vegemite(vegan)
vegemite()所属R语言包：vegan
Prints a Compact, Ordered Vegetation Table
打印一款结构紧凑，有序的植被表
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The function prints a compact vegetation table, where species are rows, and each site takes only one column without spaces. The vegetation table can be ordered by explicit indexing, by environmental variables or results from an ordination or cluster analysis.
该函数打印一个紧凑的植被表，物种的行，并且每个站点只需要一列没有空格。植被可以通过明确的索引排序表，通过环境变量或协调或聚类分析的结果。
用法----------Usage----------
vegemite(x, use, scale, sp.ind, site.ind, zero=".", select ,...)
coverscale(x, scale=c("Braun.Blanquet", "Domin", "Hult", "Hill", "fix","log"),
maxabund)
参数----------Arguments----------
参数：x
Vegetation data.
植被数据。
参数：use
Either a vector, or an object from cca, decorana etc. or hclust or a dendrogram for ordering sites and species.
无论是矢量，或cca，decorana等hclust或dendrogram订购网站和物种的对象。
参数：sp.ind
Species indices.
种指数。
参数：site.ind
Site indices.
网站的索引。
参数：zero
Character used for zeros.
字符用于零。
参数：select
Select a subset of sites. This can be a logical vector (TRUE for selected sites), or a vector of indices of selected sites. The order of indices does not influence results, but you must specify use or site.ind to reorder sites.
选择网站的一个子集。这可以是一个逻辑向量（TRUE为选定的网站），或选定的网站的向量的索引。索引的顺序不影响结果，但你必须指定use或site.ind重新排序的网站。
参数：scale
Cover scale used (can be abbreviated).
覆盖规模（可以缩写）。
参数：maxabund
Maximum abundance used with scale = "log". Data maximum in the selected subset will be used if this is missing.
最大丰度与scale = "log"。如果没有这个，将使用最大的select版的子集数据。
参数：...
Arguments passed to coverscale (i.e., maxabund).
参数传递coverscale（即，maxabund）。
Details
详细信息----------Details----------
The function prints a traditional vegetation table. Unlike in ordinary data matrices, species are used as rows and sites as columns. The table is printed in compact form: only one character can be used for abundance, and there are no spaces between columns. Species with no occurrences are dropped from the table.
的功能打印传统的植被表格。不同于普通数据矩阵，物种作为行和列的网站。表印在紧凑的形式：只有一个字符，可用于丰富，列之间没有空格。从表中没有出现的物种下降。
The parameter use can be a vector or an object from hclust, a dendrogram or any ordination result recognized by scores (all ordination methods in vegan and some of those not in vegan). If use is a vector, it is used for ordering sites. If use is an object from ordination, both sites and species are arranged by the first axis. When use is an object from hclust or a dendrogram, the sites are ordered similarly as in the cluster dendrogram. If ordination methods provide species scores, these are used for ordering species. In all cases where species scores are missing, species are ordered by their weighted averages (wascores) on site scores. There is no natural, unique ordering in hierarchic clustering, but in some cases species are still nicely ordered (please note that you can reorder.dendrogram to have such a natural order). Alternatively, species and sites can be ordered explicitly giving their indices or names in parameters sp.ind and site.ind. If these are given, they take precedence over use. A subset of sites can be displayed using argument select, but this cannot be used to order sites, but you still must give use or site.ind.
