New Zealand Freshwater Fish Database User Guide

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Tarawera River

NIWA Client Report: HAM2005-033September 2005Updated July 2008

NIWA Project: BBEF062

New Zealand Freshwater Fish Database User Guide

Jody Richardson

NIWA Client Report: HAM2005-033September 2005Updated July 2008

NIWA Project: BBEF062

National Institute of Water & Atmospheric Research LtdGate 10, Silverdale Road, HamiltonP O Box 11115, Hamilton, New ZealandPhone +64-7-856 7026, Fax +64-7-856 0151www.niwa.co.nz

All rights reserved. This publication may not be reproduced or copied in any form without the permission of the client. Such permission is to be given only in accordance with the terms of the client's contract with NIWA. This copyright extends to all forms of copying and any storage of material in any kind of information retrieval system.

Contents

1. Introduction 12. The web site 12.1 Opening page 12.2 Search the NZFFD and create a file to download 2

2.2.1 Pattern matching 42.2.2 Card number 52.2.3 Catchment name 52.2.4 Catchment number 62.2.5 Sampling locality 102.2.6 NZMS260 Map Number 102.2.7 Fishing method 112.2.8 Fish species 112.2.9 Limit options 122.2.10 REC segment number 12

2.3 View the contents of a single card 123. The database assistant program 123.1 Opening, merging, and saving files 133.2 Moving data to Excel 133.3 Analysis 143.4 Maps 15

3.4.1 View menu 153.4.2 Format menu 183.4.3 Insert menu 203.4.4 File menu 213.4.5 The database and REC icons 21

3.5 Entering data 224. Obtaining additional data 255. Appendix I – Organization codes 266. Appendix II – How to assign catchment numbers 297. Appendix III – How to save viewed cards into a word document 31

Reviewed by: Approved for release by:

Andrew Davey Ian Jowett

Formatting checked

1. Introduction

The New Zealand Freshwater Fish Database (NZFFD) records the occurrence of fish in fresh waters of New Zealand, including major offshore islands, and was established in 1977. Data collected include the site location, the species present and their abundance, as well as information such as the fishing method used and a qualitative assessment of the site’s physical features. Data, which are recorded in the field on pre-printed forms, are contributed voluntarily by NIWA, fish and game councils, the Department of Conservation, regional councils, environmental consultants, universities, and interested individuals. The NZFFD is maintained on computer at NIWA Wellington, with libraries of the field forms held at Hamilton and Christchurch. On-line access to the NZFFD is available on request, (http://www.niwascience.co.nz/services/free/nzffd/register) although users must first accept the conditions listed an end user licence agreement (EULA) regarding use, etc. of the data.

The purpose of this guide is to assist users of the NZFFD to perform effective searches from the web site, to get the most out of the assistant program, and to painlessly enter their own data. It assumes users have already agreed to the EULA and have obtained a login and password to the web site from the database administrator. Users within NIWA can login from http://neptune.niwa.co.nz/fwdb/ without a password.

2. The web site

2.1 Opening page

There are a number of self-explanatory link buttons at the bottom of the opening page of the web site after you have logged on (Figure 1). Options under the search and view buttons are discussed in detail below. The assistant program was written specifically for use with the NZFFD and users should download it onto their own computers. Note that the assistant is zipped and you must extract the files before use. If you cannot write *.exe files to your computer because of your company’s IT policy, then you will need to ask for assistance and permission from them to unzip the assistant correctly. The assistant contains an on-line help facility, but some of the general features are discussed in Section 3. The atlas and quick guides provide information about and for identifying New Zealand’s freshwater fish species, respectively.

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Figure 1: Opening page of the NZFFD web site showing user options and links to useful information.

2.2 Search the NZFFD and create a file to download

This option is designed to let you filter the NZFFD to retrieve only the data you want at that time (Figure 2). Note that we have had reports of searches not being performed correctly from users employing the Firefox web browser, and we therefore suggest you use Explorer.

The filter field options are based on the most frequent requests prior to the web site being established. The search filter field options are discussed in detail in Sections 2.2.2 to 2.2.9. These are preceded by an explanation of pattern matching that can be used with some filter fields. Each section includes information on what that field represents and how to use it for searching; where examples are given the information that should be entered is shown in quotes, but the quote symbols should not actually be entered on the computer. Successful searches will use various combinations of fields to limit and speed the search, and it helps to think about which combination will give the best and fastest results; searching with numbers is much faster than using names. Pattern matching (see Section 2.2.1) can be used to obtain data from large areas when using the catchment number or map filter options.

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You might want to download the entire database (simply click get records with all the filter options blank) and store a copy in a suitable format for searching with the assistant or packages such as Microsoft Access. However, don’t forget that the NZFFD is updated weekly to include any new records and corrections to existing records, and that you will need to perform this download on a regular basis if your own copy is to remain in date.

Figure 2: Search page of the NZFFD web site showing the filter options available to users.

Note that any search is not complete until “done” appears in the lower left hand corner of your screen even though the header and some data appear almost immediately. The header tells you how many records were found out of how many were available and the date of the search. If you try and save the data before “done” appears, you may not get a complete retrieval. The search results should be saved as a text file (by clicking File/Save as and selecting Text File from the Save as type menu) for loading into other applications on your own computer. It’s a really good idea to give the file a meaningful name and to note where that file is being saved (you can alter this in the Save in menu at the top of Save Web Page box.

