Biomass, abundance, and catch time series table

Biomass, abundance, and catch time series table

table_biomass_abundance_catch(
  dat,
  unit_label = c(biomass = "mt", abundance = "fish", catch = "mt"),
  era = NULL,
  interactive = TRUE,
  group = NULL,
  method = "sum",
  module = NULL,
  label = NULL,
  make_rda = FALSE,
  tables_dir = getwd()
)

Arguments

dat

Data frame or list. A tibble or named list of tibbles (input as list()) returned from convert_output.

If inputting a list of tibbles, the first tibble's reference point defined in ref_line is used to plot a reference line or calculate relative spawning biomass.

unit_label

Character vector. Abbreviated unit label for each quantity

Default: c("biomass" = "mt", "abundance" = "fish", "catch" = "mt")

era

String. Era of data.

Default: "time"

Options: "early", "time", "fore" (forecast), or NULL (all data)

interactive

Logical. TRUE/FALSE; indicate whether the environment is interactive.

Default: FALSE

group

A string of a single column that groups the data.

Set group = "none" to summarize data over all indexing values.

Default: NULL Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL

method

A string describing the method of summarizing data when group is set to "none".

Default: "sum"

Options: "sum" or "mean"

module

Character vector. (Optional) Module name found in dat$module_name. If selecting >1 module, place them in a vector like c("module1", "module2").

Default: NULL

If the interactive and >1 module_name is found, user will select the module_name in the console. @seealso filter_data()

label

The label that will be chosen from the input file. If unspecified, the function will search the "label" column and use the first matching label in this ordered list: "landings_weight", "landings_numbers", "landings_expected", "landings_predicted", "landings".

Default: NULL

make_rda

Logical. TRUE/FALSE; indicate whether to save the object and make an automated caption and alternative text in the form of an rda object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir".

Default: FALSE.

tables_dir

The location of the folder containing the table rda files ("tables") that will be created if the argument make_rda = TRUE. Default: the working directory (getwd())

Value

A table of biomass, abundance, catch, and spawning biomass.

Details

There are options to return a gt::gt() object or export an rda object containing a gt-based table, caption, and LaTeX-based table.

See also

convert_output(), filter_data(), process_table(), export_kqs(), insert_kqs(), create_rda()

Examples

table_biomass_abundance_catch(stockplotr::example_data)
#> ℹ Processing ^biomass$
#> ! Multiple module names found in data. 
#> ℹ Environment not interactive. Selecting SPR_SERIES.
#> ℹ Processing ^abundance
#> ! Multiple module names found in data. 
#> ℹ Environment not interactive. Selecting SPR_SERIES.
#> ℹ Processing catch$|landings_observed
#> ! Multiple module names found in data. 
#> ℹ Environment not interactive. Selecting CATCH.


  
Year
      
Biomass (mt) 
      
Abundance Midyear (fish) 
      
Landings Observed Weight (mt)  (se)
    
