Wrapper around an XML representation of a Markdown document. It contains four publicly accessible slots: path, frontmatter, body, and ns.
Details
This class is a fancy wrapper around the results of to_xml() and
has methods that make it easier to add, analyze, remove, or write elements
of your markdown document.
Note
this requires the sourcepos attribute to be recorded when the
object is initialised. See protect_unescaped() for details.
See also
to_md_vec() for a way to generate the same vector from a
nodelist without a yarn object
Public fields
path[
character] path to file on diskfrontmatter[
character] text block at head of filefrontmatter_format[
character] 'YAML', 'TOML' or 'JSON'body[
xml_document] an xml document of the (R)Markdown file.ns[
xml_document] an xml namespace object defining "md" to commonmark.
![[Deprecated]](figures/lifecycle-deprecated.svg)
Methods
Method new()
Create a new yarn document
Usage
yarn$new(path = NULL, encoding = "UTF-8", sourcepos = FALSE, ...)Arguments
path[
character] path to a markdown episode file on diskencoding[
character] encoding passed toreadLines()sourcepospassed to
commonmark::markdown_xml(). IfTRUE, the source position of the file will be included as a "sourcepos" attribute. Defaults toFALSE....arguments passed on to
to_xml().
Examples
path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
ex1
path2 <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex2 <- tinkr::yarn$new(path2)
ex2Method reset()
reset a yarn document from the original file
Examples
path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
# OH NO
ex1$body
ex1$body <- xml2::xml_missing()
ex1$reset()
ex1$bodyMethod write()
Write a yarn document to Markdown/R Markdown
Usage
yarn$write(path = NULL, stylesheet_path = stylesheet())Method show()
show the markdown contents on the screen
Usage
yarn$show(lines = TRUE, stylesheet_path = stylesheet())Arguments
linesa subset of elements to show. Defaults to
TRUE, which shows all lines of the output. This can be either logical or numeric.stylesheet_pathpath to the xsl stylesheet to convert XML to markdown.
Examples
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex2 <- tinkr::yarn$new(path)
ex2$head(5)
ex2$tail(5)
ex2$show()Method head()
show the head of the markdown contents on the screen
Usage
yarn$head(n = 6L, stylesheet_path = stylesheet())Method tail()
show the tail of the markdown contents on the screen
Usage
yarn$tail(n = 6L, stylesheet_path = stylesheet())Method md_vec()
query and extract markdown elements
Usage
yarn$md_vec(xpath = NULL, stylesheet_path = stylesheet())Arguments
xpatha valid XPath expression
stylesheet_pathpath to the xsl stylesheet to convert XML to markdown.
Examples
path <- system.file("extdata", "example1.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
# all headings
ex$md_vec(".//md:heading")
# all headings greater than level 3
ex$md_vec(".//md:heading[@level>3]")
# all links
ex$md_vec(".//md:link")
# all links that are part of lists
ex$md_vec(".//md:list//md:link")
# all code
ex$md_vec(".//md:code | .//md:code_block")Method add_md()
add an arbitrary Markdown element to the document
Arguments
mda string of markdown formatted text.
wherethe location in the document to add your markdown text. This is passed on to
xml2::xml_add_child(). Defaults to 0, which indicates the very top of the document.
Examples
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex <- tinkr::yarn$new(path)
# two headings, no lists
xml2::xml_find_all(ex$body, "md:heading", ex$ns)
xml2::xml_find_all(ex$body, "md:list", ex$ns)
ex$add_md(
"# Hello\n\nThis is *new* formatted text from `{tinkr}`!",
where = 1L
)$add_md(
" - This\n - is\n - a new list",
where = 2L
)
# three headings
xml2::xml_find_all(ex$body, "md:heading", ex$ns)
xml2::xml_find_all(ex$body, "md:list", ex$ns)
tmp <- tempfile()
ex$write(tmp)
readLines(tmp, n = 20)Method append_md()
append abritrarily markdown to a node or set of nodes
Arguments
mda string of markdown formatted text.
nodesan XPath expression that evaulates to object of class
xml_nodeorxml_nodesetthat are all either inline or block nodes (never both). The XPath expression is passed toxml2::xml_find_all(). If you want to append a specific node, you can pass that node to this parameter.spaceif
TRUE, inline nodes will have a space inserted before they are appended.
Details
this is similar to the add_md() method except that it can do
the following:
append content after a specific node or set of nodes
append content to multiple places in the document
Examples
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex <- tinkr::yarn$new(path)
# append a note after the first heading
txt <- c("> Hello from *tinkr*!", ">", "> :heart: R")
ex$append_md(txt, ".//md:heading[1]")$head(20)Method prepend_md()
prepend abritrarily markdown to a node or set of nodes
Arguments
mda string of markdown formatted text.
nodesan XPath expression that evaulates to object of class
xml_nodeorxml_nodesetthat are all either inline or block nodes (never both). The XPath expression is passed toxml2::xml_find_all(). If you want to append a specific node, you can pass that node to this parameter.spaceif
TRUE, inline nodes will have a space inserted before they are prepended.
