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fishing_area_species(): 渔区主要物种分析

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

英文原页：fishing_area_species()

说明

该函数分析渔区数据，并根据各物种按总产量（吨）的排名，为rank_range所选名次的物种生成图表。

English

This function analyzes the fishing area data and generates plots for specified species based on their ranking in terms of total tonnes.

用法 

fishing_area_species(
  area_data,
  rank_range = 1:10,
  rank_years = NULL,
  plot = TRUE,
  table = TRUE,
  timeseries_analysis = TRUE,
  line_width = 1.5,
  point_size = 1.8,
  point_alpha = 0.7,
  point_shape = 1,
  line_alpha = 0.7,
  axis_text_size = 10,
  axis_title_size = 10,
  strip_text_size = 10,
  axis_text_face = "plain",
  axis_title_face = "bold",
  strip_text_face = "bold",
  smooth_method = "loess",
  smooth_linetype = "dashed",
  line_linewidth = 1.5,
  text_hjust = 0.9,
  text_vjust = -4,
  text_size = 4.5,
  text_color = "black",
  facet_ncol = 2,
  h_value = 0.15,
  ZH = FALSE,
  lang = NULL,
  pptx = getOption("faofishingreport.pptx", FALSE),
  plot_show = fao_setting("plot_show")
)

参数

area_data
包含渔区数据的数据框，例如fishing_area_data()返回的area_data。
English A data frame containing the fishing area data.
rank_range
要显示的物种名次，按产量排序（见rank_years）：列出名次即可，例如1:10（默认）为前十名，c(5, 6)为第五和第六名，c(1, 10)为第一和第十名。超出物种数量的名次不显示。0.9.0及以前的版本中，两个数表示起止名次（c(1, 10)为前十名）。
English The ranks of the species to show, ranked by their catch (see rank_years): the ranks listed, e.g. 1:10 (default) for the first ten, c(5, 6) for the fifth and sixth, or c(1, 10) for the first and the tenth. Ranks beyond the number of species are left out. Until version 0.9.0 two numbers gave the first and the last rank (c(1, 10) was the first ten).
rank_years
按最近几年的渔获量对物种条目排名时所用的年数，例如5表示最近五年（与fao_report()中的表格相同）。默认为NULL：按所有年份的渔获量排名。两种情况下图表都显示完整的序列。
English The number of recent years whose catch ranks the species items, e.g. 5 for the last five years (as in the tables of fao_report()). Default is NULL: the catch of all years. The charts show the whole series either way.
plot
逻辑值，是否生成并保存图表。默认为TRUE。
English A logical value indicating whether to generate and save plots.
table
逻辑值，是否生成表格并保存到tables/目录（species_ranked_table.csv和species_coefs_data.csv）。默认为TRUE。
English A logical value indicating whether to generate and save tables
timeseries_analysis
逻辑值，决定分面图（area/area_species_wrap.png）的内容：为TRUE（默认）时显示线性趋势线和突变点（用水平线段标出相邻突变点之间各时段的平均产量，用虚线标出各时段的起始年份）；为FALSE时改为显示平滑曲线（见smooth_method）。带突变点的分面图使用固定的线宽、字号和两列布局，只有text_hjust、text_vjust、text_size和text_color对它起作用。无论取值如何，都会计算突变点，并写入返回值和表格。
English A logical value indicating whether to analysis timeseries.
line_width
数值，时间序列图（area/area_species.png）中折线的宽度。默认为1.5。
English A numeric value specifying the line width. Default is 1.5.
point_size
数值，点的大小（时间序列图和不带突变点的分面图）。默认为1.8。
English A numeric value specifying the point size. Default is 1.8.
point_alpha
数值，点的透明度（0为完全透明，1为不透明）。默认为0.7。
English A numeric value specifying the point alpha. Default is 0.7.
point_shape
数值或字符，点的形状（R的点符号，如1为空心圆，16为实心圆）。默认为1。
English A numeric or character value specifying the shape of the points. Default is 1.
line_alpha
数值，折线的透明度（时间序列图和不带突变点的分面图）。默认为0.7。
English A numeric value specifying the line alpha. Default is 0.7.
axis_text_size
数值，坐标轴刻度文字的大小。默认为10。
English A numeric value specifying the size of the axis text. Default is 10.
axis_title_size
数值，坐标轴标题的大小。默认为10。
English A numeric value specifying the size of the axis title. Default is 10.
strip_text_size
数值，分面标签文字的大小。默认为10。