1876
42,640.00
0.00
1.00 (0.01)
1877
42,640.00
0.00
1.00 (0.01)
1878
42,640.00
0.00
1.00 (0.01)
1879
42,640.00
0.00
1.00 (0.01)
1880
42,552.20
0.00
11.55 (0.01)
1881
42,464.70
0.00
22.10 (0.01)
1882
42,377.40
0.00
32.65 (0.01)
1883
42,290.30
0.00
43.20 (0.01)
1884
42,203.40
0.00
53.75 (0.01)
1885
42,116.60
0.00
64.30 (0.01)
1886
42,029.80
0.00
74.85 (0.01)
1887
41,943.10
0.00
85.40 (0.01)
1888
41,856.30
0.00
95.95 (0.01)
1889
41,769.60
0.00
106.50 (0.01)
1890
41,682.90
0.00
117.05 (0.01)
1891
41,596.10
0.00
127.60 (0.01)
1892
41,509.20
0.00
138.15 (0.01)
1893
41,422.20
0.00
148.71 (0.01)
1894
41,335.20
0.00
159.26 (0.01)
1895
41,248.10
0.00
169.81 (0.01)
1896
41,159.50
0.00
180.60 (0.01)
1897
41,072.50
0.00
191.11 (0.01)
1898
40,985.40
0.00
201.61 (0.01)
1899
40,898.00
0.00
212.16 (0.01)
1900
40,810.50
0.00
222.71 (0.01)
1901
40,722.80
0.00
233.25 (0.01)
1902
40,635.10
0.00
243.80 (0.01)
1903
40,547.20
0.00
254.34 (0.01)
1904
40,459.30
0.00
264.89 (0.01)
1905
40,371.30
0.00
275.44 (0.01)
1906
40,283.10
0.00
285.98 (0.01)
1907
40,194.80
0.00
296.53 (0.01)
1908
40,106.50
0.00
307.07 (0.01)
1909
40,018.00
0.00
317.62 (0.01)
1910
39,929.40
0.00
328.16 (0.01)
1911
39,840.80
0.00
338.71 (0.01)
1912
39,752.00
0.00
349.26 (0.01)
1913
39,663.10
0.00
359.80 (0.01)
1914
39,574.20
0.00
370.35 (0.01)
1915
39,485.10
0.00
380.89 (0.01)
1916
39,433.90
0.00
386.50 (0.01)
1917
38,375.50
0.00
526.49 (0.01)
1918
39,120.40
0.00
423.92 (0.01)
1919
39,815.70
0.00
333.51 (0.01)
1920
40,649.00
0.00
230.55 (0.01)
1921
40,138.80
0.00
293.82 (0.01)
1922
39,115.10
0.00
424.83 (0.01)
1923
39,087.40
0.00
427.41 (0.01)
1924
38,288.40
0.00
532.91 (0.01)
1925
38,301.30
0.00
528.51 (0.01)
1926
38,334.30
0.00
521.71 (0.01)
1927
37,512.90
0.00
632.08 (0.01)
1928
37,569.80
0.00
620.09 (0.01)
1929
36,923.40
0.00
707.58 (0.01)
1930
37,223.80
0.00
660.05 (0.01)
1931
37,361.90
0.00
641.11 (0.01)
1932
37,697.70
0.00
598.39 (0.01)
1933
38,619.00
0.00
478.74 (0.01)
1934
33,857.40
0.00
1,179.95 (0.01)
1935
35,001.60
0.00
982.24 (0.01)
1936
37,478.00
0.00
626.31 (0.01)
1937
34,893.20
0.00
1,015.77 (0.01)
1938
34,032.20
0.00
1,123.74 (0.01)
1939
31,902.40
0.00
1,534.78 (0.01)
1940
33,346.60
0.00
1,316.87 (0.01)
1941
34,397.40
0.00
1,176.76 (0.01)
1942
30,442.90
0.00
2,206.06 (0.01)
1943
29,337.70
0.00
2,375.88 (0.01)
1944
31,555.00
0.00
1,621.40 (0.01)
1945
31,858.50
0.00
1,508.26 (0.01)
1946
26,241.80
0.00
2,805.53 (0.01)
1947
27,185.60
0.00
2,222.58 (0.01)
1948
20,655.20
0.00
4,280.45 (0.01)
1949
21,775.70
0.00
3,069.20 (0.01)
1950
20,427.30
0.00
3,461.25 (0.01)
1951
