CODA: California Oak Disease and Arthropod Host Index Database Version 3.3 USER'S MANUAL January 1998 Tedmund J. Swiecki Elizabeth A. Bernhardt P H Y T O S P H E R E R E S E A R C H 1027 Davis Street, Vacaville, CA 95687-5495 email -- phytosphere@phytosphere.com WWW -- http://phytosphere.com (c) 1996, 1997, 1998, 2000 Phytosphere Research. All rights reserved. IMPORTANT - Please read carefully before loading software Terms of Use and Disclaimer The CODA database and its compiled access program are protected by copyright law. You may not copy the software to sell, lease, or rent to others. The data and program may not be modified in any way, nor incorporated into any other product without the express written consent of Phytosphere Research. Phytosphere Research disclaims all warranties as to this software and documentation, whether express or implied, including without limitation any implied warranties of merchantability, fitness for a particular purpose, functionality, or data integrity. In no event shall Phytosphere Research be liable for any indirect, incidental, collateral, exemplary, consequential, or special damages or losses arising out of your use of the software or the information in the database. Your use of the CODA software signifies your assent to these terms. Conventions used in this manual: -- Single key names are in all capitals and surrounded by <>: , , -- Pressing the ENTER key is shown as -- Typed DOS commands are in capitals, and are shown on a separate line: CD CODA California Oak disease and Arthropod Host index Database USER'S MANUAL Version 3.3 Table of Contents Terms of use and disclaimer PART 1. Loading and running CODA Background Description of the database and program Program availability and technical support Program updates and development System requirements Loading the CODA access program Loading the CODA database files Starting the CODA access program Running the CODA database In brief Help Note fields Main window Host window - Agent window - Synonym window - Find an agent window - Reference window - Bibliographic window Searching through the CODA database Selecting by host or agent Using the filter function Printing reports Printing a single record report Printing a filter search report Using the key Troubleshooting Program files fail to decompress Problems starting CODA Obsolete or corrupted files in directory Improper DOS version CONFIG.SYS files statement Insufficient memory Too many environment variables Using minimum system configuration files Program functions execute slowly PART 2. CODA Technical Reference Distribution Situation Stages Symptom matrix Maturity Site Symptoms and signs General symptoms General symptoms: Gall types Diseases: Types of decay Diseases: Types of cankers Diseases: Pathogen signs Arthropods: Injury symptoms Arthropods: Types of leaf mines Arthropods: Arthropod signs and products Alphabetical listing of symptoms Status Agent description codes Additional notes Agent genus & species notations Agent family field for fungal species PART 1. LOADING AND RUNNING CODA This portion of the User's Manual describes how to load and run the CODA database, and includes a troubleshooting section. A technical reference which lists and explains the codes and descriptions in CODA is found in Part 2 of this manual. BACKGROUND The CODA database and its access program were originally developed for the Forest and Rangeland Resource Assessment Program (now the Forest Resource Assessment Program [FRAP]) of the California Department of Forestry and Fire Protection (CDF) under contract 8CA74545. CODA was originally released in July 1990. Distribution, support, and updating of the CODA database from January 1992 through July 1993 was funded by contract 8CA17093 from CDF to Phytosphere Research. Ongoing maintenance and distribution of CODA is currently supported by Phytosphere Research as a public service. The database was developed by Ted Swiecki and Elizabeth Bernhardt (Phytosphere Research), Richard Arnold (Entomological Consulting Services, Ltd.), and Jim Kellogg (Tierra Data Systems), and is described in detail in the following report available from CDF-FRAP, P.O. Box 944246, Sacramento, CA 94244-2460. Swiecki, T. J.; Bernhardt, E. A.; Arnold, R. A. 1990. Impacts of diseases and arthropods on California's rangeland oaks. DESCRIPTION OF THE DATABASE AND PROGRAM Oaks in California are colonized, damaged, eaten, or decomposed by a wide variety of agents. The California Oak Disease and Arthropod (CODA) host index is a comprehensive database of reported interactions between oak trees and their associated arthropods (insects and mites), microorganisms, and disease agents (both biotic and abiotic). The current release of CODA includes data on over 880 arthropods, and 370 species of fungi, for a total of over 2580 interactions with the 55 oak species, hybrids, and varieties listed in the database. The information in CODA comes from over 300 published and unpublished sources. The CODA database gives you access to the most complete compilation of information on diseases and arthropods affecting both native and introduced oaks in California. Furthermore, you can quickly sift through the database to extract the information that you need to answer a variety of questions. For example, you can quickly construct a list of agents that might be responsible