Regardless of your search criteria, the output comes in a standard format, with one line of data for each species occurrence. This is dictated by the NZFFD structure, but can be altered within the assistant (see Section 3.2). Note you must scroll across the page

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to see the whole line of data, including the fish information. The data items that are listed reflect those most clients requested prior to the web site being established (Table 1). Other data for records can be obtained by viewing individual cards (see Section 2.3) and transcribing the information or by following the instructions in Section 4.

Table 1: NZFFD data items and their column headings retrieved by any web site search.

NZFFD data item HeadingCard (or record) number (see Section 2.2.2) cardMonth sampling occurred mYear sampling occurred yCatchment name (see Section 2.2.3) catchnameCatchment number (see Section 2.2.4) catchName of waterway or waterbody where sampling occurred (see Section 2.2.5) localityTime sampling occurred (24 h clock) timeOrganization who collected the data (see Appendix I) orgNZMS260 map number (see Section 2.2.6) mapEast grid reference eastNorth grid reference northAltitude of site (m) altitudeDistance inland of site (along the watercourse) (km) penetFishing method used (three letter code – see Section 2.2.7) fishmethThe area fished or the number of nets set effortIf electric fishing, number of passes performed passFish species caught (six letter code – see Section 2.2.8) spcodeSubjective species abundance(a = abundant, c = common, o = occasional, r = rare)

abund

Number of fish caught numberMinimum length (mm) minlMaximum length (mm) maxlREC segment number (see Section 2.2.10) nzreach

2.2.1 Pattern matching

You can use pattern matching for all of the fields except card number in Sections 1 and 2 on the search page. There are three types of pattern matching, the wildcard or asterisk (*) that will match zero or more occurrences of any character, square brackets [ ] that enclose options that match a single character, and the | (shift backslash) separator. For example, if I wanted data from all catchments that start with “W”, I should enter “W*” in the catchment name box. If I wanted data from the Wairau or Wairoa River catchments, I would enter “Wair[ao][ua] *” in the catchment name box. Note the space before the asterisk in this instance; if there is no space, then this search also retrieves names like Wairaurahiri. If the pattern between the brackets is a string such as “a” through “d”, then you need to put a dash between the characters [a-d]. The separator (| ) (shift backslash) can be used to list items that do not suit the other

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types of pattern matching. For example, if I wanted data from maps n34, c43 and t15, I could search all these at once by entering “n34|c43|t15” in the map number box. Further examples of pattern matching are shown in the sections below.

2.2.2 Card number

Each record in the NZFFD has a unique card number. To retrieve the data for a single card, simply type a legitimate card number in the card number box and click get records. You can use this field to search for individual cards — perhaps to check if one of your records has been added during the latest NZFFD update. Note that pattern matching will not work in this field and it is only possible to search for one card at a time.

2.2.3 Catchment name

The catchment name is the name of the river or stream that flows into the sea for that particular location, with the words river, stream, etc. abbreviated as shown in Table 2. For example, the catchment name for the Manawatu River is Manawatu R, the Pomahaka River is Clutha R, for Cosseys Creek, Wairoa R, and for Ohariu Stream, Makara S. You can use the catchment name field to search for all the records in an entire catchment, although this search will be slower than a similar search using the catchment number (see Section 2.2.4). If you wanted all the records from the Waimakariri River catchment for example, you could type “Waimakariri R” in the catchment name box and click get records. Note that this search field is not case sensitive and typing “waimakariri r” will also retrieve the same records.

If you are not sure what to put after the river name, you can use an asterisk (*) to match any combination of text after the name. In the previous case, typing “Waimakariri*” in the catchment name box would return the same search results as “Waimakariri R”. If you omit the “R” or “*”, then the search will return 0 records because there are no catchment names listed simply as Waimakariri. Beware of non-unique catchment names; there are four rivers that flow to the sea called the Wairoa River, and entering “Wairoa R” or “Wairoa*” in the catchment name box will retrieve data from all four of these catchments at once. That is why the catchment number is a more precise search field.

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Table 2: Abbreviations used in the catchment name field and their translation.

Catchname abbreviation Translation

B Bay

Bn Burn

C Creek

Cp Cape

Cv Cove

Gly Gully

Hbr Harbour

I Island

In Inlet

L Lake

Lgn Lagoon

P Point

Pen Peninsula

Psg Passage

Pt Port

R River

S Stream

Snd Sound

Swp Swamp

2.2.4 Catchment number

What are catchment numbers?

The catchment numbering system used in the NZFFD is a revised version of an original waterway numbering system developed by the Soil Conservation and River Control Council (SCRCC) in 1954. This system numbered the main river and stream catchments to define their locations and to distinguish between streams with the same names. However, the way numbers were first assigned in 1954 was inconsistent because each region did the task separately and the SCRCC simply put all the information together into a single document without alteration. I have expanded the system to include more tributaries and sub-tributaries while still keeping the first three digits assigned to the same waterways as they were in 1954. This has been done within the digit constraints discussed below. The revised numbering system is still by no means complete and contains inconsistencies, but is a vast improvement on the original system.

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The revised NZFFD system is based on six-digit decimal numbers. The first three digits denote a river or stream discharging into the sea (the name of which is shown in the catchment name field). Catchments whose first three digits are between 001 and 499 occur in the North Island, starting at Spirits Bay and proceeding clockwise around the island. Those between 500 and 999 are in the South Island, beginning in Golden Bay and again proceeding clockwise. Leading and trailing zeros are important and should not be omitted from the six-digit number.