23,414.70
0.00
2,323.44 (0.01)
1952
23,290.80
0.00
2,176.72 (0.01)
1953
23,493.20
0.00
1,928.17 (0.01)
1954
20,664.80
0.00
2,525.99 (0.01)
1955
21,217.10
0.00
2,294.32 (0.01)
1956
23,058.80
0.00
1,849.25 (0.01)
1957
19,771.00
0.00
2,639.74 (0.01)
1958
20,401.80
0.00
2,318.67 (0.01)
1959
21,995.00
0.00
1,880.98 (0.01)
1960
20,955.30
0.00
2,157.46 (0.01)
1961
18,754.20
0.00
2,548.42 (0.01)
1962
18,059.70
0.00
2,690.84 (0.01)
1963
17,227.20
0.00
2,710.56 (0.01)
1964
18,882.30
0.00
2,150.66 (0.01)
1965
19,258.70
0.00
2,109.23 (0.01)
1966
18,833.80
0.00
2,289.51 (0.01)
1967
19,522.20
0.00
2,181.42 (0.01)
1968
19,929.80
0.00
2,121.13 (0.01)
1969
19,942.20
0.00
2,249.00 (0.01)
1970
18,887.50
0.00
2,713.96 (0.01)
1971
18,916.60
0.00
2,887.68 (0.01)
1972
19,015.60
0.00
2,953.35 (0.01)
1973
17,929.20
0.00
2,950.56 (0.01)
1974
15,433.30
0.00
3,624.83 (0.01)
1975
14,514.30
0.00
3,489.85 (0.01)
1976
14,709.70
0.00
2,764.06 (0.01)
1977
15,567.60
0.00
2,267.94 (0.01)
1978
12,231.30
0.00
3,058.79 (0.01)
1979
10,294.80
0.00
3,054.97 (0.01)
1980
10,640.70
0.00
2,467.60 (0.01)
1981
11,457.60
0.00
2,041.19 (0.01)
1982
9,727.88
0.00
2,630.33 (0.01)
1983
10,589.50
0.00
2,214.19 (0.01)
1984
11,045.40
0.00
1,739.17 (0.01)
1985
10,124.50
0.00
1,839.45 (0.01)
1986
10,130.70
0.00
1,750.43 (0.01)
1987
8,739.28
0.00
2,204.84 (0.01)
1988
8,668.73
0.00
2,149.18 (0.01)
1989
8,701.67
0.00
2,152.70 (0.01)
1990
9,644.76
0.00
1,764.64 (0.01)
1991
8,967.17
0.00
1,927.37 (0.01)
1992
9,743.79
0.00
1,553.50 (0.01)
1993
10,082.60
0.00
1,503.21 (0.01)
1994
11,372.50
0.00
1,375.14 (0.01)
1995
11,084.70
0.00
1,659.05 (0.01)
1996
10,863.00
0.00
1,828.60 (0.01)
1997
10,502.20
0.00
1,947.72 (0.01)
1998
12,509.10
0.00
1,462.77 (0.01)
1999
13,228.50
0.00
1,497.11 (0.01)
2000
12,248.10
0.00
1,893.27 (0.01)
2001
12,603.40
0.00
1,845.22 (0.01)
2002
12,868.00
0.00
1,797.09 (0.01)
2003
12,995.50
0.00
2,069.58 (0.01)
2004
14,009.30
0.00
1,963.97 (0.01)
2005
12,226.60
0.00
2,734.36 (0.01)
2006
12,117.30
0.00
2,610.20 (0.01)
2007
12,477.90
0.00
2,252.84 (0.01)
2008
12,125.30
0.00
2,219.71 (0.01)
2009
13,032.60
0.00
1,767.44 (0.01)
2010
19,752.60
0.00
803.10 (0.01)
2011
22,244.50
0.00
934.51 (0.01)
2012
23,703.30
0.00
1,117.72 (0.01)
2013
20,093.40
0.00
2,253.36 (0.01)
2014
20,976.70
0.00
2,408.74 (0.01)
2015
20,958.60
0.00
2,665.17 (0.01)
2016
21,129.90
0.00
2,727.63 (0.01)
2017
20,520.40
0.00
2,930.62 (0.01)
2018
20,831.50
0.00
2,894.44 (0.01)
2019
21,423.40
0.00
2,616.91 (0.01)
2020
23,125.50
0.00
2,092.13 (0.01)
2021
20,253.80
0.00
2,879.11 (0.01)
2022
19,064.90
0.00
3,059.94 (0.01)

