R语言【paleobioDB】——pbdb_richness()：绘制指定类群的数量丰度

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。

Usage

R 复制代码

pbdb_richness (data, rank, res, temporal_extent, colour, bord, do.plot)

Arguments

参数【data】：输入的数据，数据帧格式。可以通过 pbdb_occurrences() 函数传参 **show = c("phylo", "ident")**获得数据。

参数【rank】：设置感兴趣的分类阶元。可选项包括："species"，"genus"，"family"，"order"，"class" 和 "phylum"。默认值为 "species"。

参数【temporal_extent】：设置时间范围，向量型（min，max）。

参数【res】：数值型。设置时间范围的时间段刻度。

参数【orig_ext】：1 表示出现，2 表示灭绝。

参数【colour】：改变图中柱子的颜色。默认为 skyblue2。

参数【bord】：设置图形边界的颜色。

参数【do.plot】：TRUE /FALSE。默认为 TRUE。

Value

返回一个数据帧和一个图像，展示了指定类群阶元在特定时间段内和分辨率上的丰富度变化。

Example

R 复制代码

library(paleobioDB)
library(RCurl)

options(RCurlOptions = list(cainfo = system.file("CurlSSL", "cacert.pem", package = "RCurl")))

data<-  pbdb_occurrences (limit="all", vocab="pbdb",
base_name="Canidae", show=c("phylo", "ident"))

pbdb_richness (data, rank="species", res=1, temporal_extent=c(0,3))

R 复制代码

  temporal_intervals richness
1                0-1       95
2                1-2       94
3                2-3       98

Page

R 复制代码

function (data, rank, res = 1, temporal_extent = c(0, 10), colour = "#0000FF30", 
    bord = "#0000FF", do.plot = TRUE) 
{
    temporal_range <- pbdb_temp_range(data = data, rank = rank, 
        do.plot = FALSE)
    te <- temporal_extent
    time <- seq(from = min(te), to = (max(te)), by = res)
    means <- NULL
    for (i in 1:length(time) - 1) {
        x <- (time[i + 1] + time[i])/2
        means <- c(means, x)
    }
    a <- NULL
    for (i in 1:(length(time) - 1)) {
        b <- temporal_range[, 1] > time[i] & temporal_range[, 
            2] <= time[i + 1]
        a <- cbind(a, b)
    }
    richness <- colSums(a + 0, na.rm = T)
    temporal_intervals <- paste(time[-length(time)], time[-1], 
        sep = "-")
    richness <- data.frame(temporal_intervals, richness)
    if (do.plot == TRUE) {
        plot.new()
        par(mar = c(5, 5, 1, 5), font.lab = 1, col.lab = "grey20", 
            col.axis = "grey50", cex.axis = 0.8)
        plot.window(xlim = c(max(te), min(te)), xaxs = "i", ylim = c(0, 
            (max(richness[, 2])) + (max(richness[, 2])/10)), 
            yaxs = "i")
        abline(v = seq(min(te), max(te), by = res), col = "grey90", 
            lwd = 1)
        abline(h = seq(0, max(richness[, 2]) + (max(richness[, 
            2])/10), by = (max(richness[, 2])/10)), col = "grey90", 
            lwd = 1)
        xx <- c(means[1], means, means[length(means)])
        yy <- c(0, richness[, 2], 0)
        polygon(xx, yy, col = colour, border = bord)
        axis(1, line = 1, las = 2, labels = temporal_intervals, 
            at = means)
        axis(2, line = 1, las = 1)
        mtext("Million years before present", line = 3.5, adj = 1, 
            side = 1)
        mtext("Richness", line = 3.5, adj = 0, side = 2)
    }
    return(richness)
}