The next two digits refer to tributaries of the main stem, numbered from the mouth and proceeding upstream in the order the tributaries join the main stem. The last digit refers to a sub-tributary, again numbered in the upstream order they join the tributary. For example, for catchment number 570.133, 570 denotes the Motueka River (which discharges into the sea), 13 a tributary of the Motueka (the Wangapeka), and 3, the Dart which discharges into the Wangapeka. This number also tells us the Wangapeka joins the Motueka downstream of the Tadmor River (570.150) (because 130 comes before 150) and that the Dart joins the Wangapeka before Gibbs Creek (570.137).

Because this system has a limited amount of numbers, it has been necessary to group some catchments under a single number. For example, streams draining to the coast between the Moutere River and Waimea Inlet are all assigned to catchment 572. In the Waimea catchment, it has been necessary to group all the Roding River catchment under a single number, 575.021, without being able to assign separate numbers to the Lee or Serpentine River, for example. When this situation occurs, the number assigned is that of the first numbered waterway that this stream would flow into; the Lee flows into the Roding and so is assigned the number for the Roding River.

How to use catchment numbers for searching

Catchment numbers are a fast and flexible way of searching the NZFFD. There are catchment number look-up tables on the web site search page, in the database assistant, or you can download the current version of the revised catchment number dictionary from the web site. Detailed instructions for assigning catchment numbers are shown in Appendix II.

When used in combination with catchment or locality names or other fields, it is possible to hone your search to small areas of interest. Or you can use the wildcard pattern (an asterisk) to retrieve data from entire catchments. You can also use bracket pattern matching in the catchment number box to search large areas of New Zealand or the separator to search several discrete catchments at once.

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Examples:

How do I retrieve all the records from the entire Manawatu River catchment? Enter “325*” in the catchment number box. This retrieves all records with catchment numbers beginning with 325, i.e., 325.000 to 325.999. You can perform the same search (more slowly) by entering “Manawatu R” or “Manawatu*” in the catchment name box.

How do I retrieve records from the Wangapeka River catchment? Enter “570.13*” in the catchment number box. This retrieves all records with catchment numbers beginning with 570.13, i.e., 570.130 to 570.139.

How do I retrieve all records from catchments between and including Kapitea and Canoe Creek on the west coast of the South Island? Enter “91[0-9]*” in the catchment number box. This finds all the records from catchments 910.000 to 919.999 inclusive.

How would I retrieve all records from the Waitaki to Clutha catchments inclusive? The catchment number for the Waitaki is 711 and for the Clutha is 752. We want these and all catchments in between. There are two ways to perform this search:

1. Enter “7*” in the catchment number box to retrieve all records from catchments 700.000 to 799.999, load the resulting *.txt file into Excel (either directly or via the assistant (see Section 3.2)), sort by catchment number and delete all the records outside the desired range (711.000 to 752.999). You could then save the results as a *.csv file to reload back into the assistant.

2. Enter “71[1-9]*” in the catchment number box (to get all the records from catchments 711.000 to 719.999) and save the results in a *.txt file. Then enter “7[2-4]*” to get all the records from catchments 720.000 to 749.999 and save the results in another *.txt file. Finally, enter 75[0-2]* to pick up the data from catchments 750.000 to 752.999 and save the results in a third file. Merge these files together within the assistant (see Section 3.1) to obtain a single *.fdb file with all the data. The reason we have to do this in three steps is that the brackets only enclose a wildcard for a single character.

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How do I retrieve records from just the Waimakariri and Clutha River catchments. Enter “664*|752*” in the catchment number box.

How do I retrieve records from just the main stem sites of the Manawatu River? Enter “325.000” in the catchment number box and “Manawatu River” in the sampling locality box. This limits the search to sites matching both the number and name criteria.

How do I retrieve records from main stem sites of the Manawatu River below Manawatu Gorge? Enter “325.000” in the catchment number box, “Manawatu River” in the sampling locality box and “0” to “99” in the inland distance boxes. This limits the search to main stem sites less than 99 km inland (about the distance inland at the base of the gorge).

How do I retrieve records from Davy Creek? Enter “570.133” in the catchment number box and “Davy Creek” in the sampling locality box. Records retrieved match both criteria.

How do I retrieve records from the entire Davy Creek catchment? Enter “570.133” in the catchment number box and “Davy Creek*” in the sampling locality box. Because there are no named tributaries of Davy Creek, these will be named Davy Creek tributary in the NZFFD (see Section 2.2.5 for how to name sampling localities). The wildcard (asterisk) after Davy Creek means that any string of characters beginning with Davy Creek is retrieved, including sites named Davy Creek tributary. When other named tributaries are present, you must also search for these records by performing more searches using the same catchment number with the locality names. The retrieved files of data can be merged into single file later (see Section 3.1 for how to merge files).

How do I retrieve data from the Kaikokopu Stream catchment? Enter “326.000” in the catchment number box and “Kaikokopu S” in the catchment name box. Because there are several main stems assigned to number 326.000, it is necessary to specify which catchment you want. All sites in the catchment we want will have Kaikokopu S assigned as the catchment name (see Section 2.2.3 for how catchment names are assigned).

How do I retrieve data from Lake Kaikokopu. Enter “326.000” in the catchment number box and “Lake Kaikokopu” in the sampling locality box. Entering “Kaikokopu S” in the catchment name box is redundant unless there is another lake in the vicinity named Lake Kaikokopu.

