Using Code Templates in RStudio
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+Site built with pkgdown 2.0.9.
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+4. Make a Package • rUM
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+Introduction
+
+Saving your data and analyses into an R package helps to create
+reproducible research. Someone who wants to reproduce your work can load
+a package to have access to your data and your paper(s).
+rUM can help you by creating a project
+that has all the files/directories needed for an R package including a
+vignette folder that contains the outline of a paper.
+
+
+How do I make a package project?
+
+All you need to do is add vignette = TRUE when you use
+the make_project() function. Once the project is created,
+run the run_me.R file. For example type:
+
+-
+
rUM::make_project("~/Desktop/my.example", "R", example = TRUE, vignette = TRUE).
+This creates a new project with all the files for a package in the
+current directory. The vignette includes an example table and figure and
+all the R Markdown syntax for adding hyperlinks to the table and
+figures.
+- After the new project is open, run the
+RUN_ME_FIRST.R file. The easiest way to do this is by
+typing
source("RUN_ME_FIRST.R") into the RStudio IDE
+console and then pressing enter. If you are working in RStudio it will
+ask you if it can/should close windows for two deleted files. Say
+Yes. They are a couple temporary files that we used to
+set options the project.
+
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+
+
+
+- Set the license for your package. REMEMBER: Do share
+sensitive data. Talk to the data privacy officer at your
+institution/organization before sharing any data. Ask them for advice on
+setting a software license. If you are not planning on publicly
+sharing your data consider using a proprietary license. For example,
+type
+
usethis::use_proprietary_license("Your Name Goes Here"). To
+learn more about licences look at the documentation for
+use_proprietary_license() by typing:
+?usethis::use_proprietary_license. You can also learn more
+at choosealicense.com or here
+but talk to the legal counsel at your institution/organization before
+making a decision.
+
+
+
+Can I write my vignette with Quarto?
+
+Yes! When you install rUM we make sure
+you have a modern version of the R quarto package but we do
+not install the most modern copy of the Quarto language itself (which
+lives outside of R). You can make sure that your version of Quarto is
+modern enough by running quarto::quarto_version(). If your
+version is not 1.4.549 or higher, install the latest version of Quarto
+directly from here.
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+5. Include an example in the analysis paper outline • rUM
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+ 5. Include an example in the analysis paper
+outline
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+ Source: vignettes/O5_show_example.Rmd
+ O5_show_example.Rmd
+
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+
+
+
+Introduction
+
+If you would like to see an example paper, that has code blocks to
+produce a summary table and a graphic, include the
+example = TRUE argument when you use the
+make_project() function. For example, if you type
+rUM::make_project("~/Desktop/my.example", "R", example = TRUE),
+in the Results section of the paper you will see code
+like:
+
+#| tbl-cap: |
+#| Your real caption belongs here. Remember that cross references to tables
+#| use labels for the code chunk starting with tbl-.
+
+
+# To learn how to use tbl_summary look at https://www.danieldsjoberg.com/gtsummary/
+analysis |>
+ tbl_summary(
+ include = c(everything()), # choose your variables here
+ # change auto_man to the name of your column variable or delete by = auto_man
+ by = auto_man, # split table by group
+ missing = "no" # don't list missing data separately
+ ) %>%
+ # add_n() %>% # add column with total number of non-missing observations
+ # add_p() %>% # test for a difference between groups
+ modify_header(label = "") %>% # update the column header to be blank
+ bold_labels()
+and
+
+
+#| fig-cap: |
+#| Your real caption belongs here. Remember that cross references to figures
+#| use labels for the code chunk starting with fig-.
+
+# To learn how to use ggplot start here: https://ggplot2.tidyverse.org/#learning-ggplot2
+analysis |>
+ ggplot() +
+ labs(
+ title = "Your short title goes here.",
+ caption = "Your data sources/citation goes here."
+ ) +
+ geom_blank()
+ # remove geom_blank() and add details here
+You will also notice that there are sentences, which begin with “As
+can be seen in” that contain cross-reference hyperlinks to the tables
+and figures.
+
+Simpler Tables
+
+The example table is created using a package called
+gtsummary. It makes completely customizable, beautiful,
+summary tables which support hyperlinks/cross-references in the
+sentences you write in your paper.
+A simpler option is to use the table1() function from
+the table1 package. It makes excellent tables with nearly
+no typing. If you would like to try it, paste the code below into the
+tbl-table1 code chunk. Unfortunately table1
+does not have good support for hyperlinks/cross-references from your
+writing/prose.