for damage symptoms on a given oak species. You could also easily determine whether an agent that attacks valley oak is known to affect coast live oak. The information in CODA can be viewed on your computer screen, or can be printed out in various types of reports. The information in CODA is contained in a set of linked databases with data on the host species, associated agents, details of each interaction, and bibliographic references. The CODA program automatically accesses information from all of the databases. PROGRAM AVAILABILITY AND TECHNICAL SUPPORT Copies of the CODA database are currently available through the internet. The most current data files and the CODA access program can be downloaded from our World Wide Web site at: http://phytosphere.com/phytosp3.htm The web page lists the most current data release, explains how to download and install the data files. Call or email us if you have any questions about the web site or your CODA software, or if you have information to submit for inclusion in the CODA database. Technical support questions can be addressed to Ted Swiecki. Phone: (707) 452-8735 (9 am - 6 pm Pacific time). e-mail: Phytosphere@phytosphere.com PROGRAM UPDATES AND DEVELOPMENT Updated versions of the CODA data files are released periodically for download from our web site. At present, no further development of the access progam is planned, due to a lack of funding. We are looking into placing the CODA database online with a web-based search platform, but we have not yet identified an organization that will provide the resources necessary to do this. For now, the CODA access software provides the best way to access the CODA database. The purpose of the CODA software is to increase awareness about the impacts of diseases and arthropods on oaks in California, and to provide accurate information about the arthropods, microorganisms, and abiotic factors that affect oak health. If you have information about any California oak disease or arthropod interaction that is not contained in the database, or is at variance with the current database information, please send this information to Ted Swiecki at Phytosphere Research. Data submission forms will be provided upon request. SYSTEM REQUIREMENTS The CODA host index access program runs on PCs running DOS version 3.3 or higher or Windows. It can be run on Apple Macintosh computers using PC-emulation software. The program requires at least 5 megabytes of hard disk free space and about 512K of free conventional memory. If there is less than this amount of free conventional memory due to memory-resident (TSR) software, the program may fail to load. If this problem occurs, exit unnecessary memory-resident applications before starting the program. See Troubleshooting for further details. LOADING THE CODA ACCESS PROGRAM Step 1. Remove old CODA version If you had a version of CODA older than version 3.3 on your computer, you must either delete all of the old files from the CODA directory or load the new copy of CODA into a different directory on your hard disk. If you attempt to load the new version of CODA without erasing the old program files in the CODA directory, the program will not operate properly. If you erase all the old CODA files, you will also need to load the updated database files as noted in the section below. Step 2. Copy CODA program files We recommend that you store CODA files in a separate directory called CODA on your hard disk. Copy or move the downloaded file CODAPROG.EXE to the CODA directory. Step 3. Decompress program files The compressed program files within CODAPROG.EXE can be expanded by running this program from within Windows (e.g., double click on CODAPROG.EXE in Program Manager in Windows 3.x). Alternatively, from a DOS prompt within the CODA directory, type: OPENCODA The compressed program files will be expanded and the following CODA program and data files will now be loaded in your CODA directory: HI.EXE CODA.BAT Once you have loaded the program, it is not necessary to reload it when updating the data files. LOADING THE CODA DATABASE FILES Once you have a copy of the CODA access program version 3.3 installed on your computer, you still need to load the data files to run the CODA database. If you have been running CODA, you can also follow the steps below to update the CODA data files to the most current release. Step 1. Download the compressed data files from the web site (http://phytosphere.com/phytosp3.htm) following the instructions on the page. The compressed data files are stored in a file named CODAnnnn.EXE where nnnn is the data release date (e.g. 0797 is the July 1997 release). Step 2. Copy the CODAnnnn.EXE file to the directory that contains the CODA software (usually C:\CODA). Step 3. From a DOS prompt within the CODA directory, type the name of the CODAnnnn.EXE file. Alternatively, from the Windows (3.x) File Manager, you may simply double click on the filename. If you use File Manager, be sure to press F5 (or click Window/Refresh) so that the newly expanded files will show up. The files UPDATE.BAT and CODAFILE.EXE should now be in the CODA directory. Step 4. From a DOS prompt within the CODA directory, type UPDATE. If using the Windows (3.x) File Manager instead, you may simply double click on the file UPDATE.BAT. The update program will erase the old database index