参数usehclust，dendrogram或scores（所有协调方法vegan认可的任何协调结果和一些可以是一个向量或对象那些没有在vegan）。如果use是一个矢量，它是用于订购网站。如果use是一个对象，从统筹安排，地点和物种的第一个轴。当use是一个对象，从hclust或dendrogram，该网站是有序的，同样作为聚类中的聚类分析。如果协调方法提供了物种的分数，这些用于订购物种。在所有情况下，缺少种分数，物种是按加权平均值（wascores）现场评分。有顺序的层次聚类是不自然的，独特的，但在某些情况下，物种仍然很好订购（请注意，你可以reorder.dendrogram有这样的自然顺序）。另外，物种和网站，可以明令指数或名称的参数sp.ind和site.ind。如果这些都给出了，它们的优先级高于use。使用参数select，可以显示网站的一个子集，但不能用于订购网站，但你还必须给use或site.ind。
If scale is given, vegemite calls coverscale to transform percent cover scale or some other scales into traditional class scales used in vegetation science (coverscale can be called directly, too). Braun-Blanquet and Domin scales are actually not strict cover scales, and the limits used for codes r and + are arbitrary. Scale Hill may be inappropriately named, since Mark O. Hill probably never intended this as a cover scale. However, it is used as default 'cut levels' in his TWINSPAN, and surprisingly many users stick to this default, and this is a de facto standard in publications. All traditional scales assume that values are cover percentages with maximum 100. However, non-traditional alternative log can be used with any scale range. Its class limits are integer powers of 1/2 of the maximum (argument maxabund), with + used for non-zero entries less than 1/512 of the maximum (log stands alternatively for logarithmic or logical). Scale fix is intended for "fixing" 10-point scales: it truncates scale values to integers, and replaces 10 with X and positive values below 1 with +.
如果scale，vegemite调用coverscale改造植物科学中使用的传统的课堂秤％的覆盖规模或其他一些规模（coverscale可以直接调用，太） 。的的博朗布兰奎特和Domin尺度实际上是不严格的封面尺度，以及用于代码的限制r和+是任意的。规模Hill不恰当地命名的，因为马克·奥·希尔可能从来没有打算为掩护规模。然而，在他的TWINSPAN，出奇的多用户坚持这个默认的默认“下调两级至”，这是一个事实上的标准出版物。所有传统的尺度值是盖的百分比，最多100个。然而，非传统替代log可以用于任何规模的范围。及其类限制的1/2的整数次幂的最大值（参数maxabund），用+用于非零项小于1/512的最大值（log代表交替对数或逻辑）。规模fix的目的是为“固定”10点尺度：，截断规模为整数的值，并取代10 X和正面的价值观低于1 +。
值----------Value----------
The function is used mainly to print a table, but it returns (invisibly) a list with items:
该功能主要用于打印表，但它返回（不可见）的列表项：
参数：species
Ordered species indices
序种指数
参数：sites
Ordered site indices
有序网站指数
These items can be used as arguments sp.ind and site.ind to reproduce the table. In addition to the proper table, the function prints the numbers of species and sites and the name of the used cover scale at the end.
这些项目可以作为参数sp.ind和site.ind复制的表。除了适当的表中，该函数打印的物种和网站和结束时的名称所用的罩规模的数目。
注意----------Note----------
This function was called vegetab in older versions of vegan. The new name was chosen because the output is so compact (and to avoid confusion with the vegtab function in the labdsv package).
此功能被称为vegetab在旧版本的vegan。选择新的名字，因为输出是非常紧凑（vegtab功能labdsv包，以避免混乱）。
（作者）----------Author(s)----------
Jari Oksanen
参考文献----------References----------
science; I used:
Vegetation. Sidgwick & Jackson.
参见----------See Also----------
cut and approx for making your own "cover scales", wascores for weighted averages.
cut和approx为自己的“封面尺度，wascores加权平均值。
实例----------Examples----------
data(varespec)
## Print only more common species [＃打印仅较常见的物种。]
freq <- apply(varespec > 0, 2, sum)
vegemite(varespec, scale="Hult", sp.ind = freq > 10)
## Order by correspondence analysis, use Hill scaling and layout:[＃对应分析，使用山缩放和布局：]
dca <- decorana(varespec)
vegemite(varespec, dca, "Hill", zero="-")
## Show one class from cluster analysis, but retain the ordering above[＃显示从聚类分析的一类，但保留的订货以上]
clus <- hclust(vegdist(varespec))
cl <- cutree(clus, 3)
sel <- vegemite(varespec, use=dca, select = cl == 3, scale="Br")
# Re-create previous[重新创建以前]
vegemite(varespec, sp=sel$sp, site=sel$site, scale="Hult")
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-10-1 15:15:16