table_biomass_abundance_catch(stockplotr::example_data,
  unit_label = c("biomass" = "kg", "abundance" = "eggs", "catch" = "kg"),
  module = c("TIME_SERIES", "CATCH", "TIME_SERIES"),
  interactive = FALSE
)
#> ℹ Processing ^biomass$
#> ℹ Processing ^abundance
#> ℹ Processing catch$|landings_observed


  
Year
      
Biomass (kg) 
      
Abundance Midyear (eggs) 
      
Landings Observed Weight (kg)  (se)
    
1876
42,648.70
71,607.00
1.00 (0.01)
1877
42,647.80
71,606.00
1.00 (0.01)
1878
42,647.10
71,605.20
1.00 (0.01)
1879
42,646.60
71,607.20
1.00 (0.01)
1880
42,646.40
71,608.80
11.55 (0.01)
1881
42,636.70
71,598.90
22.10 (0.01)
1882
42,618.30
71,579.00
32.65 (0.01)
1883
42,591.90
71,550.30
43.20 (0.01)
1884
42,558.20
71,513.90
53.75 (0.01)
1885
42,517.80
71,470.90
64.30 (0.01)
1886
42,471.60
71,422.00
74.85 (0.01)
1887
42,419.90
71,367.70
85.40 (0.01)
1888
42,363.50
71,308.80
95.95 (0.01)
1889
42,302.80
71,245.90
106.50 (0.01)
1890
42,238.30
71,179.20
117.05 (0.01)
1891
42,170.30
71,109.40
127.60 (0.01)
1892
42,099.40
71,036.60
138.15 (0.01)
1893
42,025.70
70,961.20
148.71 (0.01)
1894
41,949.60
70,883.60
159.26 (0.01)
1895
41,871.40
70,804.00
169.81 (0.01)
1896
41,791.20
70,722.50
180.60 (0.01)
1897
41,709.20
70,639.30
191.11 (0.01)
1898
41,625.70
70,554.60
201.61 (0.01)
1899
41,540.90
70,468.70
212.16 (0.01)
1900
41,454.90
70,381.80
222.71 (0.01)
1901
41,367.90
70,293.80
233.25 (0.01)
1902
41,279.90
70,205.00
243.80 (0.01)
1903
41,191.10
70,115.50
254.34 (0.01)
1904
41,101.50
70,025.20
264.89 (0.01)
1905
41,011.30
69,934.50
275.44 (0.01)
1906
40,920.50
69,843.20
285.98 (0.01)
1907
40,829.20
69,751.50
296.53 (0.01)
1908
40,737.50
69,659.60
307.07 (0.01)
1909
40,645.40
69,567.30
317.62 (0.01)
1910
40,553.00
69,475.10
328.16 (0.01)
1911
40,460.30
69,382.50
338.71 (0.01)
1912
40,367.40
69,290.10
349.26 (0.01)
1913
40,274.30
69,197.70
359.80 (0.01)
1914
40,181.20
69,105.60
370.35 (0.01)
1915
40,088.00
69,013.60
380.89 (0.01)
1916
39,994.70
68,922.00
386.50 (0.01)
1917
39,906.10
68,836.20
526.49 (0.01)
1918
39,698.50
68,607.60
423.92 (0.01)
1919
39,603.30
68,522.80
333.51 (0.01)
1920
39,601.90
68,549.70
230.55 (0.01)
1921
39,698.80
68,685.00
293.82 (0.01)
1922
39,733.30
68,732.90
424.83 (0.01)
1923
39,646.60
68,632.00
427.41 (0.01)
1924
39,565.00
68,546.90
532.91 (0.01)
1925
39,394.60
68,361.20
528.51 (0.01)
1926
39,243.40
68,208.00
521.71 (0.01)
1927
39,113.40
68,086.40
632.08 (0.01)
1928
38,896.40
67,861.30
620.09 (0.01)
1929
38,711.50
67,682.90
707.58 (0.01)
1930
38,466.30
67,436.60
660.05 (0.01)
1931
38,289.70
67,280.90
641.11 (0.01)
1932
38,153.60
67,178.80
598.39 (0.01)
1933
38,079.00
67,154.00
478.74 (0.01)
1934
38,131.50
67,284.10
1,179.95 (0.01)
1935
37,549.60
66,636.30
982.24 (0.01)
1936
37,203.90
66,326.80
626.31 (0.01)
1937
37,229.20
66,500.50
1,015.77 (0.01)
1938
36,923.00
66,251.00
1,123.74 (0.01)
1939
36,543.90
65,881.60
1,534.78 (0.01)
1940
35,846.20
65,098.80
1,316.87 (0.01)
1941
35,417.40
64,563.80
1,176.76 (0.01)
1942
35,141.60
63,999.40
2,206.06 (0.01)
1943
34,030.70
62,203.10
2,375.88 (0.01)
1944
32,781.00
59,931.40
1,621.40 (0.01)
1945
32,118.30
58,134.60