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2.2.5 Sampling locality

The sampling locality is the name, as it appears on the NZMS260 map series, of the waterway or waterbody where sampling took place. It is written out in full and as it appears on the map, and does not include comments that can be deciphered from the map reference such as “downstream of bridge” or “beside school camp”. If the site has no name on the map, then it is called a tributary of the nearest named water e.g., Wairoa River tributary or Lake Kaikokopu tributary, etc. Most unnamed or man-made ponds are called “Unnamed pond”, and similarly for small unnamed wetlands and swamps — “Unnamed wetland”.

The examples shown in Section 2.2.4 demonstrated how to use the sampling locality in combination with the catchment number to perform precise searches. You could also use this field in combination with the NZMS260 map number to search for unnamed streams that flow directly to the sea. For example, if I wanted to find whether a stream that flows into Anchorage Bay in Akaroa Harbour had been sampled, I could enter “Unnamed stream*” in the sampling locality box and “n37” as the map number to see what unnamed streams on this map had been sampled. Note the use of an asterisk after the word “stream”; this is important as usually the nearest locality is given for unnamed streams, e.g., Unnamed stream Anchorage Bay.

2.2.6 NZMS260 Map Number

This is the number of the NZMS260 series map where the sampling site is located. The letter is in lower case and there are 2 digits, e.g., m02, l26, s15, etc. There is a drop down map of New Zealand on the search page that shows where each map is located. You can use the wildcard (*) and pattern matching in this field to search large areas of the country, or enter a single map to select just that data, e.g., “m02”.

Examples

How do I retrieve all the data from Banks Peninsula? Looking at the drop down map shows Banks Peninsula occurs on maps m36, n36, m37 and n37. To search all of these maps at once, type “[m-n]3[6-7]” in the map number box. Note that you will need to do some post-retrieval editing because a few of these records will be on the Canterbury Plains as these maps also include areas off the peninsula.

How do I retrieve all sites from Northland sampled between 1980 and the present? Northland occurs on maps m02 to r08 roughly. To search this whole area, enter “[m-r]0[2-8]” in the map number box and “1980” in the from box under the year option. This search will retrieve all the data on maps m02 to r02 through m08 to r08 dated from 1980 to the present.

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How would I retrieve all records in the Haast Pass vicinity that drain into the Clutha River? Haast Pass occurs on g38, so enter that in the map number box. To limit this search to the Clutha catchment, also enter “752*” in the catchment number box.

2.2.7 Fishing method

You can also filter your search by the fishing method used, either on its own or in combination with other filter fields. There is a drop down menu of the method codes, and you can use pattern matching in this field, e.g., to search for all electric fishing records (backpack, mains set, boat, and unknown type) select “other” in the top box and enter “ef*” in the lower box. This pattern also works for all types of nets or traps by entering “*n” or “*t” in the lower box, respectively. To search for all records where back pack electric fishing or Gee minnow traps were used, select “other” in the top box and enter “efp|gmt” in the lower box.

2.2.8 Fish species

Fish species data on the NZFFD are coded with a six-letter code to save space and data entry time. The code includes the first three letters of the genus and first three letters of the species name, e.g., angdie for Anguilla dieffenbachii. As new species of fish are still being recognized and described, if the code for a new species has already been used, then the next letter in the species name is used. For example, the code for Galaxias macronasus is galmar because galmac has already been assigned to G. maculatus. There is a drop down menu of species codes listed in common name order on the search page. The pattern matching options do not work in this field, but you can use this field to filter the data for single species or combinations of species and in combination with other filter fields.

Examples

I want all the records for banded kokopu in New Zealand. Set the species code to “Banded kokopu (galfas)” by scrolling down the menu and clicking that species.

I want to find sites in New Zealand where koaro and brown trout co-exist. Select “Other” as the species code, type “galbre saltu” in the lower box and tick “and”.

Are there any records of giant kokopu or giant bully in the Tarawera River catchment? Set the catchment number to “153*”, the species code to “Other”, type “galarg gobgob” in the lower box and tick “or”.

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2.2.9 Limit options

You can use these filter options to limit your search to certain years, altitudes or distances inland, as per some of the examples shown above. If using an upper limit, add 1 to the number you enter in this box. For example, if you want all records from 1980 to 2000, then you should enter “1980” in the from box for year and “2001” in the to box for year, or all records between 20 and 50 km inland, enter “20” in the from box for inland distance and “51” in the to box for inland distance.

2.2.10 REC segment number

This data field appears at the end of each line of the search output and relates to the Rivers Ecosystem Classification (REC) database which is also managed by NIWA. Every waterway in New Zealand has been mapped and segmented, and a unique number assigned to each segment of waterway. The nzreach number shown on the NZFFD search output corresponds to the REC segment number where the sampling site was located. Having access to this number and the REC database allows users access to information on catchment geology, vegetation type, catchment size, rainfall, etc. for the segment in question. If this number is a 0 it means there is no REC segment number for that site, and if nzreach = 9, then there are errors in the REC database at that point and no number can be correctly assigned. At present, you cannot search the NZFFD using this data field.

2.3 View the contents of a single card

This option allows you to view all the data (except comments) for a single card. You might use this option to check who collected the data or what the substrate was, for example. The next and previous icons on the results page allow you to scroll through sequentially numbered cards. If you want to append copies of cards to your publications, this is where you should obtain them, as they will now (having been added to the computerized version of the NZFFD) conform to all database protocols and have official NZFFD card numbers. Instructions for saving viewed cards into Word documents are given in Appendix III.