files (if you are updating a previous release), decompress the new database files and overwrite the old ones, and finally erase the CODAFILE.EXE and UPDATE.BAT files. Step 5. You can now start the CODA program in the usual way (discussed below). There will be a delay as the index files are recreated the first time you use the program after updating. Step 6. Once you are satisfied that the load or update was successful, you may want to erase the CODAnnnn.EXE file. PLEASE NOTE: The CODAnnnn.EXE file contains only the data files used by the CODA access program. You must have the CODA version 3.3 access program to run the CODA program, so don't erase all the old files in the CODA directory!! STARTING THE CODA ACCESS PROGRAM Windows NT 4 note: Before starting CODA for the first time, edit your CONFIG.NT files (in the winnt\system32 and winnt\repair folders) to read files=40 instead of files=20. To start the program from a DOS prompt, make the CODA directory the current directory and type: CODA You can also launch the program from within Windows like any other DOS program. In Windows, double click on CODA.BAT in Windows Explorer or use run from the start menu. The first time the program is started, there will be a delay as the program creates index files needed by the program. These 8 index files (files with the extension .NTX) are stored to your hard disk in the same directory as the other CODA system files. If any of these index files is erased from the hard disk, CODA will recreate the missing file(s) when the program is started. NOTE: The index files are unique to the current set of data files. Loading any updated data files from disk can disrupt the indexing, making it appear that records have been lost. If updated data files are loaded, or if the index files become corrupted for any reason, erase all the files with the extension .NTX from the CODA directory and restart the program. RUNNING THE CODA DATABASE PROGRAM In brief Information in the CODA database is displayed through a series of nested windows. The main window is displayed when the program starts. Windows with information on the host, agent, and references are displayed by pressing the , , and function keys, respectively. Pressing will expand the note field in any window that has an associated note. The key displays a help screen that lists the functions that can be performed from each window. You will note that the program interface is somewhat dated. For instance, all actions are performed by keystrokes only; the mouse is not used. It's a bit of a throwback to simpler times, but is still quite functional.. Help A list of options that can be performed from each window can be viewed on a pop-up help window by pressing the key. To clear the help window without performing any operation, press the space bar. Note fields The main window, host window, agent window, and bibliographic window may have associated notes in a note field at the bottom of the screen. Long notes may not be displayed completely from these screens. To see the entire note field in any of these windows, press . This places the window in "Note edit" mode. The up and down arrow keys and the and keys will allow you to scroll up and down in the note field. When you are finished viewing the note, press to return to the normal viewing mode. Main window The main window displays information about a particular host-agent interaction. This window contains fields that describe the agent, distribution, situation, susceptible life stages of the host, site and maturity of tissue attacked, symptoms and signs, status of the agent, and displays a partial list of references. The fields shown in this window are explained in more detail in Part 2 of this manual. Several functions can be performed directly from the main window. -- Database records can be displayed arranged by host or agent using the and function keys and the directional keys (see Selecting by host and agent). -- The filter searching function can be accessed by pressing (see Using the filter function). -- Abbreviated codes are translated on-screen by pressing (View codes). -- For agents with more than one synonym, additional synonyms can be seen by pressing . -- Notes associated with a record can be viewed by pressing (view Note). -- A printed report can be produced for the currently displayed record (see Printing reports). In addition, all of the other information windows are accessed from the main window using the function keys described below. Host window - The host window gives additional information about the host species, including its range, habit, and characteristics. Agent window - The agent window gives more detailed information about the agent, which may include a description in the note field (press to completely view long notes). From the agent window, you can view the synonym window by pressing . Synonym window - Nested within the agent window, the synonym window lists further information for the synonyms of the agent which are listed in CODA. At present, the list of synonyms for each agent is not comprehensive, but is based primarily on names used in earlier literature for California records. Find an agent window - If you press from the Agent window, a separate window will appear which allows you to jump to any agent genus by typing in the first few letters of the genus name. You may