A guide to computer packages

9.2.8 A guide to computer packages

0 0 0.2 0.4 0.6 0.8 1 Table 9.1 tabulates available computer packages Time (year)

against features discussed in this chapter, such as the strength of assumptions about distributions

Fig. 9.7 Total mortality rate of Hong Kong white- and growth. Table 9.1 also shows that nearly all of spotted rabbitfish following cohort slicing of length–

the published methods may these days be pro- frequency samples aged using non-parametric methods

grammed into a spreadsheet such as Excel, with with an adjustment for overlap (see text). Plot shows

Visual Basic routines written to step across the estimated numbers of two cohorts (open circles = 0 + co-

hort; closed circles = 1 + cohort) over 13 samples. Points range of required L • and k values and to call the

at right-hand side of plot are used to estimate mortality built-in Excel optimization routines (‘Solver’). The rates (solid lines). An example spreadsheet may be down-

routine can record the GOF at each step for later loaded from www.fisheries.ubc.ca/projects/lbased.htm.

plotting and interpretation. The advantage of this Table 9.1 Guide to computer packages for length–frequency analysis.

Nmsep Mix Mfan ASSUMPTIONS

Method MPA

parametric/ NP

PPP non-parametric

TYPE graphical/

G C C C G G C C C computational

DISTRIBUTIONS weak/strong

SSS GROWTH

W W/S S SAMPLES

weak/strong W/S

SSM SPREADSHEET?

Single/multiple M

S/M

S/M

Hard Easy No PACKAGE CODE

Hard/Easy/No Easy

5 3 4 Notes : Key to methods: MPA = Modal Progression Analysis (MPA); Efan = ELEFAN; SLCA = Shepherd’s Length-

Composition Analysis; Proj = Projection Matrix; PPap = Probability Paper; Bhatt = Bhattacharya’s method; Nmsep = Normsep; MIX; Mfan = MULTIFAN. Key to packages: (1) Compleat Elefan (ICLARM); (2) LFDA 3.0 (RRAG); (3) MIX (Ichthus); (4) MULTIFAN (Otter); (5) FiSAT (FAO).

Chapter 9

approach is that the user retains complete control which dissected 12 age groups from Bluefin tuna over the algorithm and the interpretations of alter- (Thunnus thynnus) samples (Fournier et al. 1990). native maxima. One disadvantage is that some The software contains some neat graphical short packages contain undocumented improvements cuts together with powerful optimization rou- and corrections to published methods that spread- tines. MULTIFAN runs in a DOS Window in Win- sheet programmers may find it hard to obtain dows 95 of NT. A powerful modern version is information about. Moreover, many existing under development, but its website implies that it packages were generally written for DOS and most will cost over US$10 000. As to costs: LFDA is free- have not been updated to Windows versions.

ware, FiSAT costs US$40, MIX costs around

A DOS computer package called LFDA (Length US$140, while MULTIFAN is very expensive at Frequency Data Analysis) is available from the about US$1500. Renewable Resources Assessment Group at Imperial College, London, UK (www.ic.ac.uk). It

includes SLCA, the Projection Matrix and the 9.3 WHEN LENGTH IS KING

ELEFAN algorithm, along with various options for estimating mortality, and has some elegant con- Some analyses may only be performed using tour plots of the GOF surfaces. Although LFDA, length-based techniques. This section outlines dating from an earlier epoch of computers, only three of these methods: the first the estimation of runs a maximum of 10 by 10 values of L • and k, yield-per-recruit in multispecies fishery using a analyses can be repeated over a series of values to single gear such as trawl (see also Shepherd and create very detailed GOF surfaces, and was used to Pope, Chapter 8, this volume); the second, a way of generate Plate 1. As far as I am aware, LFDA has not estimating the offshore migration rate, a common been recoded for Windows, but it runs effectively problem in many inshore tropical fisheries; and in a DOS window in Windows 98.

the third, using a length-based analysis to estimate Using maximum-likelihood and automatic trophic level. direct computer search, the MIX pro- gramme (Ichthus Software, Hamilton, Ontario,

9.3.1 Ringing the changes on

Canada; Macdonald and Green 1988; http://

Thomson and Bell: multispecies

icarus.math.mcmaster.ca/peter/mix/mix31.html ) finds a mixture of overlapping components which

yield-per-recruit

maximizes goodness-of-fit with the length– Fishing gear such as the mesh in a trawl selects fish frequency data. The distributions can be normal, by size, not age. Converting size to age for one log normal, exponential or gamma. A Windows species in the standard way means that yield- version is available.

per-recruit (YPR) calculations comparing long-

FAO distributes DOS software called FiSAT term average yield under a range of mesh sizes and (FAO-ICLARM Stock Assessment Tools; fishing rates can be made for this fishing gear. But if http://www.fao.org/fi/statist/fisoft/iclarm.asp ) more than one species is caught in the trawl, the which implement an updated and improved same size of fish can represent different ages in dif- ELEFAN method, including the seasonal ferent species. This means that the yield for each growth model option and a plot of the GOF species must be calculated for each length class. surface. FiSAT also includes SLCA and the Once this is done, the yields can be added to pro- Bhattacharaya method. A Windows version is in vide multispecies yield-per-recruit estimate for development.

the trawl gear.

