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Summarize active vessels

Source: R/vessel_count.R
vessel_count.Rd

vessel_count counts the number of active vessels in the main table. It can summarize by period if date is provided, group by any number of grouping variables, and filter by period or value. There are several options for customizing table/plot output.

Usage

vessel_count(
  dat,
  project,
  v_id,
  date = NULL,
  period = NULL,
  group = NULL,
  sub_date = NULL,
  filter_date = NULL,
  date_value = NULL,
  filter_by = NULL,
  filter_value = NULL,
  filter_expr = NULL,
  facet_by = NULL,
  combine = FALSE,
  position = "stack",
  tran = "identity",
  format_lab = "decimal",
  value = "count",
  type = "bar",
  scale = "fixed",
  output = "tab_plot"
)

Arguments

dat

Primary data containing information on hauls or trips. Table in FishSET database contains the string 'MainDataTable'.

project

String, name of project.

v_id

Variable in dat containing vessel identifier to count.

date

Date variable to aggregate by.

period

Time period to aggregate by. Options include "year", "month", "week" (weeks in the year), "weekday", "weekday_abv", "day_of_month", "day_of_year", and "cal_date" (calender date).

group

Names of grouping variables. For line plots (type = "line") two grouping variables can be entered, the first is passed to "color" and second to "linetype". Only one grouping variable can be used for barplots (type = "bar"), which is passed to "fill". When combine = TRUE all variables in group will be joined. Grouping by "year", "month", and "week" are available if a date variable is added to sub_date.

sub_date

Date variable used for subsetting, grouping, or splitting by date.

filter_date

The type of filter to apply to `MainDataTable`. To filter by a range of dates, use filter_date = "date_range". To filter by a given period, use "year-day", "year-week", "year-month", "year", "month", "week", or "day". The argument date_value must be provided.

date_value

This argument is paired with filter_date. To filter by date range, set filter_date = "date_range" and enter a start- and end-date into date_value as a string: date_value = c("2011-01-01", "2011-03-15").

To filter by period (e.g. "year", "year-month"), use integers (4 digits if year, 1-2 digits if referencing a day, month, or week). Use a vector if filtering by a single period: date_filter = "month" and date_value = c(1, 3, 5). This would filter the data to January, March, and May.

Use a list if using a year-period type filter, e.g. "year-week", with the format: list(year, period). For example, filter_date = "year-month" and date_value = list(2011:2013, 5:7) will filter the data table from May through July for years 2011-2013.

filter_by

String, variable name to filter `MainDataTable` by. the argument filter_value must be provided.

filter_value

A vector of values to filter `MainDataTable` by using the variable in filter_by. For example, if filter_by = "GEAR_TYPE", filter_value = 1 will include only observations with a gear type of 1.

filter_expr

String, a valid R expression to filter `MainDataTable` by using the variable in filter_by.

facet_by

Variable name to facet by. Accepts up to two variables. These can be variables that exist in dat, or a variable created by vessel_count() such as "year", "month", or "week" if a date variable is added to sub_date. The first variable is facetted by row and the second by column.

combine

Whether to combine variables listed in group. This is passed to the "fill" or "color" aesthetic for plots.

position

Positioning of bar plot. Options include 'stack', 'dodge', and 'fill'.

tran

A function to transform the y-axis. Options include log, log2, log10, and sqrt.

format_lab

decimal or scientific

value

Whether to return "count" or "percent" of active vessels. Defaults to "count".

type

Plot type, options include "bar" (the default) and "line".

scale

Scale argument passed to facet_grid. Options include "free", "free_x", "free_y". Defaults to "fixed".

output

Whether to display "plot", "table". Defaults to both ("tab_plot").

Value

When output = "tab_plot" a list containing a table and plot are returned. If output = "table" only the summary table is returned, if output = "plot" only the plot.

Details

vessel_count gives the number (or percent) of active vessels using a column of unique vessel IDs. The data can be filtered by date and/or by a variable. (console users may want to use a separate filtering function, like dplyr::filter, before running vessel_count: note that this is okay but will lead to different output if using log_rerun). filter_date specifies the type of date filter to apply--by date-range or by period. date_value should contain the values to filter the data by. To filter by a variable, enter its name as a string in filter_by and include the values to filter by in filter_value.

Up to two grouping variables can be entered. Grouping variables can be merged into one variable using combine = TRUE; in this case any number of variables can be joined, but no more than three is recommended.

For faceting, any variable (including ones listed in group) can be used, but "year", "month", "week" are also available provided a date variable is added to sub_date. Currently, combined variables cannot be faceted.

Examples

if (FALSE) {
# grouping by two variables
vessel_count(pollockMainDataTable, v_id = "VESSEL_ID", 
             group = c("GEAR_TYPE", "IFQ"))
             
# filter by variable
vessel_count(pollockMainDataTable, v_id = "VESSEL_ID", group = "GEAR_TYPE",
             filter_by = "IFQ", filter_value = "Y")
             
# filter by month
vessel_count(pollockMainDataTable, v_id = "VESSEL_ID", group = "GEAR_TYPE",
             sub_date = "HAUL_DATE", date_filter = "month", date_value = 1:5)
             
#' # filter by date
vessel_count(pollockMainDataTable, v_id = "VESSEL_ID", group = "GEAR_TYPE",
             sub_date = "HAUL_DATE", date_filter = "date_range", 
             date_value = c("2011-01-01", "2011-02-05"))

# summarize by month
vessel_count(pollockMainDataTable, v_id = 'VESSEL_ID', date = 'DATE_FISHING_BEGAN', 
             period = 'month', group = 'DISEMBARKED_PORT', position = 'dodge', 
             output = 'plot')
}