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cmsy_compare(): 比较多次CMSY++运行结果，或与其他评估比较

Source: vignettes/articles/zh/reference/cmsy_compare.Rmd
cmsy_compare.Rmd

英文原页：cmsy_compare()

说明

本函数绘制多次cmsy_run()运行（例如采用不同起始年份或先验的敏感性分析）中同一批种群的B/Bmsy和F/Fmsy，也可以加入其他评估的结果，并给出它们最后一年数值的表格。

English

This function draws B/Bmsy and F/Fmsy of the same stocks from several runs of cmsy_run() (e.g. with different start years or priors, a sensitivity analysis) and, optionally, from other assessments, and gives a table of their last-year values.

用法 

cmsy_compare(
  ...,
  stocks = NULL,
  external = NULL,
  lang = NULL,
  annotations = getOption("faofishingreport.cmsy_annotations", FALSE),
  pptx = getOption("faofishingreport.pptx", FALSE),
  plot_show = fao_setting("plot_show"),
  silent = fao_setting("silent")
)

参数

...
cmsy_run()的结果，可以命名，也可以不命名（例如default = run1, start_1980 = run2）。
English Results of cmsy_run(), named or not (e.g. default = run1, start_1980 = run2).
stocks
要比较的种群（可选）：Stock标识，或物种的FAO英文或中文名称、学名或FAO三字母代码。默认为NULL，即所有已运行的种群。
English Optional stocks to compare: Stock identifiers or species, by English or Chinese FAO name, scientific name or FAO 3-alpha code. Default is NULL, all stocks that ran.
external
其他估计结果的数据框（可选），包含Stock、Year、B_Bmsy（可选F_Fmsy）和source列（source为图例中显示的名称，例如另一项评估的机构或模型）。
English Optional data frame of other estimates, with columns Stock, Year, B_Bmsy (and optionally F_Fmsy) and source (the name shown in the legend, e.g. the agency or model of the other assessment).
lang
图表文字和名称的语言：“en”（英文）、“zh”（中文）或”both”（中英双语）。默认为NULL，即使用fao_settings()设置的语言（未更改时为”en”）。
English The language of the chart text and names: “en” (English), “zh” (Chinese) or “both” (Chinese and English). Default is NULL, which uses the language set with fao_settings() (“en” unless changed).
annotations
在坐标轴标题和坐标轴标签之外添加的文字：FALSE（默认）不添加，TRUE全部添加，或”title”、“subtitle”、“caption”、“legend”和”labels”（图内文字）中的任意几项。可以用options(faofishingreport.cmsy_annotations = TRUE)更改本次R会话的默认值。
English The text added to the axis titles and labels: FALSE (default) none, TRUE all, or any of “title”, “subtitle”, “caption”, “legend” and “labels” (text inside the chart). The default can be changed for the session with options(faofishingreport.cmsy_annotations = TRUE).
pptx
逻辑值。为TRUE时，图表还另存为可编辑的PowerPoint文件，保存在figures/pptx/cmsy/compare/。默认为FALSE，可以用fao_settings(pptx = TRUE)为所有函数统一更改。
English A logical value. If TRUE, the charts are also saved as editable PowerPoint files in figures/pptx/cmsy/compare/. Default is FALSE, which can be changed for all functions with fao_settings(pptx = TRUE).
plot_show
逻辑值。为TRUE时，每张图在保存的同时也画在绘图窗口中（例如RStudio的Plots窗格），便于立即查看。默认为FALSE，可以用fao_settings(plot_show = TRUE)为所有函数统一更改。无论是否显示，图表都会保存为文件（plot = TRUE）。
English A logical value. If TRUE, each chart is also drawn in the plot window (e.g. the Plots pane of RStudio) as it is saved, to look at it at once. Default is FALSE, which can be changed for all functions with fao_settings(plot_show = TRUE). The charts are saved as files (plot = TRUE) either way.
silent
逻辑值。为TRUE时不输出种群匹配情况的提示信息。默认为FALSE，或fao_settings(silent = )设置的值。
English A logical value. If TRUE, the messages on how the stocks were matched are not printed. Default is FALSE, or the value set with fao_settings(silent = ).

返回值

以不可见方式返回一个列表，包含last_year（每个种群和每次运行一行）和plots。

English

Invisibly, a list with last_year (one row per stock and run) and plots.

示例 

# Sensitivity to the start year
run_1950 <- cmsy_run(input, stocks = "CAP_27", seed = 1)
run_auto <- cmsy_run(input, stocks = "CAP_27", seed = 1, auto_start = TRUE)
cmsy_compare(`from 1950` = run_1950, `CMSY++ start year` = run_auto, annotations = "legend")

# Sensitivity to a CMSY++ setting (see cmsy_defaults())
run_cv <- cmsy_run(input, stocks = "CAP_27", seed = 1, auto_start = TRUE, settings = list(CV.C = 0.3))
cmsy_compare(default = run_auto, `CV.C = 0.3` = run_cv)$last_year

# With another assessment of the same stock, read from a file with the columns
# Stock, Year, B_Bmsy (optionally F_Fmsy) and source
other <- read.csv("other_assessment.csv")
cmsy_compare(CMSY = run_auto, external = other, annotations = "legend")