Compare `f7d65b7 ... +19 ... de1c525`

#' library("taxize")
#' spp <- names_list("species", 500)
#' # phylomatic(taxa = spp, get = "GET")
#' (out <- phylomatic(taxa = spp, get = "POST"))
#' (out <- phylomatic(taxa = spp, get = "POST", db = "itis"))
#' plot(out)
#'
#' # Pass in a tree from a URL on the web
#' spp <- c("Abies_nordmanniana", "Abies_bornmuelleriana", "Abies_cilicica", "Abies_cephalonica",
#' "Abies_numidica", "Abies_pinsapo", "Abies_alba")
#' url <- "http://datadryad.org/bitstream/handle/10255/dryad.8791/final_tree.tre?sequence=1"
#' phylomatic(taxa=spp, treeuri=url)
#' }

phylomatic <- function(taxa, taxnames = TRUE, get = 'GET',

@@ -7,25 +7,25 @@

#' @param taxa quoted tsn number (taxonomic serial number)
#' @param format output format, isubmit (you can paste in to the Phylomatic
#'     website), or 'rsubmit' to use in fxn phylomatic_tree
#' @param db One of "ncbi", "itis", or "apg". if you use "apg", no HTTP 
#' requests are made (no internet connection needed), whereas if you use 
#' "ncbi" or "itis" you do need an internet connection. IMPORTANT: 
#' @param db One of "ncbi", "itis", or "apg". if you use "apg", no HTTP
#' requests are made (no internet connection needed), whereas if you use
#' "ncbi" or "itis" you do need an internet connection. IMPORTANT:
#' see **Authentication** below if using "ncbi".
#' @param ... curl options passed on to [taxize::tax_name()]
#' @return string (e.g., "pinaceae/pinus/pinus_contorta"), in Phylomatic 
#' @return string (e.g., "pinaceae/pinus/pinus_contorta"), in Phylomatic
#' submission format
#' @section Authentication:
#' NCBI Entrez doesn't require that you use an API key, but you get
#' higher rate limit with a key, from 3 to 10 requests per second, so do 
#' get one. Run [taxize::use_entrez()] or see 
#' higher rate limit with a key, from 3 to 10 requests per second, so do
#' get one. Run `taxize::use_entrez()` or see
#' https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
#' for instructions.
#' 
#' NCBI API key handling logic is done inside of the `taxize` package, used 
#'
#' NCBI API key handling logic is done inside of the `taxize` package, used
#' inside this function.
#' 
#' Save your API key with the name `ENTREZ_KEY` as an R option in your 
#' `.Rprofile` file, or as environment variables in either your `.Renviron` 
#'
#' Save your API key with the name `ENTREZ_KEY` as an R option in your
#' `.Rprofile` file, or as environment variables in either your `.Renviron`
#' file or `.bash_profile` file, or `.zshrc` file (if you use oh-my-zsh) or
#' similar. See [Startup] for help on R options and environment
#' variables. You cannot pass in your API key in this function.

@@ -35,7 +35,7 @@

#' or environment variables.
#'
#' We strongly recommend using environment variables over R options.
#' 
#'
#' Note that if you don't have an ENTREZ_KEY set, you'll get a message
#' about it, but only once during each function call. That is, there
#' can be of these messages per R session, across function calls.

@@ -61,17 +61,12 @@


    if (db %in% c("ncbi", "itis")) {
      family <- ck$handle_conditions(
        taxize::tax_name(
          query = taxa_genus, get = "family", db = db, messages = FALSE, 
          ...)$family)
        taxize::tax_name(taxa_genus, get = "family", db = db,
          messages = FALSE, ...)$family)
    } else {
      tplfamily <- tpl[ match(taxa_genus, tpl$genus), "family" ]
      dd <- taxize::apg_families[ match(tplfamily, taxize::apg_families$this), ]
      if (nchar(as.character(dd$that), keepNA = FALSE) == 0) {
        family <- dd$this
      } else {
        family <- dd$that
      }
      family <- taxize::apg_families[ 
        match(tplfamily, taxize::apg_families$accepted_name), ]$accepted_name
    }
    stringg <- c(family, strsplit(nnn, " ")[[1]])
    stringg <- tolower(as.character(stringg))

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50.00% ø -6.73%

skip_on_ci some tests

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Files		•	•	•	Coverage
R	-15	-19	ø	+4	^-6.73% 50.00%
Project Totals (6 files)	156	78	0	78	50.00%

35	35		#' or environment variables.
36	36		#'
37	37		#' We strongly recommend using environment variables over R options.
38		-	#'
	38	+	#'
39	39		#' Note that if you don't have an ENTREZ_KEY set, you'll get a message
40	40		#' about it, but only once during each function call. That is, there
41	41		#' can be of these messages per R session, across function calls.