Details
this is similar to the add_md() method except that it can do
the following:
prepend content after a specific node or set of nodes
prepend content to multiple places in the document
Examples
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex <- tinkr::yarn$new(path)
# prepend a table description to the birds table
ex$prepend_md("Table: BIRDS, NERDS", ".//md:table[1]")$tail(20)Method protect_math()
Protect math blocks from being escaped
Examples
path <- system.file("extdata", "math-example.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
ex$tail() # math blocks are escaped :(
ex$protect_math()$tail() # math blocks are no longer escaped :)Method protect_curly()
Protect curly phrases {likethat} from being escaped
Examples
path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
ex$protect_curly()$head()Method protect_unescaped()
Protect unescaped square braces from being escaped.
This is applied by default when you use yarn$new(sourcepos = TRUE).
Examples
path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path, sourcepos = TRUE, unescaped = FALSE)
ex$tail()
ex$protect_unescaped()$tail()Method get_protected()
Return nodes whose contents are protected from being escaped
Arguments
typea character vector listing the protections to be included. Defaults to
NULL, which includes all protected nodes:math: via the
protect_math()functioncurly: via the
protect_curly()functionunescaped: via the
protect_unescaped()function
Examples
path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path, sourcepos = TRUE)
# protect curly braces
ex$protect_curly()
# add math and protect it
ex$add_md(c("## math\n",
"$c^2 = a^2 + b^2$\n",
"$$",
"\\sum_{i}^k = x_i + 1",
"$$\n")
)
ex$protect_math()
# get protected now shows all the protected nodes
ex$get_protected()
ex$get_protected(c("math", "curly")) # only show the math and curlyExamples
## ------------------------------------------------
## Method `yarn$new`
## ------------------------------------------------
path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
ex1
#> <yarn>
#> Public:
#> add_md: function (md, where = 0L)
#> append_md: function (md, nodes = NULL, space = TRUE)
#> body: xml_document, xml_node
#> clone: function (deep = FALSE)
#> frontmatter: --- title: "What have these birds been studied for? Quer ...
#> frontmatter_format: YAML
#> get_protected: function (type = NULL)
#> head: function (n = 6L, stylesheet_path = stylesheet())
#> initialize: function (path = NULL, encoding = "UTF-8", sourcepos = FALSE,
#> md_vec: function (xpath = NULL, stylesheet_path = stylesheet())
#> ns: http://commonmark.org/xml/1.0
#> path: /usr/local/lib/R/site-library/tinkr/extdata/example1.md
#> prepend_md: function (md, nodes = NULL, space = TRUE)
#> protect_curly: function ()
#> protect_math: function ()
#> protect_unescaped: function ()
#> reset: function ()
#> show: function (lines = TRUE, stylesheet_path = stylesheet())
#> tail: function (n = 6L, stylesheet_path = stylesheet())
#> write: function (path = NULL, stylesheet_path = stylesheet())
#> yaml: active binding
#> Private:
#> encoding: UTF-8
#> md_lines: function (path = NULL, stylesheet = NULL)
#> sourcepos: FALSE
path2 <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex2 <- tinkr::yarn$new(path2)
ex2
#> <yarn>
#> Public:
#> add_md: function (md, where = 0L)
#> append_md: function (md, nodes = NULL, space = TRUE)
#> body: xml_document, xml_node
#> clone: function (deep = FALSE)
#> frontmatter: --- title: "Untitled" author: "M. Salmon" date: "Septemb ...
#> frontmatter_format: YAML
#> get_protected: function (type = NULL)
#> head: function (n = 6L, stylesheet_path = stylesheet())
#> initialize: function (path = NULL, encoding = "UTF-8", sourcepos = FALSE,
#> md_vec: function (xpath = NULL, stylesheet_path = stylesheet())
#> ns: http://commonmark.org/xml/1.0
#> path: /usr/local/lib/R/site-library/tinkr/extdata/example2.Rmd
#> prepend_md: function (md, nodes = NULL, space = TRUE)
#> protect_curly: function ()
#> protect_math: function ()
#> protect_unescaped: function ()
#> reset: function ()
#> show: function (lines = TRUE, stylesheet_path = stylesheet())
#> tail: function (n = 6L, stylesheet_path = stylesheet())
#> write: function (path = NULL, stylesheet_path = stylesheet())
#> yaml: active binding
#> Private:
#> encoding: UTF-8
#> md_lines: function (path = NULL, stylesheet = NULL)
#> sourcepos: FALSE
## ------------------------------------------------
## Method `yarn$reset`
## ------------------------------------------------
path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
# OH NO
ex1$body
#> {xml_document}
#> <document xmlns="http://commonmark.org/xml/1.0">
#> [1] <paragraph>\n <text xml:space="preserve">In the </text>\n <link destin ...
#> [2] <heading level="3">\n <text xml:space="preserve">Getting a list of 50 s ...