return to the agent window by pressing . Reference window - The reference window shows all of the sources of information upon which the CODA host-agent interaction record is based. More information about any citation can be displayed by highlighting the citation using the up and down arrow keys and pressing . Bibliographic window This window is nested within the reference window and displays a full citation for the reference, along with specific notes for the citation, if any. Long notes can be completely viewed by pressing . SEARCHING THROUGH THE CODA DATABASE The CODA program provides several ways to search through the records in the database. Data may be accessed by the host oak species, the agent (pathogen or insect), or by the symptoms, distribution, or other fields describing the agent or host-agent interaction. Selecting by host or agent When paging through the database, interactions shown on the main screen are indexed alphabetically either by agent or host. An indicator in the upper right corner of the screen shows the current indexing method (BY HOST or BY AGENT). - To index by agent, press . The database records will now be sorted alphabetically by agent, with all of the reported hosts arranged under each agent. If you press the up and down arrow keys, you will step through the database, displaying all of the hosts affected by each agent. If you press and , you will step through the database, moving alphabetically between different agents. - To jump to a specific agent, press , type in the agent genus, and press . You may also type just the first few letters of the genus name, and CODA will jump to the first agent which starts with the letters entered. - To index by host, press . The database records will now be sorted alphabetically by host species, with all of the reported agents arranged under each host. If you press the up and down arrow keys, you will step through the database, displaying all of the agents known to affect each host. If you press and , you will step through the database, moving alphabetically between different hosts. - To jump to a specific host species, press , type in the first letters of the host species name, and press . TIP: If the above explanation leaves you confused, don't worry - just try it. The indexing of the database is quite easy to understand when you use it, but is dreadfully difficult to explain. Using the filter function The filter function provides another way to select specific records. It allows you to display or print records from the database that match certain criteria that you may set. For example, you can search for all of the agents that cause defoliation of blue oak, or you can search for agents by common names or synonyms. - Pressing will cause the filter screen to be displayed. If you wish to exit the filter screen without engaging the filter, press . Pressing any key except , , or moves the highlight between the different filter groups, which show the different fields that may be searched in a single filter operation. To filter out records based on criteria from any of the filter groups, highlight the appropriate group and press . Use the up and down arrow keys to move between fields of the filter group. Enter the filter criteria names and/or codes in the appropriate field(s). Valid codes are listed in Part 2 of this manual. When you are finished entering your filter criteria, press . You may enter names and codes in upper or lower case. You may also use partial spellings for the names and codes. For example, typing "dou" in the Quercus: field will retrieve records for Q. douglasii. In the agent common name field and the symptom matrix, the program will search for any occurrence of the character string you type in the field. This is known as a substring search. For example, typing "scale" under agent common name will retrieve any record with the word scale in the common name, such as oak pit scale or Kuwana oak scale. Typing "rot" in the branch or trunk symptom block will retrieve all listed types of rot: brown rot (BROT), white rot (WROT), pocket rot (PROT), and general unspecified rot (ROT). If any records match the criteria you set, a window will be displayed that asks whether you want to send your output to the screen or the printer. If there are no records that match your filter criteria, the screen display will automatically return to the main window. -Screen display - If you select option <1>, output to screen, each record matching the filter criteria will be displayed in order as you press the up or down arrow keys. A Filter On indicator will appear in the upper right corner of the screen to show that the filter is on. The filter will automatically turn off as soon as the last matching record is displayed. To turn off the filter early, press . You can access all of the other information windows and the main window functions while the filter is on, except the and keys. Pressing the and keys will turn off the filter. -Printed reports - You should generally preview the results of a filter search on the screen before printing a report, since certain searches may generate a great deal of printed output. There are two main options (short and long) for printing a report, and output can be sent directly to your printer or to a file using either option. The type of output produced using these different options is