improve documentation #50

README.Rmd

@@ -240,6 +240,12 @@ Before running `grateful` you might want to run [`funchir::stale_package_check`]
 If getting an error like "Error in (function (pkg, lib.loc = NULL): there is no package called...", that means that some of your scripts is loading a package that is no longer available in your computer, so {grateful} cannot grab its citation. To fix this, there are several options. First, you could omit that package (or those packages, if more than one) from {grateful} citations using `cite_packages(omit = c("package1", "package2")`. Alternatively, try checking if that package is still needed for your project and you want to cite it, otherwise remove or comment that line where the package is loaded. If you still use and want to cite that package, install it, and then run `cite_packages` again.
 
 
+### Projects with large number of packages or files
+
+When a project includes many used packages (or files), `renv` may issue a warning. Use `options(renv.config.dependencies.limit = 10000)` to overcome the warning and scan the project for all packages used. Alternatively, use `.renvignore` to ignore certain files or folders (see `renv` [help](https://rstudio.github.io/renv/reference/dependencies.html#ignoring-files)).
+
+
+
 ### Citing 'grateful'
 
 ```{r eval=TRUE, comment=NA}

README.md

@@ -173,10 +173,10 @@ Use `scan_packages`
 ``` r
 scan_packages()
          pkg version
-1     badger   0.2.3
-2       base   4.4.0
-3      knitr    1.47
-4    pkgdown   2.0.9
+1     badger   0.2.4
+2       base   4.4.1
+3      knitr    1.48
+4    pkgdown   2.1.0
 5    remotes   2.5.0
 6       renv   1.0.7
 7  rmarkdown    2.27
@@ -318,6 +318,15 @@ to cite it, otherwise remove or comment that line where the package is
 loaded. If you still use and want to cite that package, install it, and
 then run `cite_packages` again.
 
+### Projects with large number of packages or files
+
+When a project includes many used packages (or files), `renv` may issue
+a warning. Use `options(renv.config.dependencies.limit = 10000)` to
+overcome the warning and scan the project for all packages used.
+Alternatively, use `.renvignore` to ignore certain files or folders (see
+`renv`
+[help](https://rstudio.github.io/renv/reference/dependencies.html#ignoring-files)).
+
 ### Citing ‘grateful’
 
 ``` r

Rmd_Quarto/grateful-Quarto.qmd

@@ -2,7 +2,7 @@
 title: "Using {grateful} with Quarto"
 format: pdf
 bibliography: grateful-refs.bib
-# csl: "`r grateful::get_csl('journal-of-ecology', out.dir = '.')`"
+# csl: https://www.zotero.org/styles/journal-of-ecology
 ---
 
 Load packages
@@ -30,10 +30,23 @@ visreg(model)
 
 ### Software used
 
+**Paragraph output:**
+
 ```{r}
 #| echo: false
 grateful::cite_packages(output = "paragraph", pkgs = "Session", out.dir = ".")
 ```
 
+**Table output:**
+
+```{r}
+#| echo: false
+pkgs <- grateful::cite_packages(output = "table", pkgs = "Session", out.dir = ".")
+knitr::kable(pkgs)
+```
+
+
+
+
 ## References
 

Rmd_Quarto/grateful-Rmarkdown.Rmd

@@ -2,7 +2,7 @@
 title: "Using {grateful} with Rmarkdown"
 output: pdf_document
 bibliography: grateful-refs.bib
-# csl: "`r grateful::get_csl('journal-of-ecology', out.dir = '.')`"
+# csl: https://www.zotero.org/styles/journal-of-ecology
 ---
 
 Load packages
@@ -29,9 +29,23 @@ visreg(model)
 
 ### Software used
 
+**Paragraph output:**
+
 ```{r echo=FALSE}
 grateful::cite_packages(output = "paragraph", pkgs = "Session", out.dir = ".")
 ```
 
 
+**Table output:**
+
+```{r}
+#| echo: false
+pkgs <- grateful::cite_packages(output = "table", pkgs = "Session", out.dir = ".")
+knitr::kable(pkgs)
+```
+
+
+
 ## References
+
+

Rmd_Quarto/separate_bibliographies/.gitignore

@@ -0,0 +1,2 @@
+_extensions
+multibib.lua