English A numeric value specifying the size of the strip text. Default is 10.
axis_text_face
坐标轴刻度文字的字形。默认为”plain”（常规）。
English The font face of the axis text. Default is “plain”.
axis_title_face
坐标轴标题的字形。默认为”bold”（粗体）。
English The font face of the axis title. Default is “bold”.
strip_text_face
分面标签文字的字形。默认为”bold”（粗体）。
English The font face of the strip text. Default is “bold”.
smooth_method
字符串，平滑曲线的方法，同ggplot2::geom_smooth()的method（如”loess”、“lm”、“gam”），用于不带突变点的分面图（timeseries_analysis = FALSE）。默认为”loess”。
English A character string specifying the smoothing method to be used. Default is “loess”.
smooth_linetype
字符串，平滑曲线的线型（如”dashed”、“solid”、“dotted”）。默认为”dashed”。
English A character string specifying the line type for the smoothing curve. Default is “dashed”.
line_linewidth
数值，不带突变点的分面图（timeseries_analysis = FALSE）中折线的宽度。默认为1.5。
English A numeric value specifying the line width for the line geom. Default is 1.5.
text_hjust
数值，分面图中占比标签（各物种历年产量占渔区总产量的比例）的水平对齐方式；标签锚定在1957年、产量为0处。默认为0.9。
English A numeric value specifying the horizontal justification of the text geom. Default is 0.9.
text_vjust
数值，占比标签的垂直对齐方式。默认为-4。
English A numeric value specifying the vertical justification of the text geom. Default is -4.
text_size
数值，占比标签的字号。默认为4.5。
English A numeric value specifying the size of the text geom. Default is 4.5.
text_color
字符串，占比标签的颜色。默认为”black”。
English A character string specifying the color of the text geom. Default is “black”.
facet_ncol
数值，facet_wrap分面的列数，用于不带突变点的分面图（timeseries_analysis = FALSE）。默认为2。
English A numeric value specifying the number of columns to be used in facet_wrap. Default is 2.
h_value
突变点检验（strucchange::breakpoints()的参数h）中相邻突变点之间时段的最短长度：小于1时为占序列长度的比例，大于等于1时为年数。默认为0.15，即每个时段至少占序列长度的15%。
English The minimum segment size passed to strucchange::breakpoints(): a fraction of the series length (default 0.15) or a number of years.
ZH
逻辑值。为TRUE时，图表文字和名称使用中文。默认为FALSE。ZH = TRUE等同于lang = "zh"。
English A logical value. If TRUE, chart text and names are in Chinese. Default is FALSE. ZH = TRUE is the same as lang = "zh".
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：ZH = TRUE时使用”zh”，否则使用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 “zh” if ZH = TRUE, and otherwise the language set with fao_settings() (“en” unless changed).
pptx
逻辑值。图表总是以PNG格式保存在figures/png/；为TRUE时还另存为可编辑的PowerPoint文件，保存在figures/pptx/。默认为FALSE，可以用fao_settings(pptx = TRUE)为所有函数统一更改。
English A logical value. Charts are always saved as PNG in figures/png/; if TRUE they are also saved as editable PowerPoint files in figures/pptx/. 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.

返回值

一个列表，包含area_species（渔区内每个物种条目逐年的产量）、area_species_ranked（所选名次的各物种逐年的产量，其余合并为一类）、area_species_ranked_total（所选物种的总产量和排名）和coefs_data（相邻突变点之间各时段的起始年start_year、结束年end_year和平均产量intercept）。plot和table为TRUE时保存图表和表格。

English

A list with area_species (yearly catch of every species item in the area), area_species_ranked (yearly catch of the ranked species, with the others grouped), area_species_ranked_total (total catch and rank of the selected species) and coefs_data (start year, end year and mean catch of each period between breakpoints). Charts and tables are saved if plot and table are TRUE.

另请参阅

Other fishing area analyses: fishing_area_country(), fishing_area_data()

示例 

FAO27 <- fishing_area_data("Atlantic, Northeast")
fishing_area_species(FAO27$area_data, rank_range = 1:10)    # the ten main species
fishing_area_species(FAO27$area_data, rank_range = 11:20)   # the next ten