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April 8, 2017 19:02
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Read <table> HTML tag with {XML} library
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| # Read <table> HTML tag with {XML} library | |
| # ==================================================== | |
| # Load library | |
| library(XML) | |
| # ======================= | |
| # Read the web page [accessed 08-Apr-2017] | |
| # ======================= | |
| link <- "http://www.theplantlist.org/1.1/statistics/" | |
| # NOTE: is ethical to store the page and not read it unnecessarily too many times, | |
| # overloading their server | |
| link.scrap <- htmlParse(link) | |
| # ======================= | |
| # Read all tables from the page, | |
| # then select desired table | |
| # ======================= | |
| tbls.lst <- readHTMLTable(link.scrap) | |
| my.tbl.1 <- tbls.lst[[1]] # select first table | |
| # Note that some unwanted columns were read as well | |
| my.tbl.1 | |
| ## V1 V2 V3 V4 | |
| ##1 <U+25D5> Accepted 350,699 33.0% | |
| ##2 <U+25D5> Synonym 470,624 44.2% | |
| ##3 <U+25D5> Unplaced 243 0.0% | |
| ##4 <U+25D5> Unassessed 242,469 22.8% | |
| # Also all data was read as character! | |
| str(my.tbl.1) | |
| ##'data.frame': 4 obs. of 4 variables: | |
| ## $ V1: Factor w/ 1 level "<U+25D5>""| __truncated__: 1 1 1 1 | |
| ## $ V2: Factor w/ 4 levels "Accepted","Synonym",..: 1 2 4 3 | |
| ## $ V3: Factor w/ 4 levels "242,469","243",..: 3 4 2 1 | |
| ## $ V4: Factor w/ 4 levels "0.0%","22.8%",..: 3 4 1 2 | |
| # ======================= | |
| # Read specific table(s) from the page | |
| # using directly the table's XPath selector | |
| # ======================= | |
| # ----------------------- | |
| # Simple reading using XPath selector | |
| # ----------------------- | |
| # gives the same results as above | |
| my.tbl.2 <- xpathApply(doc = link.scrap, | |
| path = '//*[@id="columns"]/section/div[1]/table', | |
| fun = readHTMLTable)[[1]] | |
| # ----------------------- | |
| # Adjusting for header, column classes & other tweaks | |
| # ----------------------- | |
| my.tbl.3 <- xpathApply(doc = link.scrap, | |
| path = '//*[@id="columns"]/section/div[1]/table', | |
| fun = readHTMLTable, | |
| header = c("Status", "Total", "Total_prc"), | |
| colClasses = list(NULL, "character", "FormattedInteger", "Percent"), | |
| stringsAsFactors = FALSE, | |
| skip.rows = 1L, | |
| trim = TRUE)[[1]] | |
| my.tbl.3 | |
| ## Status Total Total_prc | |
| ##1 Accepted 350699 33.0 | |
| ##2 Synonym 470624 44.2 | |
| ##3 Unplaced 243 0.0 | |
| ##4 Unassessed 242469 22.8 | |
| # The type of data is as desired now | |
| str(my.tbl.3) | |
| ##'data.frame': 4 obs. of 3 variables: | |
| ## $ Status : chr "Accepted" "Synonym" "Unplaced" "Unassessed" | |
| ## $ Total : int 350699 470624 243 242469 | |
| ## $ Total_prc: num 33 44.2 0 22.8 | |
| # ----------------------- | |
| # Select multiple tables via their XPath selectors | |
| # ----------------------- | |
| # Use a vector of XPath selectors | |
| tbls.lst.2 <- xpathApply(doc = link.scrap, | |
| path = c('//*[@id="columns"]/section/div[1]/table', | |
| '//*[@id="columns"]/section/table[1]'), | |
| fun = readHTMLTable, | |
| stringsAsFactors = FALSE) | |
| tbls.lst.2 | |
| ##[[1]] | |
| ## V1 V2 V3 V4 | |
| ##1 <U+25D5> Accepted 350,699 33.0% | |
| ##2 <U+25D5> Synonym 470,624 44.2% | |
| ##3 <U+25D5> Unplaced 243 0.0% | |
| ##4 <U+25D5> Unassessed 242,469 22.8% | |
| ##[[2]] | |
| ## V1 V2 V3 V4 V5 V6 V7 V8 | |
| ##1 High confidence 149,349 229,242 0 0 378,591 35.6% | |
| ##2 Medium confidence 193,013 214,107 0 0 407,120 38.3% | |
| ##3 Low confidence 8,337 27,275 243 242,469 278,324 26.2% |
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