#> [3] <paragraph>\n <text xml:space="preserve">For more details about the fol ...
#> [4] <code_block info="r" xml:space="preserve" name=""># polygon for filterin ...
#> [5] <paragraph>\n <text xml:space="preserve">For the sake of simplicity, we ...
#> [6] <code_block info="r" xml:space="preserve" name="">species <- ebd %> ...
#> [7] <paragraph>\n <text xml:space="preserve">The species are Carrion Crow, ...
#> [8] <heading level="3">\n <text xml:space="preserve">Querying the scientifi ...
#> [9] <paragraph>\n <text xml:space="preserve">Just like rOpenSci has a taxon ...
#> [10] <paragraph>\n <text xml:space="preserve">We shall use </text>\n <code ...
#> [11] <paragraph>\n <text xml:space="preserve">We first define a function ret ...
#> [12] <paragraph>\n <text xml:space="preserve">We use </text>\n <code xml:sp ...
#> [13] <code_block info="r" xml:space="preserve" name="">.get_papers <- func ...
#> [14] <code_block xml:space="preserve" name="">## [1] "Great spotted cuckoo n ...
#> [15] <paragraph>\n <text xml:space="preserve">If we were working on a scient ...
#> [16] <paragraph>\n <text xml:space="preserve">We then apply this function to ...
#> [17] <code_block info="r" xml:space="preserve" name="">get_papers <- ratel ...
#> [18] <code_block xml:space="preserve" name="">## [1] 522\n</code_block>
#> [19] <code_block info="r" xml:space="preserve" name="">all_papers <- uniqu ...
#> [20] <code_block xml:space="preserve" name="">## [1] 378\n</code_block>
#> ...
ex1$body <- xml2::xml_missing()
ex1$reset()
ex1$body
#> {xml_document}
#> <document xmlns="http://commonmark.org/xml/1.0">
#> [1] <paragraph>\n <text xml:space="preserve">In the </text>\n <link destin ...
#> [2] <heading level="3">\n <text xml:space="preserve">Getting a list of 50 s ...
#> [3] <paragraph>\n <text xml:space="preserve">For more details about the fol ...
#> [4] <code_block info="r" xml:space="preserve" name=""># polygon for filterin ...
#> [5] <paragraph>\n <text xml:space="preserve">For the sake of simplicity, we ...
#> [6] <code_block info="r" xml:space="preserve" name="">species <- ebd %> ...
#> [7] <paragraph>\n <text xml:space="preserve">The species are Carrion Crow, ...
#> [8] <heading level="3">\n <text xml:space="preserve">Querying the scientifi ...
#> [9] <paragraph>\n <text xml:space="preserve">Just like rOpenSci has a taxon ...
#> [10] <paragraph>\n <text xml:space="preserve">We shall use </text>\n <code ...
#> [11] <paragraph>\n <text xml:space="preserve">We first define a function ret ...
#> [12] <paragraph>\n <text xml:space="preserve">We use </text>\n <code xml:sp ...
#> [13] <code_block info="r" xml:space="preserve" name="">.get_papers <- func ...
#> [14] <code_block xml:space="preserve" name="">## [1] "Great spotted cuckoo n ...
#> [15] <paragraph>\n <text xml:space="preserve">If we were working on a scient ...
#> [16] <paragraph>\n <text xml:space="preserve">We then apply this function to ...
#> [17] <code_block info="r" xml:space="preserve" name="">get_papers <- ratel ...
#> [18] <code_block xml:space="preserve" name="">## [1] 522\n</code_block>
#> [19] <code_block info="r" xml:space="preserve" name="">all_papers <- uniqu ...
#> [20] <code_block xml:space="preserve" name="">## [1] 378\n</code_block>
#> ...
## ------------------------------------------------
## Method `yarn$write`
## ------------------------------------------------
path <- system.file("extdata", "example1.md", package = "tinkr")
ex1 <- tinkr::yarn$new(path)
ex1
#> <yarn>
#> Public:
#> add_md: function (md, where = 0L)
#> append_md: function (md, nodes = NULL, space = TRUE)
#> body: xml_document, xml_node
#> clone: function (deep = FALSE)
#> frontmatter: --- title: "What have these birds been studied for? Quer ...