The most sophisticated computer package The basic length-based yield equation was available is MULTIFAN (Otter Software, Victoria, devised by Thomson and Bell, and is thoroughly BC, Canada. http://otter-rsch.com/index.html), described in Sparre and Venema (1992). A version initially published with an impressive example of this multispecies yield-per-recruit analysis is

Size-based Methods in Fisheries Assessment

Present obtained from time series, or, as in this case, by

running a Beverton and Holt biomass-per-recruit (BPR) analysis for each species at the current esti- mated F and age of entry zero. Relative recruit- ment indices were then obtained by using the estimated biomass of the species, since B/R = BPR

VPR and so R = B/BPR. Uncertainty (not shown here) Multi-

3.75 was addressed using Monte Carlo simulations

3 based on random sampling of 74 parameter distri-

2.25 butions. In this analysis yield-per-recruit has been

3 4 5 0.75 converted to value-per-recruit by multiplying each

6 7 8 0 species and size class by its market price. Mesh size (cm)

9 10 The location of the present Hong Kong trawl fishery is indicated on the value-per-recruit sur-

face of Fig. 9.8 by an arrow. The analysis suggests

Present

that, provided relative recruitment is not altered, the value of the existing fishery could be almost doubled by doubling the mesh size in the trawl (Pitcher et al. 1998).

VPR Multi-

9.3.2 Estimating the offshore

0 3 migration rate using length and age

6 Often, fish migrate offshore into deeper water as

2.25 7 they get older and larger, partly as the appropriate

F 3 9 Mesh size (cm)

refuge from predators changes and partly as a

3.75 10 search for larger food. By moving offshore, these may remove themselves from the sampling area,

and this offshore migration rate may mask the true is plotted against mesh size in cm, and fishing mortality

Fig. 9.8 Multi-species value-per-recruit (VPR) surface (front and back views) for the 17 Hong Kong species. VPR

total mortality rate and decrease the apparent rate, F (vertical axis is value). Approximate present

growth rate. If a sample of fish has been aged using position of fishery indicated by arrow. (Source: from

otoliths or other hard parts, the differences be- Pitcher et al. 1998.)

tween cohorts constructed from the biased growth parameters obtained from this method and those from the samples can be used to estimate the off-

available in the FiSAT package, but the equa- shore migration rate with age (Pitcher et al. 1998). tions can fairly easily be programmed into a The method assumes that the probability of fish spreadsheet.

migrating offshore out of the sampling zone

An example of the results from a spreadsheet increases linearly with size from a start length length-based multispecies analysis applied to (P = 0.0) to an end length (P = 1.0) at which all fish Hong Kong trawl fisheries is shown in Fig. 9.8. The have left. work covered 17 species (14 fish and 3 inverte-

First, the von Bertalanffy growth parameter, k, brates) caught in the Hong Kong trawl sector. The and L • is estimated from length–frequency analy- overall multispecies YPR was obtained by sum- sis and an auximetric plot that compares with pub- ming the contributions of each of the species, lished values. (For the lizardfish (Saurida tumbil) weighted by their relative recruitment, as advised in Fig. 9.9, L • = 69 cm and k = 0.228.) Keeping the by Murawski (1984). Relative recruitment can be same L • , a curve fitted to otolith-derived ages gave

Chapter 9

1.0 Table 9.2 Estimated instantaneous rates of offshore migration for three species of Hong Kong fishes.

0.8 Age (year)

L infinity

Relative frequency

Probability of migrating

0.2 start and end length, or an automatic search for a minimum performed.

Examples of the goodness-of-fit surface for

6 10 14 18 22 26 30 34 38 three Hong Kong fishes are shown in Plate 2 and Length (cm)

the calculated instantaneous migration rates with age are shown in Table 9.2. The results show

Fig. 9.9 Diagram showing the estimation of offshore that the small leiognathid ponyfish, which only migration rate with age for Saurida tumbil (lizardfish)

reaches about 14 cm maximum length, moves in Hong Kong. The analysis is performed on the first two

offshore at about the same rate once adult at 1+. age groups. Start and end lengths for migration proba-

The croaker moves rapidly out of the inshore area bility (thick inclined line) are adjusted until means and

standard deviations of two cohorts (solid bell-shaped soon after it is a year old, while most lizard fish re-

curves) fit observed truncated distributions (broken main inshore until their second year.

curves). True mean lengths are 17.5 and 36 cm, while the mean lengths of fish remaining are 14.1 and 19.1 cm.