3. The database assistant program

The database assistant program was written by Ian Jowett and is designed specifically for use with the NZFFD, mainly to transcribe the web site output into a more useable format, to further filter and analyse the data, to produce distribution maps for reports

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and presentations, and for entering your own data. The assistant has a comprehensive on-line help facility that is activated by pressing F1 or Help. However, instructions on how to use the main features are described in the following sections. Currently, we are using version 6.1 of the assistant.

3.1 Opening, merging, and saving files

You can open *.txt (files saved from a web site search), *.csv (specifically formatted comma delimited files) or *.fdb files (files saved within the assistant program) with the database assistant. Simply click Open and select the file from the appropriate directory. Usually, it’s a good idea to save *.txt or *.csv files as an *.fdb file for later use within the assistant program. To do this, click Save and assign your file an appropriate name.

If you have several files from web site searches that you want to merge into one file (often searching a big area or many catchments will require performing more than one search, even using pattern matching), then Open the first *.txt file and Save it with an appropriate name, Open the next file and Save it with the same name, clicking the Append option when prompted. Keep repeating this until all the files are merged into one. You need to do this BEFORE copying the data to Excel or else the species on subsequent files will be out of order compared to the first file. For valid *.csv formats, see the assistant help file.

If you want to view the data in the assistant, use the Form (Figure 3) or Edit buttons. Forms can be printed or copied for transfer to other software such as Word. However, if you want to append forms that have official NZFFD numbers and data for all the fields to publications, you should retrieve them from the web site (see Section 2.3).

3.2 Moving data to Excel

You can load your *.txt files of saved search results from the web site directly into Excel by opening the files as fixed width and checking that all the column lines are in the right places by scrolling across the page and deleting or adding lines as necessary. If you do this, you will still have one line of data for each species occurrence.

If you want the data formatted so each species appears as a column of data (generally a much more useful format), then you should use the assistant to transfer the data; after you Open the file in the assistant, click File, Copy to clipboard, and then paste this into a new Excel file. Now you will have one line of data for each record, with the species data as columns of information. If both the number caught and abundance

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estimate are recorded for a species, then the number is shown. If there is no number but an abundance estimate, then that is shown. If the species is listed as being present without any quantitative data, then “present” appears in the column for that record. Note that some attributes (month, organization, time, pass, min length, and max length) are lost when you perform this transfer. From Excel, you can save the file in an appropriate format for GIS software such as ArcView.

Figure 3: A form viewed with the assistant. This form contains complete information because the data were entered using New and it has been assigned an official NZFFD card number; it is ready to be added to the NZFFD.

3.3 Analysis

Selecting the Analysis menu in the assistant allows you to further filter the data and to get a species list and frequency report for that file. You can filter by one or two fields, and use two wildcards, the asterisk (which operates as on the web site) and a question mark (which acts as a wildcard for a single character). For example, if I had searched

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the NZFFD for all Clutha catchment records, but now wanted to see how many of those records contained any species of Galaxiid, after opening my *.txt file in the assistant, I would use the Analysis and Filter data options with species set to “gal*” to see how many records there were (using the Edit, Form, or Map buttons to view the results).

A list of species and their frequency can be obtained by selecting that option from the Analysis menu. This can be copied to the clipboard for pasting in Excel or Word. To convert this information to a table after pasting in Word, select the text, and under Table, click convert text to table, choosing a tab to separate the text.

3.4 Maps

The map button in the assistant allows you to view your output spatially and to produce distribution maps for publication (See example on document cover). Version 6.1 of the assistant includes several new mapping procedures, mainly separating the changes you might make to information that comes from NZFFD searches (data markers) and information that you might add to the map yourself, such as lines and arrows. Before clicking the map button, you can turn on the river network by clicking View/Expanded stream network. Now when you click the Map button you should see your sites (if you have a file open and have selected to view New Zealand or the appropriate island) as well as a vast network of rivers and streams.

To zoom into an area of interest, click the Zoom icon ( ) and use the cursor to select the area you want, or use the up and down arrow icons ( ) to increase or decrease the viewing area by 2. You can only zoom in the rectangular shape of the window. However, you can also move the edges of the window before Saving or Copying to the clipboard to further refine the map size. To get back to previous views, click the Previous scale icon ( ). You can also move around the map with the hand (pan) icon ( ).

When viewing maps, clicking the right mouse button causes a menu to appear that relates only to the current view, even when you are zoomed in. This menu allows you to see details about those particular sites and to copy and save that picture. Various format options (see Section 3.4.2) are also available on this menu.

3.4.1 View menu

Under the View menu you can choose how you want the map to appear, add labels, and go to specific places.

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Map

Under the Map menu (also shown as on the toolbox), you can select what options to show on the map, such as a scale or roads, by clicking the appropriate box (Figure 4). When these boxes are clicked, you can also alter their appearance under the Format menu (Section 3.4.2). The colour of the land and water and the line weight used for the coastline can also be changed in this menu.

Figure 4: The Map option menu allows you to decide what features to show on the map.

Topomap

If you select the Topomap option, then a large-scale topographical map is shown. This map is designed for large-scale views only and loses quality when you zoom in.

Place names

A list of place names associated with the NZMS260 map series and other databases is available under this option, and you can use it to display and label certain features on your map such as lakes or rain gauges (Figure 5). You can also choose to mark these

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places with any sort of marker or not. If you have the Retain on map (editable) box clicked, then you can select, delete, edit, change or move individual place names. To change the appearance of any text, select it, and then use the text font icon on the toolbox for your alterations. Use the text edit icon ( ) to change the wording of selected text. To change the appearance of all the text, click Edit/select all (or ^A) and then . To get rid of all the labels, type ^A, then delete. If you don’t have the Retain on map box clicked, then you need to go back in the menu and untick the boxes to remove labels.

