weekly_effort
summarizes CPUE (or other numeric variables) in the
main table by week. It can summarize by grouping variables and filter by period
or value. There are several options for customizing the table and plot output.
Usage
weekly_effort(
dat,
project,
cpue,
date,
group = NULL,
sub_date = NULL,
filter_date = NULL,
date_value = NULL,
filter_by = NULL,
filter_value = NULL,
filter_expr = NULL,
facet_by = NULL,
conv = "none",
tran = "identity",
format_lab = "decimal",
combine = FALSE,
scale = "fixed",
output = "tab_plot",
format_tab = "wide"
)
Arguments
- dat
Primary data containing information on hauls or trips. Table in FishSET database contains the string 'MainDataTable'.
- project
String, name of project.
- cpue
Variable(s) in
dat
containing catch per unit effort.- date
A variable in
dat
containing dates to aggregate by.- group
Grouping variable name(s). Up to two grouping variables are available. For plotting, if a single CPUE column is entered the first grouping variable is passed to the "color" aesthetic and the second to "linetype". If multiple CPUE columns are entered, a new variable named "species" is created and passed to "fill", the first group variable to "linetype", and second is dropped.
- 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 argumentdate_value
must be provided.- date_value
This argument is paired with
filter_date
. To filter by date range, setfilter_date = "date_range"
and enter a start- and end-date intodate_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"
anddate_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"
anddate_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, iffilter_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. Facetting by
"year"
is available if a date variable is added tosub_date
. Facetting by"species"
is available if multiple cpue columns are included in"cpue"
. The first variable is facetted by row and the second by column.- conv
Convert catch variable to
"tons"
,"metric_tons"
, or by using a function entered as a string. Defaults to"none"
for no conversion.- tran
A function to transform the y-axis. Options include log, log2, log10, sqrt.
- format_lab
Formatting option for y-axis labels. Options include
"decimal"
or"scientific"
.- combine
Whether to combine variables listed in
group
. This is passed to the "color" aesthetic for plots.- scale
Scale argument passed to
facet_grid
. Defaults to"fixed"
.- output
Whether to display
"plot"
,"table"
. Defaults to both ("tab_plot"
).- format_tab
How table output should be formatted. Options include 'wide' (the default) and 'long'.
Value
weekly_effort()
calculates mean CPUE by week. This function doesn't
calculate CPUE; the CPUE variable must be created in advance (see cpue
).
When multiple CPUE variables are entered, a new column named "species"
is created and used to group values in plots.
The "species" column can also be used to split (or facet) the plot. For table output,
the "species" column will be kept if format_tab = "long"
, i.e. a column of
species names ("species") and a column containing the mean CPUE ("mean_cpue"). When
format_tab = "wide"
, each CPUE variable is given its own value column.
The data can be filtered by date and/or by a variable. 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
;
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" and "species" are also available. Facetting by "year" requires a date
variable be added to sub_date
. Currently, combined variables cannot be
faceted. A list containing a table and plot are printed to the console and
viewer by default.