Appendices {#sec-Appendices}

	## Supplementary materials such as raw data, additional tables or figures, questionnaires, etc.

	{{< pagebreak >}}

	# Other information {#sec-Other_information}

	## Funding

	* Give the source of funding and the role of the funders for the present study and, if applicable, for the original study on which the present article is based

	Note: An Explanation and Elaboration article discusses each checklist item and gives methodological background and published examples of transparent reporting. The STROBE checklist is best used in conjunction with this article (freely available on the Web sites of PLoS Medicine at http://www.plosmedicine.org/, Annals of Internal Medicine at http://www.annals.org/, and Epidemiology at http://www.epidem.com/). Information on the STROBE Initiative is available at www.strobe-statement.org.




	--------------------------------------------------------------------------------

	{{< pagebreak >}}

	# Report sections

	STROBE <https://www.strobe-statement.org/index.php?id=available-checklists>

	STROBE Statement --- checklist of items that should be included in reports of observational studies

	Added some additional items.

	1. Title Page:
	1. Title of the Report
	1. Author(s) Name(s)
	1. Affiliation(s)
	1. Date
	1. Title and abstract/Executive summary
	1. Indicate the study's design with a commonly used term in the title or the abstract
	1. Provide in the abstract an informative and balanced summary of what was done and what was found
	1. Abstract:
	1. A brief summary of the report, typically around 150-250 words, highlighting the purpose, methods, results, and conclusions.
	1. Table of Contents (optional):
	1. List of sections and subsections with page numbers for easy navigation.
	1. List of Figures and Tables (optional):
	1. If your report contains numerous figures and tables, provide a list with their titles and page numbers.
	1. List of Abbreviations (optional):
	1. Define any acronyms or abbreviations used in the report.
	1. Introduction
	1. Background/rationale
	1. Explain the scientific background and rationale for the investigation being reported
	1. Objectives
	1. State specific objectives, including any prespecified hypotheses
	1. Literature Review:
	1. Review of relevant prior research and theories.
	1. Identification of gaps in existing knowledge.
	1. Methods
	1. Study design
	1. Present key elements of study design early in the paper
	1. Setting
	1. Describe the setting, locations, and relevant dates, including periods of recruitment, exposure, follow-up, and data collection
	1. Participants
	1. Cohort study --- Give the eligibility criteria, and the sources and methods of selection of participants. Describe methods of follow-up
	1. Case-control study --- Give the eligibility criteria, and the sources and methods of case ascertainment and control selection. Give the rationale for the choice of cases and controls
	1. Cross-sectional study --- Give the eligibility criteria, and the sources and methods of selection of participants
	1. Cohort study --- For matched studies, give matching criteria and number of exposed and unexposed
	1. Case-control study --- For matched studies, give matching criteria and the number of controls per case
	1. Variables
	1. Clearly define all outcomes, exposures, predictors, potential confounders, and effect modifiers. Give diagnostic criteria, if applicable
	1. Data sources/ measurement
	1. *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
	1. For each variable of interest, give sources of data and details of methods of assessment (measurement). Describe comparability of assessment methods if there is more than one group
	1. Bias
	1. Describe any efforts to address potential sources of bias
	1. Study size
	1. Explain how the study size was arrived at
	1. Quantitative variables
	1. Explain how quantitative variables were handled in the analyses. If applicable, describe which groupings were chosen and why
	1. Statistical methods
	1. Describe all statistical methods, including those used to control for confounding
	1. Describe any methods used to examine subgroups and interactions
	1. Explain how missing data were addressed
	1. Cohort study --- If applicable, explain how loss to follow-up was addressed
	1. Case-control study --- If applicable, explain how matching of cases and controls was addressed
	1. Cross-sectional study --- If applicable, describe analytical methods taking account of sampling strategy
	1. Describe any sensitivity analyses
	1. Results
	1. Participants
	1. *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
	1. Report numbers of individuals at each stage of study --- eg numbers potentially eligible, examined for eligibility, confirmed eligible, included in the study, completing follow-up, and analysed
	1. Give reasons for non-participation at each stage
	1. Consider use of a flow diagram
	1. Descriptive data
	1. *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
	1. (a) Give characteristics of study participants (eg demographic, clinical, social) and information on exposures and potential confounders
	1. (b) Indicate number of participants with missing data for each variable of interest
	1. (c) Cohort study --- Summarise follow-up time (eg, average and total amount)
	1. Outcome data
	1. *Give information separately for cases and controls in case-control studies and, if applicable, for exposed and unexposed groups in cohort and cross-sectional studies.
	1. Cohort study --- Report numbers of outcome events or summary measures over time
	1. Case-control study --- Report numbers in each exposure category, or summary measures of exposure
	1. Cross-sectional study --- Report numbers of outcome events or summary measures
	1. Main results
	1. Give unadjusted estimates and, if applicable, confounder-adjusted estimates and their precision (eg, 95% confidence interval). Make clear which confounders were adjusted for and why they were included
	1. Report category boundaries when continuous variables were categorized
	1. If relevant, consider translating estimates of relative risk into absolute risk for a meaningful time period
	1. Other analyses
	1. Report other analyses done --- eg analyses of subgroups and interactions, and sensitivity analyses
	1. Discussion
	1. Key results
	1. Summarise key results with reference to study objectives
	1. Limitations
	1. Discuss limitations of the study, taking into account sources of potential bias or imprecision. Discuss both direction and magnitude of any potential bias
	1. Interpretation
	1. Give a cautious overall interpretation of results considering objectives, limitations, multiplicity of analyses, results from similar studies, and other relevant evidence
	1. Generalisability
	1. Discuss the generalisability (external validity) of the study results
	1. Conclusion:
	1. Summary of the main findings.
	1. Implications of the study.
	1. Suggestions for future research.
	1. References:
	1. List of all sources cited in the report, following a specific citation style (e.g., APA, MLA, Chicago).
	1. Appendices (if applicable):
	1. Supplementary materials such as raw data, additional tables or figures, questionnaires, etc.
	1. Other information
	1. Funding
	1. Give the source of funding and the role of the funders for the present study and, if applicable, for the original study on which the present article is based

	Note: An Explanation and Elaboration article discusses each checklist item and gives methodological background and published examples of transparent reporting. The STROBE checklist is best used in conjunction with this article (freely available on the Web sites of PLoS Medicine at http://www.plosmedicine.org/, Annals of Internal Medicine at http://www.annals.org/, and Epidemiology at http://www.epidem.com/). Information on the STROBE Initiative is available at www.strobe-statement.org.