Figure 5: The place names menu allows you to show the names of selected features on your map, in this case the names of streams, dams, and towns have been selected, and their location will be marked with a black cross. The Retain on map (editable) option must be clicked if you want to alter the names once they are displayed.

Find place and Go to coordinate

The Find Place menu allows you find specified places listed in the place names dictionary. You can sort this list by any category simply by clicking the header. Once you have found your place, double clicking the name will take you directly there. You could also type in the name, click next, and then to go there. Your specified place

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will be denoted by a red dot in the centre of the map view (if your dot looks like its in the middle of the sea, then you need to alter the view to show that island. Likewise, the Go to coordinate option requires typing in a map coordinate and clicking okay. The map view will show that point as a red dot in the centre of the map view.

3.4.2 Format menu

Under the Format menu (Figure 6) you can choose how features you have elected to show on the map appear.

Figure 6: A map of banded kokopu distributions showing options available in the format menu. On this display, only 6 and 7th order rivers have been selected from the expanded stream network using the Rivers option under the format menu.

Rivers

Within the River menu, you can choose what colour, line weight, and complexity of river network to show on the map. All rivers and streams have been assigned an order between 1 (smallest) to 7 (largest) and with the Show rivers of order button you can change the river network complexity by selecting an appropriate river order. For large

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areas, it is generally best to choose a large river order otherwise the map becomes too cluttered. However, this will depend on how much detail you need on your distribution maps. If the expanded stream network has not been selected, only 5 to 7 order rivers will be displayed.

Data markers

Data markers are the markers used to denote locations of sites in files you have open, whether they are *.txt files saved from a web site search, a previously saved *.fdb file, or new data you have entered during that session. The Data marker menu (shown as

on the toolbox) allows you to select the shape, colour, and size of markers. It also allows you to display the markers for single species or combinations of species under the Show location of option, and various labels with the Location labels option.

Multiple species

To show more than one species on a single map (as on the cover of this document), you need to have the Retain on map (editable) box clicked on the Data marker menu page when you produce the first map after scrolling down the species list (only species that are present in the open file are shown) (Figure 7). To show the next species, select a different shape or colour of marker before clicking Ok.

Note that data markers are plotted with the most recently selected species on top, i.e., if you have plotted two species that occur at the same site, the marker for the second species will be plotted on top of the marker for the first species. However, you can zoom in and move markers with the cursor to show multiple species markers at a single site if you have the Retain on map box clicked for the second species. This would be a tedious process for large map areas and for cosmopolitan species, so be wary of what species you plot together. If you have decided to show any labels on your map and have the Retain on map box ticked when you produce the map, you can then click on these labels to move, edit, or delete them.

Legends

To add a legend your map, click Insert/Marker and click on your map where you want the legend to be placed. Change the appearance of that marker by selecting it with the cursor and clicking Edit Text/marker icon on the toolbox ( ). Add appropriate text next to the marker with the Add text icon ( ) and repeat as necessary to show all the species you have plotted together. You can align your markers and text by selecting the appropriate ones with ^click or shift click and then right clicking your mouse. Choose Align and select the right options to line them up. Note, you can also add text

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to your marker when you change its appearance with the icon, but the symbol and marker will not be linked so you will still need to align them.

Figure 7: Options available under the Data marker menu in the assistant. The display shows how to plot just shortfin eel records with a solid red circle from a file for the Clutha River catchment; the Retain on map option is clicked so another species can be displayed on the same map after performing this operation.

3.4.3 Insert menu

From this menu you can insert text, a line or arrow, and markers. Inserting markers was described above, but you can also insert text and lines/arrows under this menu (or with and icons, respectively, on the toolbox). To change the appearance of text, after you have entered it, select it with the cursor, and use the icon on the toolbox to change the style, size, and colour of the text. To edit the text, you need to select it and then use the Edit Text/marker icon on the toolbox ( ). You can also delete text after it has been selected. To change the appearance of lines/arrows, select the line/arrow you have drawn and use the draw a line or arrow icon ( ) on the toolbox) to alter.

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Although the assistant program was developed for use with the NZFFD, you can also use it to produce distribution maps for anything with the Insert/import file menu. For example, if you wanted to show locations of a particular species of invertebrate you could import a file of grid references that could be plotted on a map that you had already formatted to meet your specifications (using the Zoom, Format, and File/Save as menus). The types of file that can be imported are shown on the menu. If you are saving a text file of grid references from an Excel spreadsheet for importing to the assistant, create a file delimited by tabs or commas.

3.4.4 File menu

The file menu is where you save or export your maps to other applications; there are also icons on the toolbox that perform these functions. Maps can be Copied to the clipboard and pasted directly into Word and Powerpoint or saved as *.wmf for inserting into Word documents later. If you save the file as a graphics file (*.fgr), then you can use the Restore button to use the same map again and again within the assistant program. This is a useful option if you are creating distribution maps from imported files, but want the same base map to be used in each instance. To do this, create the base map with the Zoom, View and Format menus, and then save it as an *.fgr file. Import your first file and save this map. Then, Restore the original *.fgr map file and Import the second file, etc.