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65	65		#' library("taxize")
66	66		#' spp <- names_list("species", 500)
67	67		#' # phylomatic(taxa = spp, get = "GET")
68		-	#' (out <- phylomatic(taxa = spp, get = "POST"))
	68	+	#' (out <- phylomatic(taxa = spp, get = "POST", db = "itis"))
69	69		#' plot(out)
70		-	#'
71		-	#' # Pass in a tree from a URL on the web
72		-	#' spp <- c("Abies_nordmanniana", "Abies_bornmuelleriana", "Abies_cilicica", "Abies_cephalonica",
73		-	#' "Abies_numidica", "Abies_pinsapo", "Abies_alba")
74		-	#' url <- "http://datadryad.org/bitstream/handle/10255/dryad.8791/final_tree.tre?sequence=1"
75		-	#' phylomatic(taxa=spp, treeuri=url)
76	70		#' }
77	71
78	72		phylomatic <- function(taxa, taxnames = TRUE, get = 'GET',

7	7		#' @param taxa quoted tsn number (taxonomic serial number)
8	8		#' @param format output format, isubmit (you can paste in to the Phylomatic
9	9		#' website), or 'rsubmit' to use in fxn phylomatic_tree
10		-	#' @param db One of "ncbi", "itis", or "apg". if you use "apg", no HTTP
11		-	#' requests are made (no internet connection needed), whereas if you use
12		-	#' "ncbi" or "itis" you do need an internet connection. IMPORTANT:
	10	+	#' @param db One of "ncbi", "itis", or "apg". if you use "apg", no HTTP
	11	+	#' requests are made (no internet connection needed), whereas if you use
	12	+	#' "ncbi" or "itis" you do need an internet connection. IMPORTANT:
13	13		#' see Authentication below if using "ncbi".
14	14		#' @param ... curl options passed on to [taxize::tax_name()]
15		-	#' @return string (e.g., "pinaceae/pinus/pinus_contorta"), in Phylomatic
	15	+	#' @return string (e.g., "pinaceae/pinus/pinus_contorta"), in Phylomatic
16	16		#' submission format
17	17		#' @section Authentication:
18	18		#' NCBI Entrez doesn't require that you use an API key, but you get
19		-	#' higher rate limit with a key, from 3 to 10 requests per second, so do
20		-	#' get one. Run [taxize::use_entrez()] or see
	19	+	#' higher rate limit with a key, from 3 to 10 requests per second, so do
	20	+	#' get one. Run `taxize::use_entrez()` or see
21	21		#' https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
22	22		#' for instructions.
23		-	#'
24		-	#' NCBI API key handling logic is done inside of the `taxize` package, used
	23	+	#'
	24	+	#' NCBI API key handling logic is done inside of the `taxize` package, used
25	25		#' inside this function.
26		-	#'
27		-	#' Save your API key with the name `ENTREZ_KEY` as an R option in your
28		-	#' `.Rprofile` file, or as environment variables in either your `.Renviron`
	26	+	#'
	27	+	#' Save your API key with the name `ENTREZ_KEY` as an R option in your
	28	+	#' `.Rprofile` file, or as environment variables in either your `.Renviron`
29	29		#' file or `.bash_profile` file, or `.zshrc` file (if you use oh-my-zsh) or
30	30		#' similar. See [Startup] for help on R options and environment
31	31		#' variables. You cannot pass in your API key in this function.

61	61
62	62		if (db %in% c("ncbi", "itis")) {
63	63		family <- ck$handle_conditions(
64		-	taxize::tax_name(
65		-	query = taxa_genus, get = "family", db = db, messages = FALSE,
66		-	...)$family)
	64	+	taxize::tax_name(taxa_genus, get = "family", db = db,
	65	+	messages = FALSE, ...)$family)
67	66		} else {
68	67		tplfamily <- tpl[ match(taxa_genus, tpl$genus), "family" ]
69		-	dd <- taxize::apg_families[ match(tplfamily, taxize::apg_families$this), ]
70		-	if (nchar(as.character(dd$that), keepNA = FALSE) == 0) {
71		-	family <- dd$this
72		-	} else {
73		-	family <- dd$that
74		-	}
	68	+	family <- taxize::apg_families[
	69	+	match(tplfamily, taxize::apg_families$accepted_name), ]$accepted_name
75	70		}
76	71		stringg <- c(family, strsplit(nnn, " ")[[1]])
77	72		stringg <- tolower(as.character(stringg))

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