R语言【paleobioDB】——pbdb_subtaxa()：统计指定类群下的子类群数量

Package paleobioDB version 0.7.0

paleobioDB 包在2020年已经停止更新，该包依赖PBDB v1 API。

可以选择在Index of /src/contrib/Archive/paleobioDB (r-project.org)下载安装包后，执行本地安装。

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Usage

pbdb_subtaxa (data, do.plot, col)

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Arguments

参数【data】：输入的数据，数据帧格式。可以通过 pbdb_occurrences() 函数获得数据。

参数【do.plot】：TRUE/FALSE。默认为 TRUE。

参数【col】：改变图中柱子的颜色。默认为 skyblue2。

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Value

返回一张图和一个数据帧，展示了数据中的子类群数量。

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Example

library(paleobioDB)
library(RCurl)options(RCurlOptions = list(cainfo = system.file("CurlSSL", "cacert.pem", package = "RCurl")))canidae_quat<-  pbdb_occurrences (limit="all", 
base_name="Canidae",  interval="Quaternary", 
show=c("coords", "phylo", "ident"))pbdb_subtaxa (canidae_quat)

  species genera families orders classes phyla
1       0     29        1      1       1     1

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Page

function (data, do.plot = TRUE, col = "#0000FF") 
{species <- nrow(pbdb_temp_range(data = data, rank = "species", do.plot = FALSE))genera <- nrow(pbdb_temp_range(data = data, rank = "genus", do.plot = FALSE))families <- nrow(pbdb_temp_range(data = data, rank = "family", do.plot = FALSE))orders <- nrow(pbdb_temp_range(data = data, rank = "order", do.plot = FALSE))classes <- nrow(pbdb_temp_range(data = data, rank = "class", do.plot = FALSE))phyla <- nrow(pbdb_temp_range(data = data, rank = "phylum", do.plot = FALSE))subtaxa <- data.frame(species, genera, families, orders, classes, phyla)if (do.plot == TRUE) {par(mar = c(8, 4, 2, 0))barplot(unlist(subtaxa), beside = T, horiz = F, col = col, border = F, las = 2, ylab = "Number of taxa")}return(subtaxa)
}