3.4.5 The database and REC icons

The database ( ) and REC ( ) icons allow you to view information about any site in your open file. The database icon is the default when you start viewing maps, and the REC icon is only active when the expanded stream network is selected. If you want to know what species were caught at a particular site, click the database icon and then the marker in question. The resulting window shows the NZFFD card number (record number is internal to the assistant program), the locality name, catchment name, nzreach number and the species and their abundance recorded at that site (Figure 8). If there are multiple records at that location, as on the example shown in Figure 8, you can scroll through these with the arrow icons on the bottom of the display window.

The REC icon gives access to selected information from the Rivers Ecosystem Classification database. You can either click on markers or river segments to show the information (Figure 8). If you are using this icon to access REC numbers, be sure to have the river order set to 1 under the Format/River menu. Otherwise, information for the nearest displayed segment will be shown, but this might not be the segment where the sampling site occurred.

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Figure 8: Database (top) and REC (bottom) display results for a site at the mouth of the Clutha River. There is more than one NZFFD record at this site, so the arrows at the bottom of the display boxes are highlighted.

3.5 Entering data

Using the assistant to enter new data is relatively quick and painless, and renders the information into a format ready for loading directly onto the NZFFD. Only the database administrator can actually append new records to the NZFFD, and this is done after the records you send in are checked to ensure they are complete, correct, and comply with database protocols as outlined in Section 2.

The best quality NZFFD data has all fish caught identified to species and counted, the area fished measured, and information about the physical characteristics of the site enumerated from measurements, not visual estimates. The database administrator may reject poor quality records, particularly incomplete species lists and where fish are only identified to genus, or may combine information from a number of sites in close proximity into a single record if the same species were caught. If the administrator queries some of your species identifications, please don’t be offended. If a species

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occurs in a new place or unusual habitat, we need to confirm the data are correct before adding them to the NZFFD.

To begin entering new data in the assistant, simply click New and start filling in the blanks (Figure 9). If you are entering data from a filled in database booklet, use the card number shown in red on the card; if you are entering data from notes, then simply enter 1 as the first card number, and official NZFFD numbers will be assigned by the database administrator when you send in your cards for inclusion. The assistant will automatically number any subsequent cards entered during this session.

Figure 9: New data entry page in the assistant.

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You should try to fill in as much information as you can, but grid references1 and species codes are the most essential items. If fact, any records without grid references will be returned to you for completion. If you have not caught any fish at a site, then the correct code is “nospec”. Typing F1 in any box will activate the help file for that attribute, showing lookup tables, legitimate codes, formats, and other information. There are also a number of range checks built into the data entry program, e.g., checking that the total percent of substrates adds to 100. This gives you an opportunity to correct any errors you might have made in the field, hopefully while the information is still fresh in your mind.

When you have finished entering the data from one card, keep pushing enter until you get back to the card number box and then start on the next card. When you have finished entering cards for that session, you should close the window and then immediately Save the file as an *.fdb file (using a unique name and noting where it is being saved). If you exit the program without saving, you will lose all the data you entered, although you will be prompted about this when you Exit.

There are a number of ways to check your data. You can view the forms by clicking the Form button and reading through the data, noting any corrections, or you can use the View/Data check menu to see a synopsis of the information you have entered (Figure 10). This can be viewed on screen or saved and printed if you prefer reading hard copy. Your data can then be changed and corrected with the Edit button. Be sure to save the file again after you have done any editing; you can use the same file name again with the overwrite option or save to a new file. When you are satisfied with the data, the file should be emailed to the database administrator for inclusion on the NZFFD.

If you have entered your data in an Excel spreadsheet and can’t be bothered entering it again with the assistant, don’t despair! Data can also be converted from *.csv files (from Excel spreadsheets) into *.fdb files, but the data must be in one of three prescribed formats. Details and examples of these are shown in the assistant help file.

1 Chatham Island sites are a special case because the maps covering this area are not based on the NZMS260 grid. The assistant will automatically adjust for this if you enter the appropriate map (c01 or c02) in the map number box and the 3-digit easting and northing from these maps in the grid reference boxes (e.g., 444 and 695). You should also enter this grid reference (444/695) in the comments box. The catchment number for all Chatham Island sites is “Chatham”.

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Figure 10: The data check screen in the assistant. This view allows you to quickly read through your data to note any errors that can then be corrected with the edit button.

4. Obtaining additional data

Although the web site search output is limited to prescribed data items, all the data shown on NZFFD cards are stored on computer, and it is possible to request additional data. Data for just a few cards can be obtained by Viewing the individual cards and entering the data yourself. For large numbers of cards, you need to email the database administrator an Excel file containing the card numbers of those records you want the data for. The email should also specify what additional data you want and the desired format of the output (Excel spreadsheet, *.csv file, etc.). Note that NIWA may invoice you for the staff time spent processing the request.

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5. Appendix I – Organization codes

Organizations that contribute data to the NZFFD are coded with 2 to 4 letter codes that depict their whole names (Table 2). All regional councils end with “rc”, all fish and game councils with “fg”, all DOC regions begin with “doc” and all universities begin with “uo”. Current codes are shown in Table 3.

Table 3: Codes for organizations that contribute data to the NZFFD (07/2008).