#> frontmatter_format: YAML
#> get_protected: function (type = NULL)
#> head: function (n = 6L, stylesheet_path = stylesheet())
#> initialize: function (path = NULL, encoding = "UTF-8", sourcepos = FALSE,
#> md_vec: function (xpath = NULL, stylesheet_path = stylesheet())
#> ns: http://commonmark.org/xml/1.0
#> path: /usr/local/lib/R/site-library/tinkr/extdata/example1.md
#> prepend_md: function (md, nodes = NULL, space = TRUE)
#> protect_curly: function ()
#> protect_math: function ()
#> protect_unescaped: function ()
#> reset: function ()
#> show: function (lines = TRUE, stylesheet_path = stylesheet())
#> tail: function (n = 6L, stylesheet_path = stylesheet())
#> write: function (path = NULL, stylesheet_path = stylesheet())
#> yaml: active binding
#> Private:
#> encoding: UTF-8
#> md_lines: function (path = NULL, stylesheet = NULL)
#> sourcepos: FALSE
tmp <- tempfile()
try(readLines(tmp)) # nothing in the file
#> Warning: cannot open file '/tmp/RtmpCryV9T/file7ad79d5bc8e': No such file or directory
#> Error in file(con, "r") : cannot open the connection
ex1$write(tmp)
head(readLines(tmp)) # now a markdown file
#> [1] "---"
#> [2] "title: \"What have these birds been studied for? Querying science outputs with R\""
#> [3] "slug: birds-science"
#> [4] "authors:"
#> [5] " - name: Maëlle Salmon"
#> [6] " url: https://masalmon.eu/"
unlink(tmp)
## ------------------------------------------------
## Method `yarn$show`
## ------------------------------------------------
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex2 <- tinkr::yarn$new(path)
ex2$head(5)
#> ---
#> title: "Untitled"
#> author: "M. Salmon"
#> date: "September 6, 2018"
#> output: html_document
ex2$tail(5)
#> | Cyanistes caeruleus | Eurasian Blue Tit | 233 |
#> | Chroicocephalus ridibundus | Black-headed Gull | 223 |
#>
#> blabla
#>
ex2$show()
#> ---
#> title: "Untitled"
#> author: "M. Salmon"
#> date: "September 6, 2018"
#> output: html_document
#> ---
#>
#> ```{r setup, include=FALSE, eval=TRUE}
#> knitr::opts_chunk$set(echo = TRUE)
#> ```
#>
#> ## R Markdown
#>
#> This is an ~~R Markdown document~~. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
#>
#> When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
#>
#> ```{r, eval=TRUE, echo=TRUE}
#> summary(cars)
#> ```
#>
#> ## Including Plots
#>
#> You can also embed plots, for example:
#>
#> ```{python, fig.cap="pretty plot", echo=-c(1, 2), eval=TRUE}
#> plot(pressure)
#> ```
#>
#> ```{python}
#> plot(pressure)
#> ```
#>
#> Non-RMarkdown blocks are also considered
#>
#> ```bash
#> echo "this is an unevaluted bash block"
#> ```
#>
#> ```
#> This is an ambiguous code block
#> ```
#>
#> Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
#>
#> | scientific\_name | common\_name | n |
#> | :------------------------- | :------------------ | --: |
#> | Corvus corone | Carrion Crow | 288 |
#> | Turdus merula | Eurasian Blackbird | 285 |
#> | Anas platyrhynchos | Mallard | 273 |
#> | Fulica atra | Eurasian Coot | 268 |
#> | Parus major | Great Tit | 266 |
#> | Podiceps cristatus | Great Crested Grebe | 254 |
#> | Ardea cinerea | Gray Heron | 236 |
#> | Cygnus olor | Mute Swan | 234 |
#> | Cyanistes caeruleus | Eurasian Blue Tit | 233 |
#> | Chroicocephalus ridibundus | Black-headed Gull | 223 |
#>
#> blabla
#>
## ------------------------------------------------
## Method `yarn$md_vec`
## ------------------------------------------------
path <- system.file("extdata", "example1.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
# all headings
ex$md_vec(".//md:heading")
#> [1] "### Getting a list of 50 species from occurrence data"
#> [2] "### Querying the scientific literature"
#> [3] "### Querying scientific open data"
#> [4] "### Conclusion"
#> [5] "#### Scientific literature access"
#> [6] "#### Scientific data access… and publication with R"
#> [7] "#### No more birding? No, your turn!"
# all headings greater than level 3
ex$md_vec(".//md:heading[@level>3]")
#> [1] "#### Scientific literature access"
#> [2] "#### Scientific data access… and publication with R"
#> [3] "#### No more birding? No, your turn!"
