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

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

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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 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。

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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。

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Example

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))

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

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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_extenttime <- seq(from = min(te), to = (max(te)), by = res)means <- NULLfor (i in 1:length(time) - 1) {x <- (time[i + 1] + time[i])/2means <- c(means, x)}a <- NULLfor (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)
}

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