Organization Code

AB Ecology Limited abe

Aquatic Ecology Limited ael

Auckland Regional Council arc

Auckland Waikato Fish & Game awfg

Bioresearches bior

Boffa Miskell (Auckland) bma

Bay Of Plenty Regional Council bprc

Carter Holt Harvey Forests chhf

Cawthron Institute ci

Canterbury Regional Council crc

Doc Auckland doca

Doc Bay Of Plenty docb

Doc Canterbury docc

Doc East Coast doce

Doc Wellington docg

Doc Hawkes Bay doch

Doc Nelson Marlborough docn

Doc Otago doco

Doc Southland docs

Doc Tongariro Taupo doct

Doc Waikato docw

Doc Northland docx

Doc West Coast docy

Doc Wanganui docz

Eastern Fish & Game eafg

Environment Southland envs

Enviro Research Ltd erl

Environment Waikato ew

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Fletcher Challenge Forests fcf

Fred Overmars & Associates foa

Glencoal Energy Ltd gel

Hawke's Bay Fish & Game hbfg

Hawkes Bay Regional Council hbrc

Hancock Forest Management hfm

Harrison Grierson Consultants hgcl

Private Individuals indx where x is the first letter of the person’s

surname

Kessels & Associates kal

Kingett Mitchell kma

Landcare Research land

Marlborough District Council mdc

Fisheries Ministry (North) mofn

Morphum Environmental Ltd mor

Manawatu Wanganui Regional Council mwrc

North Canterbury Fish & Game ncfg

Native Freshwater Fish Club nffc

Northland Fish & Game nffg

NIWA niwa

Natural Logic Ltd. nll

Nelson Marlborough Fish & Game nmfg

North Shore City Council nscc

NZ National Aquaculture Centre nzac

NZ Forest Products nzfp

Oxford Area School oas

Opus Consultancy Services opus

Otago Regional Council orc

Otago Fish & Game otfg

Poynter & Associates paa

Central South Island Fish & Game scfg

Stark Environmental Ltd sel

Southland Fish & Game slfg

Taranaki Fish & Game tafg

Tasman District Council tdc

Tom Kroos & Associates tka

Taranaki Regional Council trc

Timberlands West Coast twc

Unknown Organization unk

Canterbury University uoc

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Massey University uom

Otago University uoo

Victoria University uov

Waikato University uow

URS New Zealand urs

West Coast Fish & Game wcfg

West Coast Regional Council wcrc

West Coast Whitebait Association wcwa

Waste Management Limited wml

Wellington Fish & Game wnfg

Wellington Regional Council wnrc

Waikato Regional Council wrc

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6. Appendix II – How to assign catchment numbers

Assigning catchment numbers is a process of determining where your site is, and the path this water would take to reach the sea. There are look-up tables in the database assistant, on the web site search page, or you can download the current version of the revised catchment number dictionary from the web site. If you use any of the above, it is important to ensure you are in the right catchment as there are many streams with the same name. An NZMS260 map number is given beside each stream name to assist with this. However, this map number references where that tributary joins the main stem or where the main stem meets the sea, and your site may occur on an entirely different map, especially if the catchment is large.

Not every waterway is listed in the dictionary. This occurs because there are more waterways than available numbers. The process of assigning a catchment number is the same regardless, and follows this procedure using maps and the catchment number dictionary:

1. Find your site on a map.2. Determine what path water from this stream would take to reach the sea. (If

the site has no outlet (e.g., a landlocked dune lake) assign the number as if there were an outlet).

3. On the list of catchment numbers, find the name of the waterway discharging into the sea for the first three digits of your number.

4. Follow this watercourse until you reach the appropriate tributary and note the number.

5. Repeat the above step until there are no further numbers.6. This is the number that would apply to your site.

Examples: Main stem that flows directly to sea — Manawatu River

1. T24 380 9272. Manawatu River/sea3. Manawatu – 325.0004. No further steps required, so Manawatu River = 325.000

Small named tributary — Davy Creek1. M28 808 9632. Davy Creek/Dart River/Wangapeka River /Motueka River/sea3. Motueka River– 570.0004. Wangapeka River – 570.1305. Dart River – 570.1336. There are no more numbers, so Davy Creek = 570.133

Small unnamed tributary — Waipunga River tributary1. V19 178 3852. Tributary/Waipunga River/Mohaka River/sea

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3. Mohaka River – 218.0004. Waipunga River – 218.2005. No further name, so number = 218.200

Lake with an outlet — Lake Tutira1. V20 561 1382. Lake Tutira/Mahiaruhe Stream/Waikoau River/Aropaoanui River/sea3. Aropaoanui River – 225.0004. Waikoau River –225.0305. Mahiaruhe Stream – 225.0326. There are no more numbers, so Lake Tutira = 225.032

Landlocked lake — Lake Henry1. D43 976 1752. Probably Lake Te Anau/Waiau River/sea3. Waiau River – 797.0004. Lake Te Anau – 797.4905. No further watercourse, so Lake Henry = 797.490

A main stem without a unique catchment number — Kaikokopu Stream1. S24 008 9022. Kaikokopu Stream/sea3. The stream lies between the Manawatu and Rangitikei rivers – 326.0004. There are no further numbers, so Kaikokopu Stream = 326.000

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7. Appendix III – How to save viewed cards into a word document

After you have entered a card number and clicked View form on the web site, follow these instructions:

1. Click Edit, Select all, Copy.

2. Open a new Word document and click Paste.

3. Select and Cut the Prev/Next line off the top of the page.

4. Select the whole document and Resize the font to Arial 9 pt or less (if there are lots of blank rows in the fish data area, you should cut some of these out first by selecting those rows with the cursor, and under the Table menu select Delete Rows).

5. Press Print preview and Shrink to fit.

6. Save with an appropriate name.

7. Repeat for each card separately.

8. Then merge, using page breaks and insert file.

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