# all links
ex$md_vec(".//md:link")
#> [1] "[second post of the series where we obtained data from\neBird](https://ropensci.org/blog/2018/08/21/birds-radolfzell/)"
#> [2] "[the fourth post of the\nseries](https://ropensci.org/blog/2018/09/04/birds-taxo-traits/)"
#> [3] "[previous post\nof the series](https://ropensci.org/blog/2018/08/21/birds-radolfzell/)"
#> [4] "[(`glue::glue_collapse(species, sep = \", \", last = \" and \")`)](https://twitter.com/LucyStats/status/1031938964796657665?s=19)"
#> [5] "[`taxize`](https://github.com/ropensci/taxize)"
#> [6] "[`spocc`](https://github.com/ropensci/spocc)"
#> [7] "[`fulltext`](https://github.com/ropensci/fulltext)"
#> [8] "[\"Investigating the impact of media on demand for wildlife: A case\nstudy of Harry Potter and the UK trade in\nowls\"](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182368)"
#> [9] "[`cites`](https://github.com/ecohealthalliance/cites/)"
#> [10] "[`rcites`](https://ibartomeus.github.io/rcites/)"
#> [11] "[`wordcloud`\npackage](https://cran.r-project.org/web/packages/wordcloud/index.html)"
#> [12] "[`wordcloud2`\npackage](https://github.com/Lchiffon/wordcloud2)"
#> [13] "[from\nPhylopic](http://phylopic.org/image/6209c9be-060e-4d7f-bc74-a75f3ccf4629/)"
#> [14] "[DataONE](https://www.dataone.org/)"
#> [15] "[searching\nDataONE\nvignette](https://github.com/DataONEorg/rdataone/blob/master/vignettes/searching-dataone.Rmd)"
#> [16] "[download data\nvignette](https://github.com/DataONEorg/rdataone/blob/master/vignettes/download-data.Rmd)"
#> [17] "[`europepmc`](https://github.com/ropensci/europepmc)"
#> [18] "[`jstor`](https://github.com/ropensci/jstor)"
#> [19] "[`suppdata`](https://github.com/ropensci/suppdata)"
#> [20] "[much\nmore](https://ropensci.org/packages/)"
#> [21] "[`dataone`\npackage](https://github.com/DataONEorg/rdataone)"
#> [22] "[`rfigshare`](https://github.com/ropensci/rfigshare)"
#> [23] "[Figshare](https://figshare.com/)"
#> [24] "[`EML` package](https://github.com/ropensci/EML)"
#> [25] "[unconf\n`dataspice` project](https://github.com/ropenscilabs/dataspice)"
#> [26] "[here](https://ropensci.org/packages/)"
#> [27] "[How to identify spots for birding using open geographical\ndata](https://ropensci.org/blog/2018/08/14/where-to-bird/)"
#> [28] "[How to obtain bird occurrence data in\nR](https://ropensci.org/blog/2018/08/21/birds-radolfzell/)"
#> [29] "[How to extract text from old natural history\ndrawings](https://ropensci.org/blog/2018/08/28/birds-ocr/)"
#> [30] "[How to complement an occurrence dataset with taxonomy and trait\ninformation](https://ropensci.org/blog/2018/09/04/birds-taxo-traits/)"
#> [31] "[our friendly discussion\nforum](https://discuss.ropensci.org/c/usecases)"
# all links that are part of lists
ex$md_vec(".//md:list//md:link")
#> [1] "[download data\nvignette](https://github.com/DataONEorg/rdataone/blob/master/vignettes/download-data.Rmd)"
#> [2] "[How to identify spots for birding using open geographical\ndata](https://ropensci.org/blog/2018/08/14/where-to-bird/)"
#> [3] "[How to obtain bird occurrence data in\nR](https://ropensci.org/blog/2018/08/21/birds-radolfzell/)"
#> [4] "[How to extract text from old natural history\ndrawings](https://ropensci.org/blog/2018/08/28/birds-ocr/)"
#> [5] "[How to complement an occurrence dataset with taxonomy and trait\ninformation](https://ropensci.org/blog/2018/09/04/birds-taxo-traits/)"
# all code
ex$md_vec(".//md:code | .//md:code_block")
#> [1] "```r\n# polygon for filtering\nlandkreis_konstanz <- osmdata::getbb(\"Landkreis Konstanz\",\n format_out = \"sf_polygon\")\ncrs <- sf::st_crs(landkreis_konstanz)\n\n# get and filter data\nf_out_ebd <- \"ebird/ebd_lk_konstanz.txt\"\n\nlibrary(\"magrittr\")\n\nebd <- auk::read_ebd(f_out_ebd) %>%\n sf::st_as_sf(coords = c(\"longitude\", \"latitude\"),\n crs = crs)\n\nin_indices <- sf::st_within(ebd, landkreis_konstanz)\n\nebd <- dplyr::filter(ebd, lengths(in_indices) > 0)\n\nebd <- as.data.frame(ebd)\n\nebd <- dplyr::filter(ebd, approved, lubridate::year(observation_date) > 2010)\n```"