described under Printing reports. PRINTING REPORTS Printing options have been greatly expanded for this release of CODA. You may either send output directly to your printer, or to a file that you can edit with your word processor prior to printing. You can also print out full bibliographic citations, as well as the information from any of the note fields. The basic output from the report function includes the information visible in the main window, namely: -- the species and common name of the host; -- description code, genus, species, and common name of the agent; -- the distribution, situation, and stages fields; -- the symptom matrix, -- reference list, and -- notes on the host-agent combination. Further printing options allow you to select what other information you want to include in the report. Printing a single record report The output for a single record can be printed out by selecting the report function from the main information window. Locate the desired record by using any of the search methods described above under Searching through the CODA database and press . You will then see a series of screens asking what type of information you want to have included in the report. These choices are described below. Full/ Brief/ Line references (F/B/L)? -- The full option prints all data fields for the references in the selected record, including the notes. -- The brief option prints the author, title, source and date fields. The note and label fields are not printed. -- The line option prints only the single line reference labels, such as those that appear on the main screen. Include agent notes (Y/N)? To include the note field that appears on the agent window in your output, press . Press if you do not wish to print the agent note. Include host notes (Y/N)? To include the note field that appears on the host window in your output, press . Press if you do not wish to print the host note. Include code descriptions? (Y/N) To include a translation of all the codes used in the record in your output, press . These printed code descriptions are the same as those seen on the screen when the view codes function is used. Press if you do not wish to print the code descriptions. Print to file (Y/N)? -- To print to a file, press . The following screen will appear: Enter \Path\file.ext: Enter a valid DOS filename (8 characters or less) that you want the report sent to. You may also specify a path and file extension. For example, to send the report to a file named CODAOUT1.DOC in a directory named WORD, enter the following: Enter \Path\file.ext: \word\codaout1.doc If you do not enter an extension, the default file extension .PRN will be used. If you do not specify a path, the file will be written to the CODA directory. If you enter a path that is not valid, the following error message will appear: Unable to open file ____ - Hit any key to continue After pressing a key, you will be returned to the main screen. You will need to resubmit your report request. After you exit CODA, you can view and print your report output file using a text editor or word processor. The output file is a text-only ASCII file. TIP: When using a word processor to format a report output file, use fixed-spaced fonts (e.g. Courier) instead of proportionally spaced fonts (e.g. Times Roman) to retain the alignment of the output fields. -- To send your report to the printer, press . The output will be sent to the default printer connected to your computer. If the printer is disconnected, off, or not ready at the time that a report is requested, the following message is displayed at the top of the screen: Printer not ready - Retry? (Y/N) To continue printing, get your printer on line and type . The report will then be sent to the printer. To abort the printing request and return to the main screen, type several times until the main screen is visible. Printing a filter search report If a filter search locates records matching the specified filter conditions, a box listing output options will appear over the filter window. There are two different options for producing printed output. If the short option <2> is selected, the following message will appear: Print to file (Y/N)? The options from this point are the same as described under Printing a single record report above. Output produced contains the fields shown in the following example report: Quercus agrifolia Agent: B P F ASC PYM Common: Coast live oak Genus: Brasiliomyces Species: trina Distribution: BA,SC Subsp: Situation: L Common: Powdery mildew Stages: M Synonym: Californiomyces trina If the long option <3> is selected, all of the options described above under Printing a single record report are available. TIP: If you use the long option to print the result of a filter search with many records, you may want to use the PRINT TO FILE option. You can then use your word processor to edit and format the file before printing. Using the key It is also possible to print the information visible on any screen by pressing the key. On some printers, especially laser printers, you may need to press the FORM FEED button on the printer to eject the printed page after pressing . On HP laser printers, two screens of information can be placed on a single page before the page should be ejected. If your printer is set up with a default character set other than the IBM set (also