Commit ⋅ ropensci/taxadb

Showing 1 of 6 files from the diff.

65.4% 60.0% -0.6%

R/get_ids.R changed.

Other files ignored by Codecov

man/get_ids.Rd has changed.

cran-comments.md has changed.

codemeta.json has changed.

README.Rmd has changed.

README.md has changed.

@@ -19,6 +19,8 @@

Loading

#' @param taxadb_db Connection to from `[td_connect()]`.
#' @param ignore_case should we ignore case (capitalization) in matching names?
#' default is `TRUE`.
#' @param warn should we display warnings on NAs resulting from multiply-resolved matches?
#' (Unlike unmatched names, these NAs can usually be resolved manually via [filter_id()])
#' @param ... additional arguments (currently ignored)
#' @return a vector of IDs, of the same length as the input names Any
#' unmatched names or multiply-matched names will return as [NA]s.

@@ -58,6 +60,7 @@

Loading

                    version = latest_version(),
                    taxadb_db = td_connect(),
                    ignore_case = TRUE,
                    warn = TRUE,
                    ...){
  format <- match.arg(format)
  n <- length(names)

@@ -67,7 +70,7 @@

Loading

  # be compatible with common space delimiters
  names <- gsub("[_|-|\\.]", " ", names)

  df <- filter_name(name = names,
  taxa <- filter_name(name = names,
                provider = provider,
                version = version,
                collect = TRUE,

@@ -76,7 +79,8 @@

Loading

    arrange(sort)

  out <- vapply(names, function(x){
    df <- df[df$scientificName == x, ]
    df <- taxa[x == taxa$scientificName, ]
    df <- df[!is.na(df$scientificName),]

    if(nrow(df) < 1) return(NA_character_)


@@ -91,12 +95,14 @@

Loading

    if(length(ids)==1){
      return(ids)
    } else {
      if(warn){
      warning(paste0("  Found ", bb(length(ids)), " possible identifiers for ",
                     ibr(x),
                     ".\n  Returning ", bb('NA'), ". Try ",
                     bb(paste0("tl('", x, "', '", provider,"')")),
                     bb(paste0("filter_id('", x, "', '", provider,"')")),
                     " to resolve manually.\n"),
              call. = FALSE)
      }
      return(NA_character_)
    }
  },

Files		•	•	•	Coverage
R	364	321	0	43	88.2%
Project Totals (16 files)	364	321	0	43	88.2%

View CI Build Download

comment: false

coverage:
  round: up
  precision: 1

  status:
    project:
      default:
        threshold: 1%
    patch:
      default:
        target: auto
        threshold: 5%
        only_pulls: true

Read the docs

Interact now

The inner-most circle is the entire project, moving away from the center are folders then, finally, a single file. The size and color of each slice is representing the number of statements and the coverage, respectively.

SVG

The top section represents the entire project. Proceeding with folders and finally individual files. The size and color of each slice is representing the number of statements and the coverage, respectively.

SVG

Each block represents a single file in the project. The size and color of each block is represented by the number of statements and the coverage, respectively.

SVG

Learn more about the coverage sunburst graph

76	79		arrange(sort)
77	80
78	81		out <- vapply(names, function(x){
79		-	df <- df[df$scientificName == x, ]
	82	+	df <- taxa[x == taxa$scientificName, ]
	83	+	df <- df[!is.na(df$scientificName),]
80	84
81	85		if(nrow(df) < 1) return(NA_character_)
82	86

91	95		if(length(ids)==1){
92	96		return(ids)
93	97		} else {
	98	+	if(warn){
94	99		warning(paste0(" Found ", bb(length(ids)), " possible identifiers for ",
95	100		ibr(x),
96	101		".\n Returning ", bb('NA'), ". Try ",
97		-	bb(paste0("tl('", x, "', '", provider,"')")),
	102	+	bb(paste0("filter_id('", x, "', '", provider,"')")),
98	103		" to resolve manually.\n"),
99	104		call. = FALSE)
	105	+	}
100	106		return(NA_character_)
101	107		}
102	108		},

Navigation	Overlay
`t` Navigate files	`h` Toggle hits
`y` Change url to tip of branch	`m` Toggle misses
`b / v` Jump to prev/next hit line	`p` Toggle partial
`z / x` Jump to prev/next missed or partial line	`1..9` Toggle flags
`shift + o` Open current page in GitHub	`a` Toggle all on
`/ or ?` Show keyboard shortcuts dialog	`c` Toggle context lines or commits

19	19		#' @param taxadb_db Connection to from `[td_connect()]`.
20	20		#' @param ignore_case should we ignore case (capitalization) in matching names?
21	21		#' default is `TRUE`.
	22	+	#' @param warn should we display warnings on NAs resulting from multiply-resolved matches?
	23	+	#' (Unlike unmatched names, these NAs can usually be resolved manually via [filter_id()])
22	24		#' @param ... additional arguments (currently ignored)
23	25		#' @return a vector of IDs, of the same length as the input names Any
24	26		#' unmatched names or multiply-matched names will return as [NA]s.

58	60		version = latest_version(),
59	61		taxadb_db = td_connect(),
60	62		ignore_case = TRUE,
	63	+	warn = TRUE,
61	64		...){
62	65		format <- match.arg(format)
63	66		n <- length(names)

67	70		# be compatible with common space delimiters
68	71		names <- gsub("[_\|-\|\\.]", " ", names)
69	72
70		-	df <- filter_name(name = names,
	73	+	taxa <- filter_name(name = names,
71	74		provider = provider,
72	75		version = version,
73	76		collect = TRUE,

1	comment: false
2
3	coverage:
4	round: up
5	precision: 1
6
7	status:
8	project:
9	default:
10	threshold: 1%
11	patch:
12	default:
13	target: auto
14	threshold: 5%
15	only_pulls: true

Updating our web app