#> [2] "```r\nspecies <- ebd %>%\n dplyr::count(common_name, sort = TRUE) %>%\n head(n = 50) %>%\n dplyr::pull(common_name)\n```"
#> [3] "`glue::glue_collapse(species, sep = \", \", last = \" and \")`"
#> [4] "`taxize`"
#> [5] "`spocc`"
#> [6] "`fulltext`"
#> [7] "`fulltext`"
#> [8] "`tidytext`"
#> [9] "`dplyr::bind_rows`"
#> [10] "`fulltext`"
#> [11] "```r\n.get_papers <- function(species){\n species %>%\n tolower() %>%\n fulltext::ft_search() %>%\n fulltext::ft_get() %>%\n fulltext::ft_collect() %>%\n fulltext::ft_chunks(c(\"title\", \"abstract\")) %>%\n fulltext::ft_tabularize() %>%\n dplyr::bind_rows()\n}\n\n.get_papers(species[1]) %>%\n dplyr::pull(title)\n```"
#> [12] "```\n## [1] \"Great spotted cuckoo nestlings have no antipredatory effect on magpie or carrion crow host nests in southern Spain\"\n## [2] \"Donor-Control of Scavenging Food Webs at the Land-Ocean Interface\"\n## [3] \"Formal comment to Soler et al.: Great spotted cuckoo nestlings have no antipredatory effect on magpie or carrion crow host nests in southern Spain\"\n## [4] \"Socially Driven Consistent Behavioural Differences during Development in Common Ravens and Carrion Crows\"\n## [5] \"Behavioral Responses to Inequity in Reward Distribution and Working Effort in Crows and Ravens\"\n## [6] \"Early Duplication of a Single MHC IIB Locus Prior to the Passerine Radiations\"\n## [7] \"Investigating the impact of media on demand for wildlife: A case study of Harry Potter and the UK trade in owls\"\n## [8] \"New Caledonian Crows Rapidly Solve a Collaborative Problem without Cooperative Cognition\"\n## [9] \"Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird\"\n## [10] \"Dietary Compositions and Their Seasonal Shifts in Japanese Resident Birds, Estimated from the Analysis of Volunteer Monitoring Data\"\n```"
#> [13] "`cites`"
#> [14] "`rcites`"
#> [15] "```r\nget_papers <- ratelimitr::limit_rate(.get_papers,\n rate = ratelimitr::rate(1, 2))\n\nall_papers <- purrr::map_df(species, get_papers)\n\nnrow(all_papers)\n```"
#> [16] "```\n## [1] 522\n```"
#> [17] "```r\nall_papers <- unique(all_papers)\n\nnrow(all_papers)\n```"
#> [18] "```\n## [1] 378\n```"
#> [19] "```r\nlibrary(\"tidytext\")\nlibrary(\"rcorpora\")\n\nstopwords <- corpora(\"words/stopwords/en\")$stopWords\n\nall_papers %>%\n dplyr::group_by(title, abstract) %>%\n dplyr::summarise(text = paste(title, abstract)) %>%\n dplyr::ungroup() %>%\n unnest_tokens(word, text) %>%\n dplyr::filter(!word %in% stopwords) %>%\n dplyr::count(word, sort = TRUE) -> words\n```"
#> [20] "```r\nhead(words, n = 10)\n```"
#> [21] "```\n## word n\n## 1 species 754\n## 2 birds 514\n## 3 virus 270\n## 4 avian 268\n## 5 bird 262\n## 6 study 243\n## 7 breeding 231\n## 8 wild 227\n## 9 populations 217\n## 10 population 213\n```"
#> [22] "`wordcloud`"
#> [23] "```r\nlibrary(\"wordcloud\")\n\nwith(words, wordcloud(word, n, max.words = 100))\n```"
#> [24] "`wordcloud2`"
#> [25] "```r\nbird <- words %>%\n head(n = 100) %>%\n wordcloud2::wordcloud2(figPath = \"bird.png\",\n color = \"black\", size = 1.5)\n# https://www.r-graph-gallery.com/196-the-wordcloud2-library/\nhtmlwidgets::saveWidget(bird,\n \"tmp.html\",\n selfcontained = F)\n```"
#> [26] "`webshot`"
#> [27] "`delay`"
#> [28] "```r\nmagick::image_read(\"screenshot.png\")\n```"
#> [29] "```r\n.get_meta <- function(species){\n\n cn <- dataone::CNode(\"PROD\")\n search <- list(q = glue::glue(\"abstract:{species}\"),\n fl = \"id,title,abstract\",\n sort = \"dateUploaded+desc\")\n\n result <- dataone::query(cn, solrQuery = search,\n as=\"data.frame\")\n\n if(nrow(result) == 0){\n NULL\n }else{\n # otherwise one line by version\n result <- unique(result)\n\n tibble::tibble(species = species,\n title = result$title,\n abstract = result$abstract)\n }\n}\n```"