known as PC-8), the lines and borders that appear on the screen may print as other characters. However, the text blocks from any screen should print normally. TROUBLESHOOTING Most of the problems discussed below apply to older systems running older versions of DOS and Windows 3.x. The CODA access program runs on most modern systems without problems, but is apparently incompatible with some older network software. -Problems starting CODA Several different types of problems may cause the CODA program to fail to start. Many of them will result in a DOS error message of the following format: Proc XX, line nn, open error file (nn) Retry? (Y/N) If this occurs, write down the error message and then type N. You may also want to type cls to clear the screen. Check through the rest of this section to determine the most likely cause of the problem. >>Obsolete or corrupted files in directory Changes have been made to most of the files for CODA version 3.3. If you have earlier CODA files in the CODA directory, the program may fail to start or the information displayed may be corrupted. If this occurs, erase all files in the CODA directory and reload the program from the downloaded CODAPROG.EXE file. If you experience problems when starting CODA, the index files which are created when the program starts may be incomplete or corrupted. The program will not function properly without correct index files. If you suspect that any index files have become corrupted for any reason, erase all the files with the extension .NTX from the CODA directory and restart the program. CONFIG.SYS files statement Your DOS CONFIG.SYS file must contain the statement FILES=30 (or higher) for CODA to run, otherwise the program will abort with an error message. Add this statement to your CONFIG.SYS file if it is lacking, or modify it if necessary. Consult your Windows manual if you do not know how to edit your CONFIG.SYS file. If you change the FILES= statement in your CONFIG.SYS file, you will need to reboot your system so that the change will take effect before running CODA. Note for Windows NT 4 users: You need to modify the CONFIG.NT file rather than the CONFIG.SYS file for CODA to run correctly. You can find two copies of this file, one in the winnt\system32 folder and one in the winnt\repair folder. We suggest that you modify both to read files=40 instead of files=20. Please note: Other switches or drivers in your CONFIG.SYS may also prevent the CODA program from starting. See further notes under Insufficient memory below. Insufficient memory The CODA program can make use of expanded memory for some of its files, but the majority of the program is loaded into conventional memory. You should have at least 512K of free conventional memory available before running CODA. If your system has device drivers or programs loaded into conventional memory (the first 640 K of memory on your system), there may not be enough room for CODA to run. In some cases the following error message may be displayed when attempting to start CODA: Not enough memory If you see this error message or the "open error" message described earlier, check the following list for ways to free up more conventional memory before starting CODA . The most appropriate method will vary with the system you are using. 1. EMM386 Driver If you are using DOS version 5.0 or higher, check to see whether the following line (or something similar) is in your CONFIG.SYS file: DEVICE=C:\DOS\EMM386.EXE If this line is present but contains the notation NOEMS, it will force the entire CODA program to load into conventional memory, which may result in the insufficient memory. Remove the NOEMS switch entirely or replace it with the switch RAM and reboot your system. 2. Exit memory-resident (TSR) applications You can unload some individual programs from memory simply by typing in the appropriate command(s) from the DOS prompt. Refer to instruction manuals for each program for the necessary commands. 3. Prevent memory-resident (TSR) applications from loading automatically Your AUTOEXEC.BAT and CONFIG.SYS files may cause a number of device drivers and memory-resident programs to be loaded automatically every time you start your computer. You can prevent unnecessary programs from loading into conventional memory by modifying your AUTOEXEC.BAT and/or CONFIG.SYS files. You may want to back up these files before making any modifications. You can modify the files using a text editor such as EDIT (DOS 5 and 6) or any other text editor. The simplest way to prevent any particular device or file from loading is by typing REM followed by a space in front of any line you wish to disable. This REMarks out the line so that it doesn't execute, but allows you to easily restore the line by removing the REM. Please remember that after saving your changes to either file, you will have to reboot your computer so that the changes will take effect. 