1,508.26 (0.01)
1946
31,491.40
56,449.80
2,805.53 (0.01)
1947
29,725.60
53,832.70
2,222.58 (0.01)
1948
28,492.80
52,408.50
4,280.45 (0.01)
1949
25,580.20
49,148.90
3,069.20 (0.01)
1950
23,835.70
47,155.60
3,461.25 (0.01)
1951
21,938.50
44,975.10
2,323.44 (0.01)
1952
21,187.10
44,210.60
2,176.72 (0.01)
1953
20,623.40
43,709.60
1,928.17 (0.01)
1954
20,284.40
43,454.00
2,525.99 (0.01)
1955
19,443.80
42,415.40
2,294.32 (0.01)
1956
18,854.20
41,572.50
1,849.25 (0.01)
1957
18,675.90
41,223.30
2,639.74 (0.01)
1958
17,808.60
39,769.00
2,318.67 (0.01)
1959
17,221.60
38,473.90
1,880.98 (0.01)
1960
17,042.80
37,801.40
2,157.46 (0.01)
1961
16,785.30
37,820.80
2,548.42 (0.01)
1962
16,423.30
40,042.40
2,690.84 (0.01)
1963
16,206.00
44,245.50
2,710.56 (0.01)
1964
16,065.30
43,752.50
2,150.66 (0.01)
1965
16,412.80
42,485.40
2,109.23 (0.01)
1966
16,826.30
42,089.80
2,289.51 (0.01)
1967
17,471.20
41,235.10
2,181.42 (0.01)
1968
18,631.40
58,012.80
2,121.13 (0.01)
1969
19,892.30
60,219.30
2,249.00 (0.01)
1970
20,742.10
54,646.00
2,713.96 (0.01)
1971
20,690.20
48,047.70
2,887.68 (0.01)
1972
20,001.20
42,353.70
2,953.35 (0.01)
1973
18,873.40
38,400.80
2,950.56 (0.01)
1974
17,414.00
35,729.20
3,624.83 (0.01)
1975
15,219.80
31,913.40
3,489.85 (0.01)
1976
13,144.30
28,450.30
2,764.06 (0.01)
1977
11,806.70
27,071.90
2,267.94 (0.01)
1978
11,132.40
27,967.10
3,058.79 (0.01)
1979
9,911.76
29,152.20
3,054.97 (0.01)
1980
8,660.89
26,363.20
2,467.60 (0.01)
1981
7,904.04
22,720.20
2,041.19 (0.01)
1982
7,514.75
21,775.40
2,630.33 (0.01)
1983
6,618.73
20,820.01
2,214.19 (0.01)
1984
6,104.36
19,647.98
1,739.17 (0.01)
1985
6,109.04
19,488.95
1,839.45 (0.01)
1986
6,178.65
22,435.70
1,750.43 (0.01)
1987
6,425.57
25,076.70
2,204.84 (0.01)
1988
6,212.39
23,146.60
2,149.18 (0.01)
1989
5,912.57
19,371.13
2,152.70 (0.01)
1990
5,528.16
17,811.82
1,764.64 (0.01)
1991
5,504.11
19,014.66
1,927.37 (0.01)
1992
5,420.45
20,371.55
1,553.50 (0.01)
1993
5,723.00
22,002.60
1,503.21 (0.01)
1994
6,053.10
21,991.09
1,375.14 (0.01)
1995
6,533.96
20,626.10
1,659.05 (0.01)
1996
6,819.65
23,872.10
1,828.60 (0.01)
1997
6,986.83
23,968.20
1,947.72 (0.01)
1998
7,039.81
24,249.00
1,462.77 (0.01)
1999
7,537.44
24,017.40
1,497.11 (0.01)
2000
8,163.01
24,540.60
1,893.27 (0.01)
2001
8,608.66
30,679.00
1,845.22 (0.01)
2002
9,146.03
31,790.70
1,797.09 (0.01)
2003
9,589.10
30,447.70
2,069.58 (0.01)
2004
9,746.01
28,742.50
1,963.97 (0.01)
2005
9,849.40
27,620.60
2,734.36 (0.01)
2006
9,201.90
25,440.70
2,610.20 (0.01)
2007
8,753.74
25,159.70
2,252.84 (0.01)
2008
9,040.86
27,474.10
2,219.71 (0.01)
2009
10,012.90
38,274.30
1,767.44 (0.01)
2010
11,949.10
47,451.80
803.10 (0.01)
2011
15,040.00
58,140.00
934.51 (0.01)
2012
17,973.90
56,834.70
1,117.72 (0.01)
2013
20,346.80
53,868.40
2,253.36 (0.01)
2014
21,348.60
50,453.70
2,408.74 (0.01)
2015
21,799.40
52,737.30
2,665.17 (0.01)
2016
21,705.90
48,104.70
2,727.63 (0.01)
2017
21,340.20
47,052.80
2,930.62 (0.01)
2018
20,599.90
46,071.70
2,894.44 (0.01)
2019
19,738.60
42,577.80
2,616.91 (0.01)
2020
18,950.00
39,265.60
2,092.13 (0.01)
2021
18,500.90
37,664.70
2,879.11 (0.01)
2022
17,372.50
36,605.10
3,059.94 (0.01)