#> [30] "```r\nget_meta <- ratelimitr::limit_rate(.get_meta,\n rate = ratelimitr::rate(1, 2))\n\nall_meta <- purrr::map_df(species, get_meta)\n\nnrow(all_meta)\n```"
#> [31] "```\n## [1] 266\n```"
#> [32] "```r\nlength(unique(all_meta$species))\n```"
#> [33] "```\n## [1] 35\n```"
#> [34] "```r\nall_meta <- unique(all_meta[,c(\"title\", \"abstract\")])\n\nnrow(all_meta)\n```"
#> [35] "```\n## [1] 104\n```"
#> [36] "```r\nall_meta %>%\n dplyr::group_by(title, abstract) %>%\n dplyr::summarise(text = paste(title, abstract)) %>%\n dplyr::ungroup() %>%\n unnest_tokens(word, text) %>%\n dplyr::filter(!word %in% stopwords) %>%\n dplyr::count(word, sort = TRUE) -> data_words\n\nhead(data_words, n = 10)\n```"
#> [37] "```\n## # A tibble: 10 x 2\n## word n\n## <chr> <int>\n## 1 data 153\n## 2 species 120\n## 3 birds 94\n## 4 breeding 87\n## 5 feeding 75\n## 6 population 65\n## 7 bird 60\n## 8 genetic 58\n## 9 study 56\n## 10 effects 54\n```"
#> [38] "```r\nwith(data_words, wordcloud(word, n, max.words = 100))\n```"
#> [39] "`fulltext`"
#> [40] "`dataone`"
#> [41] "```r\nspecies %>%\n tolower() %>%\n fulltext::ft_search() %>%\n fulltext::ft_get() %>%\n fulltext::ft_collect() %>%\n fulltext::ft_chunks(c(\"title\", \"abstract\")) %>%\n fulltext::ft_tabularize() %>%\n dplyr::bind_rows()\n```"
#> [42] "`fulltext`"
#> [43] "`europepmc`"
#> [44] "`jstor`"
#> [45] "`suppdata`"
#> [46] "`dataone`"
#> [47] "`rfigshare`"
#> [48] "`EML`"
#> [49] "`dataspice`"
#> [50] "`opencage`"
#> [51] "`bbox`"
#> [52] "`osmdata`"
#> [53] "`osmplotr`"
#> [54] "`rebird`"
#> [55] "`auk`"
#> [56] "`magick`"
#> [57] "`tesseract`"
#> [58] "`cld2`"
#> [59] "`cld3`"
#> [60] "`taxize::gnr_resolve`"
#> [61] "`taxize`"
#> [62] "`traits`"
## ------------------------------------------------
## Method `yarn$add_md`
## ------------------------------------------------
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex <- tinkr::yarn$new(path)
# two headings, no lists
xml2::xml_find_all(ex$body, "md:heading", ex$ns)
#> {xml_nodeset (2)}
#> [1] <heading level="2">\n <text xml:space="preserve">R Markdown</text>\n</he ...
#> [2] <heading level="2">\n <text xml:space="preserve">Including Plots</text>\ ...
xml2::xml_find_all(ex$body, "md:list", ex$ns)
#> {xml_nodeset (0)}
ex$add_md(
"# Hello\n\nThis is *new* formatted text from `{tinkr}`!",
where = 1L
)$add_md(
" - This\n - is\n - a new list",
where = 2L
)
# three headings
xml2::xml_find_all(ex$body, "md:heading", ex$ns)
#> {xml_nodeset (3)}
#> [1] <heading level="1">\n <text xml:space="preserve">Hello</text>\n</heading>
#> [2] <heading level="2">\n <text xml:space="preserve">R Markdown</text>\n</he ...
#> [3] <heading level="2">\n <text xml:space="preserve">Including Plots</text>\ ...
xml2::xml_find_all(ex$body, "md:list", ex$ns)
#> {xml_nodeset (1)}
#> [1] <list type="bullet" tight="true">\n <item>\n <paragraph>\n <text ...
tmp <- tempfile()
ex$write(tmp)
readLines(tmp, n = 20)
#> [1] "---"
#> [2] "title: \"Untitled\""
#> [3] "author: \"M. Salmon\""
#> [4] "date: \"September 6, 2018\""
#> [5] "output: html_document"
#> [6] "---"
#> [7] ""
#> [8] "```{r setup, include=FALSE, eval=TRUE}"
#> [9] "knitr::opts_chunk$set(echo = TRUE)"
#> [10] "```"
#> [11] ""
#> [12] "# Hello"
#> [13] ""
#> [14] "- This"
#> [15] "- is"
#> [16] "- a new list"
#> [17] ""
#> [18] "This is *new* formatted text from `{tinkr}`!"
#> [19] ""
#> [20] "## R Markdown"
## ------------------------------------------------
## Method `yarn$append_md`
## ------------------------------------------------
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex <- tinkr::yarn$new(path)
# append a note after the first heading
txt <- c("> Hello from *tinkr*!", ">", "> :heart: R")
ex$append_md(txt, ".//md:heading[1]")$head(20)
#> ---
#> title: "Untitled"
#> author: "M. Salmon"
#> date: "September 6, 2018"
#> output: html_document
#> ---
#>
#> ```{r setup, include=FALSE, eval=TRUE}
#> knitr::opts_chunk$set(echo = TRUE)
#> ```
#>
#> ## R Markdown
#>
#> > Hello from *tinkr*!
