Compile a report with different checks

This function produce an HTML report to investigate potential issues in a reference database.

refdb_report(x, file = NULL, view = TRUE)

Arguments

x

a reference database.

file

the file (path) to write the report. If NULL the report is written in the user temp directory.

view

A logical. If TRUE (default), the file is instantly opened in the web browser.

Value

The function invisibly returns the file where the report was written.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                            genus = "genus_name",
                            species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")
tmp <- tempfile()

refdb_report(lib, tmp, view = FALSE)
#> 
#> 
#> processing file: file23903a76b559.Rmd
#> 1/13                  
#> 2/13 [setup]          
#> 3/13                  
#> 4/13 [unnamed-chunk-1]
#> 5/13                  
#> 6/13 [unnamed-chunk-2]
#> 7/13                  
#> 8/13 [unnamed-chunk-3]
#> 9/13                  
#> 10/13 [unnamed-chunk-4]
#> 11/13                  
#> 12/13 [unnamed-chunk-5]
#> 13/13                  
#> output file: file23903a76b559.knit.md
#> /usr/share/positron/resources/app/quarto/bin/tools/x86_64/pandoc +RTS -K512m -RTS file23903a76b559.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpxyP55R/file23906d582482.html --lua-filter /home/francois/R/x86_64-pc-linux-gnu-library/4.5/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/francois/R/x86_64-pc-linux-gnu-library/4.5/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/francois/R/x86_64-pc-linux-gnu-library/4.5/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/francois/R/x86_64-pc-linux-gnu-library/4.5/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpxyP55R/rmarkdown-str23903b299989.html 
#> 
#> Output created: /tmp/RtmpxyP55R/file23906d582482.html