preserve YAML; add initial list of authors

r-lib · Dec 2, 2023 · ae30239 · ae30239
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diff --git a/paper/paper.Rmd b/paper/paper.Rmd
@@ -6,10 +6,29 @@ authors:
   - name: Jim Hester
     affiliation: 1
     orcid: ~
+  - name: Michael Chirico
+    affiliation: 2
+    orcid: ~
+  - name: Alexander Rosenstock
+    affiliation: 3
+    orcid: ~
+  - name: Indrajeet Patil
+    orcid: 0000-0003-1995-6531
+    affiliation: 4
 affiliations:
   - index: 1
     name: Netflix
-output: md_document
+  - index: 2
+    name: Google
+  - index: 3
+    name: Mathematisches Institut der Heinrich-Heine-Universität Düsseldorf
+  - index: 4
+    name: Center for Humans and Machines, Max Planck Institute for Human Development, Berlin, Germany
+output: 
+    md_document:
+      variant: "markdown"
+      preserve_yaml: true
+      standalone: true
 bibliography: paper.bib
 csl: apa.csl
 link-citations: yes

diff --git a/paper/paper.md b/paper/paper.md
@@ -1,12 +1,48 @@
+---
+title: "Static Code Analysis for R"
+date: "2023-12-02"
+tags: ["R", "linter", "tidyverse"]
+authors:
+  - name: Jim Hester
+    affiliation: 1
+    orcid: ~
+  - name: Michael Chirico
+    affiliation: 2
+    orcid: ~
+  - name: Alexander Rosenstock
+    affiliation: 3
+    orcid: ~
+  - name: Indrajeet Patil
+    orcid: 0000-0003-1995-6531
+    affiliation: 4
+affiliations:
+  - index: 1
+    name: Netflix
+  - index: 2
+    name: Google
+  - index: 3
+    name: Mathematisches Institut der Heinrich-Heine-Universität Düsseldorf
+  - index: 4
+    name: Center for Humans and Machines, Max Planck Institute for Human Development, Berlin, Germany
+output: 
+    md_document:
+      variant: "markdown"
+      preserve_yaml: true
+      standalone: true
+bibliography: paper.bib
+csl: apa.csl
+link-citations: yes
+---
+
 # Statement of Need
 
-R is an interpreted, dynamically typed programming language ([R Core
-Team, 2023](#ref-base2023)). It is a popular choice for statistical
-analysis and visualization, and is used by a wide range of researchers
-and data scientists. The `{lintr}` package is an open-source R package
-that provides static code analysis to check for a variety of common
-problems related to readability, efficiency, consistency, style, etc. In
-particular, it enforces the [tidyverse style
+R is an interpreted, dynamically typed programming language [@base2023].
+It is a popular choice for statistical analysis and visualization, and
+is used by a wide range of researchers and data scientists. The
+`{lintr}` package is an open-source R package that provides static code
+analysis to check for a variety of common problems related to
+readability, efficiency, consistency, style, etc. In particular, it
+enforces the [tidyverse style
 guide]((https://style.tidyverse.org/index.html)). It is designed to be
 easy to use and integrate into existing workflows, and can be run from
 the command line or used as part of an automated build or continuous
@@ -18,12 +54,14 @@ convenient for users to run `{lintr}` checks on their code as they work.
 
 As of this writing, `{lintr}` offers 115 linters.
 
-    library(lintr)
+``` r
+library(lintr)
 
-    length(all_linters())
-    #> [1] 115
+length(all_linters())
+#> [1] 115
+```
 
-Naturally, we can’t discuss all of them here. To see details about all
+Naturally, we can't discuss all of them here. To see details about all
 available linters, we encourage readers to see
 <https://lintr.r-lib.org/dev/reference/index.html#individual-linters>.
 
@@ -40,77 +78,85 @@ conditional statements is error-prone, and scalar `&&` and `||`,
 respectively, are to be preferred. The `vector_logic_linter()` linter
 detects such problematic usages.
 
-    lint(
-      text = "if (x & y) 1",
-      linters = vector_logic_linter()
-    )
-    #> <text>:1:7: warning: [vector_logic_linter] Conditional
-    #>     expressions require scalar logical operators (&& and
-    #>     ||)
-    #> if (x & y) 1
-    #>       ^
+``` r
+lint(
+  text = "if (x & y) 1",
+  linters = vector_logic_linter()
+)
+#> <text>:1:7: warning: [vector_logic_linter] Conditional
+#>     expressions require scalar logical operators (&& and
+#>     ||)
+#> if (x & y) 1
+#>       ^
+```
 
 -   **Efficiency**
 
 Sometimes the users might not be aware of a more efficient way offered
 by R for carrying out a computation. `{lintr}` offers linters to provide
 suggestions to improve code efficiency.
 