#> >
#> > :heart: R
#>
#> This is an ~~R Markdown document~~. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
#>
#> When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
## ------------------------------------------------
## Method `yarn$prepend_md`
## ------------------------------------------------
path <- system.file("extdata", "example2.Rmd", package = "tinkr")
ex <- tinkr::yarn$new(path)
# prepend a table description to the birds table
ex$prepend_md("Table: BIRDS, NERDS", ".//md:table[1]")$tail(20)
#>
#> Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
#>
#> Table: BIRDS, NERDS
#>
#> | scientific\_name | common\_name | n |
#> | :------------------------- | :------------------ | --: |
#> | Corvus corone | Carrion Crow | 288 |
#> | Turdus merula | Eurasian Blackbird | 285 |
#> | Anas platyrhynchos | Mallard | 273 |
#> | Fulica atra | Eurasian Coot | 268 |
#> | Parus major | Great Tit | 266 |
#> | Podiceps cristatus | Great Crested Grebe | 254 |
#> | Ardea cinerea | Gray Heron | 236 |
#> | Cygnus olor | Mute Swan | 234 |
#> | Cyanistes caeruleus | Eurasian Blue Tit | 233 |
#> | Chroicocephalus ridibundus | Black-headed Gull | 223 |
#>
#> blabla
#>
## ------------------------------------------------
## Method `yarn$protect_math`
## ------------------------------------------------
path <- system.file("extdata", "math-example.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
ex$tail() # math blocks are escaped :(
#>
#> $$
#> Q\_{N(norm)}=\\frac{C\_N +C\_{N-1}}2\\times
#> \\frac{\\sum *{i=N-n}^{N}Q\_i} {\\sum*{j=N-n}^{N}{(\\frac{C\_j+C\_{j-1}}2)}}
#> $$
#>
ex$protect_math()$tail() # math blocks are no longer escaped :)
#>
#> $$
#> Q_{N(norm)}=\frac{C_N +C_{N-1}}2\times
#> \frac{\sum _{i=N-n}^{N}Q_i} {\sum_{j=N-n}^{N}{(\frac{C_j+C_{j-1}}2)}}
#> $$
#>
## ------------------------------------------------
## Method `yarn$protect_curly`
## ------------------------------------------------
path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path)
ex$protect_curly()$head()
#> ---
#> title: basic curly
#> ---
#>
#> # preface {#pre-face .unnumbered}
#>
## ------------------------------------------------
## Method `yarn$protect_unescaped`
## ------------------------------------------------
path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path, sourcepos = TRUE, unescaped = FALSE)
ex$tail()
#> {#dog alt="a picture
#> of a dog"}
#>
#> \[a span with attributes\]{.span-with-attributes
#> style='color: red;'}
#>
ex$protect_unescaped()$tail()
#> {#dog alt="a picture
#> of a dog"}
#>
#> [a span with attributes]{.span-with-attributes
#> style='color: red;'}
#>
## ------------------------------------------------
## Method `yarn$get_protected`
## ------------------------------------------------
path <- system.file("extdata", "basic-curly.md", package = "tinkr")
ex <- tinkr::yarn$new(path, sourcepos = TRUE)
# protect curly braces
ex$protect_curly()
# add math and protect it
ex$add_md(c("## math\n",
"$c^2 = a^2 + b^2$\n",
"$$",
"\\sum_{i}^k = x_i + 1",
"$$\n")
)
ex$protect_math()
# get protected now shows all the protected nodes
ex$get_protected()
#> {xml_nodeset (14)}
#> [1] <text asis="true" math="true">$c^2 = a^2 + b^2$</text>
#> [2] <text xml:space="preserve" asis="true" math="true">$$</text>
#> [3] <softbreak asis="true" math="true"/>
#> [4] <text xml:space="preserve" asis="true" math="true">\\sum_{i}^k = x_i + 1 ...
#> [5] <softbreak asis="true" math="true"/>
#> [6] <text xml:space="preserve" asis="true" math="true">$$</text>
#> [7] <text curly="true">{#pre-face .unnumbered}</text>
#> [8] <text curly="true">{xml2}</text>
#> [9] <text curly="true">{tinkr}</text>
#> [10] <text curly="true" alt="a picture of a kitten">{#kitteh alt='a picture o ...
#> [11] <text curly="true" alt="a picture of a dog">{#dog alt="a picture\nof a d ...
#> [12] <text asis="true">[</text>
#> [13] <text asis="true">]</text>
#> [14] <text curly="true">{.span-with-attributes\nstyle='color: red;'}</text>
ex$get_protected(c("math", "curly")) # only show the math and curly
#> {xml_nodeset (12)}
#> [1] <text asis="true" math="true">$c^2 = a^2 + b^2$</text>
#> [2] <text xml:space="preserve" asis="true" math="true">$$</text>
#> [3] <softbreak asis="true" math="true"/>
#> [4] <text xml:space="preserve" asis="true" math="true">\\sum_{i}^k = x_i + 1 ...
#> [5] <softbreak asis="true" math="true"/>
#> [6] <text xml:space="preserve" asis="true" math="true">$$</text>
#> [7] <text curly="true">{#pre-face .unnumbered}</text>
#> [8] <text curly="true">{xml2}</text>
#> [9] <text curly="true">{tinkr}</text>
#> [10] <text curly="true" alt="a picture of a kitten">{#kitteh alt='a picture o ...
#> [11] <text curly="true" alt="a picture of a dog">{#dog alt="a picture\nof a d ...
#> [12] <text curly="true">{.span-with-attributes\nstyle='color: red;'}</text>