R语言 treebase包 search_treebase()函数中文帮助文档(中英文对照)

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search_treebase(treebase)
search_treebase()所属R语言包：treebase

                                        A function to pull in the phyologeny/phylogenies matching a search query
                                         在的phyologeny /匹配的搜索查询的系统发育的功能拉

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

A function to pull in the phyologeny/phylogenies matching a search query
在的phyologeny /匹配的搜索查询的系统发育的功能拉


用法----------Usage----------


  search_treebase(input, by, returns = c("tree", "matrix"),
    exact_match = FALSE, max_trees = Inf,
    branch_lengths = FALSE, curl = getCurlHandle(),
    verbose = TRUE, pause1 = 2, pause2 = 1, attempts = 3,
    only_metadata = FALSE)



参数----------Arguments----------

参数：input
a search query (character string)
一个搜索查询（字符串）


参数：by
the kind of search; author, taxon, subject, study, etc (see list of possible search terms, details)
的搜索类型，作者，分类单元，课题，研究，等等（见可能的搜索字词列表，详细）


参数：returns
should the fn return the tree or the character matrix?
函数返回的树或字符点阵？


参数：exact_match
force exact matching for author name, taxon, etc.  Otherwise does partial matching
力作者姓名，类群等精确匹配，否则不执行部分匹配


参数：max_trees
Upper bound for the number of trees returned, good for keeping possibly large initial queries fast
返回树木的数量上限为保持大可能的初始查询快速，良好的


参数：branch_lengths
logical indicating whether should only return trees that have branch lengths.
逻辑表明，是否应该只返回树有分支长度。


参数：curl
the handle to the curl web utility for repeated calls, see the getCurlHandle() function in RCurl package for details.
卷曲的网络实用程序反复调用句柄，请参阅getCurlHandle（）功能在RCurl包的详细信息。


参数：verbose
logical indicating level of progress reporting
逻辑指示的进度报告


参数：pause1
number of seconds to hesitate between requests
请求之间的秒数迟疑


参数：pause2
number of seconds to hesitate between individual files
秒数之间犹豫单个文件


参数：attempts
number of attempts to access a particular resource
试图访问特定的资源数量


参数：only_metadata
option to only return metadata about matching trees which lists study.id, tree.id, kind (gene,species,barcode) type (single, consensus) number of taxa, and possible quality score.
选项只返回元数据的匹配树，其中列出了类型（单，达成共识）study.id，tree.id，善良（基因，物种，条码）的类群，数量和可能出现的质量得分。


Details

详细信息----------Details----------

Choose the search type.  Options are:
请选择搜索类型。选项有：

abstract  search terms in the publication
在出版物中的抽象的搜索字词

author  match authors in the
作者在笔者匹配

subject  match subject
受比赛主题

doi  the unique object identifier for the publication
DOI的唯一对象标识符公布

ncbi  NCBI identifier number for the taxon
NCBI NCBI标识号的类群

kind.tree  Kind of tree (Gene tree, species tree,
kind.tree一种树（基因树，种的树，

type.tree  type of tree
type.tree类型的树，

ntax  number of taxa in
ntax的类群

quality  A quality score for the
品质A的质量分数为

study  match words
研究匹配的话

taxon
分类群

id.study  TreeBASE study
id.study TreeBASE研究

id.tree  TreeBASE's unique tree identifier
id.tree TreeBASE独特的树标识符

id.taxon  taxon identifier number from
id.taxon类群的标识号

tree  The title for the tree
树树的标题

type.matrix  Type of matrix  
type.matrix类型的矩阵

matrix
矩阵

id.matrix  TreeBASE's
id.matrix TreeBASE

nchar  number of
NCHAR数量

The package provides partial support for character matrices provided by TreeBASE. At the time of writing, TreeBASE permits ambiguous DNA characters in these matrices, such as 'CG' indicating either a C or G, which is not supported by any R interpreter, and thus may lead to errors.  for a description of all possible search options, see https://spreadsheets.google.com/pub?key=rL–O7pyhR8FcnnG5-ofAlw.
这个包提供了部分支持的字符矩阵所提供的TreeBASE。在写作的时候，TreeBASE在这些矩阵允许模棱两可的DNA字符，如CG表示任何一个C或G，不支持任何R解释，以及由此可能导致的错误。所有可能的搜索选项的说明，请参阅https://spreadsheets.google.com/pub?key=rL-O7pyhR8FcnnG5-ofAlw。


值----------Value----------

either a list of trees (multiphylo) or a list of character matrices
无论是列表中的树（multiphylo）或字符矩阵的列表


实例----------Examples----------


## Not run: [＃不运行：]
## defaults to return phylogeny[＃默认返回系统发育]
Huelsenbeck <- search_treebase("Huelsenbeck", by="author")

## can ask for character matrices:[＃可以要求的字符矩阵：]
wingless <- search_treebase("2907", by="id.matrix", returns="matrix")

## Some nexus matrices don't meet read.nexus.data's strict requirements,[＃一些关系矩阵不满足read.nexus.data的严格要求，]
## these aren't returned[＃这不归还]
H_matrices <- search_treebase("Huelsenbeck", by="author", returns="matrix")

## Use Booleans in search: and, or, not[＃在搜索中使用布尔值，或者，不]
## Note that by must identify each entry type if a Boolean is given[＃请注意，必须确定每个条目的类型，如果一个布尔值]
HR_trees <- search_treebase("Ronquist or Hulesenbeck", by=c("author", "author"))

## We'll often use max_trees in the example so that they run quickly,[＃我们将经常使用max_trees在本例中，让他们跑得快，]
## notice the quotes for species.[＃注意引号的物种。]
dolphins <- search_treebase('"Delphinus"', by="taxon", max_trees=5)
## can do exact matches[＃可以做精确匹配]
humans <- search_treebase('"Homo sapiens"', by="taxon", exact_match=TRUE, max_trees=10)
## all trees with 5 taxa[＃所有的树木与5类群]
five <- search_treebase(5, by="ntax", max_trees = 10)
## These are different, a tree id isn't a Study id.  we report both[＃这些都是不同的，一棵树id是不是一个研究ID。我们同时报告]
studies <- search_treebase("2377", by="id.study")
tree <- search_treebase("2377", by="id.tree")
c("TreeID" = tree$Tr.id, "StudyID" = tree$S.id)
## Only results with branch lengths[＃分支长度的只有结果]
## Has to grab all the trees first, then toss out ones without branch_lengths[＃首先抓住所有的树木，然后折腾了，没有branch_lengths]
Near <- search_treebase("Near", "author", branch_lengths=TRUE)

## End(Not run)[＃（不执行）]

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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