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)
}