-    lint(
-      text = "any(is.na(x), na.rm = TRUE)",
-      linters = any_is_na_linter()
-    )
-    #> <text>:1:1: warning: [any_is_na_linter] anyNA(x) is better
-    #>     than any(is.na(x)).
-    #> any(is.na(x), na.rm = TRUE)
-    #> ^~~~~~~~~~~~~~~~~~~~~~~~~~~
+``` r
+lint(
+  text = "any(is.na(x), na.rm = TRUE)",
+  linters = any_is_na_linter()
+)
+#> <text>:1:1: warning: [any_is_na_linter] anyNA(x) is better
+#>     than any(is.na(x)).
+#> any(is.na(x), na.rm = TRUE)
+#> ^~~~~~~~~~~~~~~~~~~~~~~~~~~
+```
 
 -   **Readability**
 
 Coders spend significantly more time reading compared to writing code
-([McConnell, 2004](#ref-mcconnell2004code)). Thus, writing readable code
-makes the code more maintainable and reduces the possibility of
-introducing bugs stemming from a poor understanding of the code.
+[@mcconnell2004code]. Thus, writing readable code makes the code more
+maintainable and reduces the possibility of introducing bugs stemming
+from a poor understanding of the code.
 
 `{lintr}` provides a number of linters that suggest more readable
 alternatives. For example, `function_left_parentheses_linter()`.
 
-    lint(
-      text = "stats::sd (c (x, y, z))",
-      linters = function_left_parentheses_linter()
-    )
-    #> <text>:1:10: style: [function_left_parentheses_linter]
-    #>     Remove spaces before the left parenthesis in a function
-    #>     call.
-    #> stats::sd (c (x, y, z))
-    #>          ^
-    #> <text>:1:13: style: [function_left_parentheses_linter]
-    #>     Remove spaces before the left parenthesis in a function
-    #>     call.
-    #> stats::sd (c (x, y, z))
-    #>             ^
+``` r
+lint(
+  text = "stats::sd (c (x, y, z))",
+  linters = function_left_parentheses_linter()
+)
+#> <text>:1:10: style: [function_left_parentheses_linter]
+#>     Remove spaces before the left parenthesis in a function
+#>     call.
+#> stats::sd (c (x, y, z))
+#>          ^
+#> <text>:1:13: style: [function_left_parentheses_linter]
+#>     Remove spaces before the left parenthesis in a function
+#>     call.
+#> stats::sd (c (x, y, z))
+#>             ^
+```
 
 -   **Tidyverse style**
 
 `{lintr}` also provides linters to enforce the style used throughout the
-`{tidyverse}` ([Wickham et al., 2019](#ref-Wickham2019)) ecosystem of R
-packages. This style of coding has been outlined in the tidyverse style
-guide (<https://style.tidyverse.org/index.html>).
-
-    lint(
-      text = "1:3 %>% mean %>% as.character",
-      linters = pipe_call_linter()
-    )
-    #> <text>:1:9: warning: [pipe_call_linter] Use explicit calls
-    #>     in magrittr pipes, i.e., `a %>% foo` should be `a %>%
-    #>     foo()`.
-    #> 1:3 %>% mean %>% as.character
-    #>         ^~~~
-    #> <text>:1:18: warning: [pipe_call_linter] Use explicit calls
-    #>     in magrittr pipes, i.e., `a %>% foo` should be `a %>%
-    #>     foo()`.
-    #> 1:3 %>% mean %>% as.character
-    #>                  ^~~~~~~~~~~~
+`{tidyverse}` [@Wickham2019] ecosystem of R packages. This style of
+coding has been outlined in the tidyverse style guide
+(<https://style.tidyverse.org/index.html>).
+
+``` r
+lint(
+  text = "1:3 %>% mean %>% as.character",
+  linters = pipe_call_linter()
+)
+#> <text>:1:9: warning: [pipe_call_linter] Use explicit calls
+#>     in magrittr pipes, i.e., `a %>% foo` should be `a %>%
+#>     foo()`.
+#> 1:3 %>% mean %>% as.character
+#>         ^~~~
+#> <text>:1:18: warning: [pipe_call_linter] Use explicit calls
+#>     in magrittr pipes, i.e., `a %>% foo` should be `a %>%
+#>     foo()`.
+#> 1:3 %>% mean %>% as.character
+#>                  ^~~~~~~~~~~~
+```
 
 # Benefits of using `{lintr}`
 
@@ -161,17 +207,4 @@ The authors declare no conflict of interest.
 
 # Acknowledgments
 
-# References
-
-McConnell, S. (2004). *Code complete*. Pearson Education.
-
-R Core Team. (2023). *R: A language and environment for statistical
-computing*. R Foundation for Statistical Computing.
-<https://www.R-project.org/>
-
-Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L. D.,
-François, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., Kuhn, M.,
-Pedersen, T. L., Miller, E., Bache, S. M., Müller, K., Ooms, J.,
-Robinson, D., Seidel, D. P., Spinu, V., … Yutani, H. (2019). Welcome to
-the <span class="nocase">tidyverse</span>. *Journal of Open Source
-Software*, *4*(43), 1686. <https://doi.org/10.21105/joss.01686>
+# References {#references .unnumbered}