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diff --git a/docs/articles/index.html b/docs/articles/index.html
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-Articles • rUM Articles • rUM
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3. Create a R Markdown File from a rUM Template
+
+ 4. Make a Package
+
+
+ 5. Include an example in the analysis paper outline
+
Introduction +
+Saving your data and analyses into an R package helps to create
+reproducible research. Someone who wants to reproduce your work can load
+a package to have access to your data and your paper(s).
+rUM can help you by creating a project
+that has all the files/directories needed for an R package including a
+vignette folder that contains the outline of a paper.
How do I make a package project? +
+All you need to do is add vignette = TRUE when you use
+the make_project() function. Once the project is created,
+run the run_me.R file. For example type:
-
+
-
+
rUM::make_project("~/Desktop/my.example", "R", example = TRUE, vignette = TRUE). +This creates a new project with all the files for a package in the +current directory. The vignette includes an example table and figure and +all the R Markdown syntax for adding hyperlinks to the table and +figures.
+ - After the new project is open, run the
+RUN_ME_FIRST.R file. The easiest way to do this is by
+typing
source("RUN_ME_FIRST.R")into the RStudio IDE +console and then pressing enter. If you are working in RStudio it will +ask you if it can/should close windows for two deleted files. Say +Yes. They are a couple temporary files that we used to +set options the project.
+
+-
+
- Set the license for your package. REMEMBER: Do share
+sensitive data. Talk to the data privacy officer at your
+institution/organization before sharing any data. Ask them for advice on
+setting a software license. If you are not planning on publicly
+sharing your data consider using a proprietary license. For example,
+type
+
usethis::use_proprietary_license("Your Name Goes Here"). To +learn more about licences look at the documentation for +use_proprietary_license()by typing: +?usethis::use_proprietary_license. You can also learn more +at choosealicense.com or here +but talk to the legal counsel at your institution/organization before +making a decision.
+
Can I write my vignette with Quarto? +
+Yes! When you install rUM we make sure
+you have a modern version of the R quarto package but we do
+not install the most modern copy of the Quarto language itself (which
+lives outside of R). You can make sure that your version of Quarto is
+modern enough by running quarto::quarto_version(). If your
+version is not 1.4.549 or higher, install the latest version of Quarto
+directly from here.
5. Include an example in the analysis paper +outline
+ + + Source:vignettes/O5_show_example.Rmd
+ O5_show_example.RmdIntroduction +
+If you would like to see an example paper, that has code blocks to
+produce a summary table and a graphic, include the
+example = TRUE argument when you use the
+make_project() function. For example, if you type
+rUM::make_project("~/Desktop/my.example", "R", example = TRUE),
+in the Results section of the paper you will see code
+like:
+#| tbl-cap: |
+#| Your real caption belongs here. Remember that cross references to tables
+#| use labels for the code chunk starting with tbl-.
+
+
+# To learn how to use tbl_summary look at https://www.danieldsjoberg.com/gtsummary/
+analysis |>
+ tbl_summary(
+ include = c(everything()), # choose your variables here
+ # change auto_man to the name of your column variable or delete by = auto_man
+ by = auto_man, # split table by group
+ missing = "no" # don't list missing data separately
+ ) %>%
+ # add_n() %>% # add column with total number of non-missing observations
+ # add_p() %>% # test for a difference between groups
+ modify_header(label = "") %>% # update the column header to be blank
+ bold_labels()and
+
+
+#| fig-cap: |
+#| Your real caption belongs here. Remember that cross references to figures
+#| use labels for the code chunk starting with fig-.
+
+# To learn how to use ggplot start here: https://ggplot2.tidyverse.org/#learning-ggplot2
+analysis |>
+ ggplot() +
+ labs(
+ title = "Your short title goes here.",
+ caption = "Your data sources/citation goes here."
+ ) +
+ geom_blank()
+ # remove geom_blank() and add details hereYou will also notice that there are sentences, which begin with “As +can be seen in” that contain cross-reference hyperlinks to the tables +and figures.
+Simpler Tables +
+The example table is created using a package called
+gtsummary. It makes completely customizable, beautiful,
+summary tables which support hyperlinks/cross-references in the
+sentences you write in your paper.
A simpler option is to use the table1() function from
+the table1 package. It makes excellent tables with nearly
+no typing. If you would like to try it, paste the code below into the
+tbl-table1 code chunk. Unfortunately table1
+does not have good support for hyperlinks/cross-references from your
+writing/prose.