4. Load memory-resident software into high memory If you are running DOS version 5.0 or higher, you may be able to use the HIMEM.SYS driver to load various memory-resident programs into high memory using the LOADHIGH command. The DEVICEHIGH command may also be used to load device drivers into upper memory. Consult your DOS manual regarding the use of these commands in your CONFIG.SYS and AUTOEXEC.BAT files. Too many environment variables The file that starts CODA (CODA.BAT) includes a DOS SET command that is needed for the program to open all the files it needs to run. If there are too many DOS environment variables set, the following message may briefly appear immediately after typing CODA: Out of environment space Although the title screen will appear following this message, the program will fail to start and will abort with an error message. If the program fails to start due to inadequate environment space, try one of the following fixes. 1. Add the following statement to your CONFIG.SYS file: shell=command.com /e:512 /p If you already have a statement of this general type in your CONFIG.SYS file, increase the value of the /e: switch by 160 or more. If the /e: switch is missing, insert it as shown above. This will increase the environment size from the default of 256 bytes to 512 bytes, and should allow the program to run if the environment size is the only limiting factor. Refer to the discussion of the command and shell statements in your DOS manual for additional details about setting the environment size. 2. Modify your CONFIG.SYS and AUTOEXEC.BAT files to reduce the number of DEVICE statements and/or SET statements by typing REM at the start of the line, as described in number 3 under Insufficient Memory above. Program functions execute slowly Due to the size of the database, operations such as the filter function may be relatively slow on computers with slow processors or slow disk access. Certain disk-intensive functions may also be slow if files are fragmented on the hard disk. Program performance will be improved if the program files are stored in contiguous blocks. You can do this by using a hard disk de-fragmentation utility program. PART 2. CODA TECHNICAL REFERENCE Much of the information in CODA is presented in an abbreviated or coded form on the screen to conserve space. Remember, you can have these codes translated on screen from the main window by pressing (View codes). When using the filter function , use this reference to determine what codes should be used when searching coded fields. The valid codes in use for each of the data fields are listed and described in this section. DISTRIBUTION This field describes the general geographic distribution of the agent in California. Regions have been drawn along county lines for convenience. BA Bay Area Alameda, Contra Costa, Marin, Napa, San Mateo, San Francisco, Santa Clara, Solano, Sonoma CC Central Coast Monterey, San Benito, San Luis Obispo, Santa Barbara, Santa Cruz, Ventura CI Central Interior Alpine, Amador, Calaveras, El Dorado, Mariposa, Nevada, Placer, Tuolumne NC North Coast Del Norte, Humboldt, Mendocino NI North Interior Lassen, Modoc, Plumas, Shasta, Sierra, Siskiyou, Trinity NV North Central Valley (Sacramento Valley) Butte, Colusa, Glenn, Lake, Sacramento, Sutter, Tehama, Yolo, Yuba SC South Coast Los Angeles, Orange, San Diego SI South Interior Imperial, Inyo, Mono, Riverside, San Bernardino SV South Central Valley (San Joaquin Valley) Fresno, Kern, Kings, Madera, Merced, San Joaquin, Stanislaus, Tulare For widely-distributed agents that are present in several regions, the following codes are used: A All regions (Widely distributed throughout the entire state) C Coastal (Includes NC, BA, CC, SC) N North (Includes NC, NI, NV, and BA) S South (Includes SC, SI, and SV) V Central Valley (Includes NV, SV) SITUATION This field describes the type of cultural situations that the host/ agent interaction is known to occur under. R Range - Mostly native (non-planted) trees growing in rangelands, woodlands, and other relatively undisturbed settings. L Landscape - Planted or native trees growing in urbanized, landscaped, or similar areas where trees are subjected to various impacts associated with human activities. N Nursery - Planted trees growing in containers or soil (e.g. liners) under nursery conditions. E Experimental - Planted or native trees, growing under various conditions where the host/agent interaction is the result of an experimental inoculation or infestation. STAGES Life stages of the tree known to be attacked by the agent. 1 Seedlings - Small seed-origin trees, generally less that 1 cm (0.5 inch) diameter at base 2 Saplings - Trees larger than seedlings, but generally less than 3 cm (1 inch) diameter at 135 cm (4.5 ft) 3 Mature trees - includes acorns attacked while attached to the tree S Stump sprouts - shoots resprouting from cut stumps D Dead wood - attached or downed Q Questionable record - This code indicates that the record is of questionable accuracy. SYMPTOM MATRIX The following fields are part of a matrix that is used to describe the location and types of damage symptoms and actual signs of the agent. These descriptions are grouped by the parts of the tree (flowers, acorns, leaves, branches, trunk, roots) affected. MATURITY This field refers to the maturity of the affected plant part that is affected, for example young leaves or mature branches. A All tissue maturities Y Young tissues M Mature tissues S Senescent (dying) tissues D Dead tissues SITE This field describes the portion of the plant part that is attacked, or where symptoms or signs are located. Some codes are specific to certain types of plant parts, as indicated below. Codes used for acorns A Cap (also known as the acorn cup) N Nut Codes used for leaves B Bottom (abaxial) surface E Entire leaf - top and bottom surfaces I Interveinal areas (between veins) M Margins (edges) of leaves P Petiole (leaf stalk) T Top (adaxial) surface V Veins of leaf Codes used for woody tissues (Branches, Trunk, Roots) C Vascular Cambium - meristematic tissue layer below the bark of stems and roots that gives rise to radial growth G Growing points - buds, apical, and lateral meristems other than the cambium H Heartwood - older wood near center of stem K Bark L Lignified (woody) tissue - heartwood/sapwood not specified or not applicable, as in small stems and roots R Root crown - base of trunk where major roots originate S Sapwood - younger wood near outside of stem Codes used with any plant part W Wound - associated with wounds or natural openings, including fire scars, branch stubs, leaf scars, pruning wounds SYMPTOMS AND SIGNS General symptoms Cavi Cavities Chlo Chlorosis - yellowing or bleaching Cspot Chlorotic (yellow or pale) spots Dcol Discoloration (other than chlorosis) Defol Defoliation - premature loss of foliage Dieb Dieback - necrosis of terminal portions Dist Distortion - irregular curling, swelling Exfol Exfoliation - abnormal peeling or flaking of bark Fail Failure - breakage or collapse of limbs, trunk or roots Mos Mosaic Necr Necrosis - death of plant parts Nspot Necrotic (dead) spots Reduc Reduced production - fewer produced than normal Sap Sap bleeding and ooze Shot Shot-hole - small circular holes in leaves Stunt Stunting - reduced size Wbrm Witch's broom - proliferation of multiple shoots Wilt Wilt Vdcol Vascular discoloration - darkening or streaking of conductive tissue General symptoms: Gall types Gall Gall, type unspecified - plant tissue overgrowth Gint Integral gall - not easily removed without cutting or breaking Gdtch Detachable gall - easily removable from plant tissues Diseases: Types of decay Rot Rot, type unspecified Prot Pocket rot - decay occurs preferentially in small pockets, forming cavities separated by thin areas of firm wood Wrot White rot - lignin is removed from wood at the same rate or faster than cellulose, resulting in a stringy or spongy, often pale-colored decay Brot Brown rot - cellulose and hemicellulose are selectively removed from the wood, resulting in a crumbly, amorphous or cubical decay. Structural strength is lost more rapidly compared with white rot. Less common in oaks than white rots. Diseases: Types of cankers Cank Canker, type unspecified Pcank Perennial canker Tcank Target canker - a regular, concentrically zonate perennial canker Diseases: Pathogen signs Aapo Ascocarp, apothecium - cup-like fruiting body Acl Ascocarp, cleistothecium - small, superficial, globose, closed fruiting body Aper Ascocarp, perithecium - small, subglobose or flask-like fruiting body Astr Ascocarp, stromatic - spores in cavities within mass of fungal tissue Acerv Acervulus - non-superficial, spore-bearing spot without distinct walls Pyc Pycnidium - small globose or flask-like fruiting body Bpil Basidiocarp, pileate - a conk-like fruiting body Bres Basidiocarp, resupinate - a sheet-like fruiting body Bstp Basidiocarp, stipitate - a mushroom-like fruiting body Mtoe Mistletoe Mycel Mycelium - fungal filaments PM Powdery mildew - superficial, powdery, usually white fungal growth on young shoots and leaves Spor Sporulation, type unspecified Sprd Sporodochium (spores formed on a cushion-like mass of conidiophores) Arthropods: Injury symptoms Bore Single boring into phloem and wood (e.g. cerambycids) Chew Chewing damage to leaves, etc.; sometimes called free-feeding Crink Leaf crinkling Ehol Emergence or exit hole Gouge Gouging or scoring Hole Hole leaf feeding Ovi Oviposition (egg-laying) slits or holes Pit Pitting Punc Punctures Roll Leaf rolling Rough Roughened bark Skel Skeletonizing - feeding that leaves major leaf veins only Stip Stipple - fine spotting Tie Leaf tying Tun Branching tunnels or galleries in phloem or bark (e.g. bark beetles) Wndw Windowing - foliar feeding pattern in which one epidermal layer and major veins remain after feeding Arthropods: Types of leaf mines Blotch Blotch leaf mine Dig Digitate (finger-like) leaf mine Line Linear leaf mine Serp Serpentine (meandering) leaf mine Arthropods: Arthropod signs and products Adult Conspicuous adult stage Case Larval cases/shelters Egg Individual eggs, egg clusters, or egg masses Excr Insect excrement (other than frass or honeydew) Frass Frass - sawdust-like wood fragments mixed with excrement produced by boring insects Hdew Honeydew - clear, sticky liquid excreted from anus of some Homoptera Larva Conspicuous larval or nymphal stage Pupa Cocoon, pupa, or pupal case Scale Scale insect nymphs or adults Silk Silken mats or pads Soot Sooty mold - black superficial mold associated with insect honeydew Spit Spittle - frothy insect secretions Wax Wax Web Web or tent-like shelters ALPHABETICAL LISTING OF SYMPTOMS Acervulus - non-superficial, spore-bearing spot without distinct walls ACERV Adult stage of arthropod ADULT Apothecia (Ascocarp) - cup-like fruiting body AAPO Blotch leaf mine BLOTC Brown rot - brittle, often blocky, dark-colored wood decay BROT Canker, type unspecified - discrete, necrotic lesion of stem tissue CANK Canker, perennial - discrete lesion that persists 2 or more years PCANK Cavities CAVI Chewing damage to leaves, etc.; sometimes called free-feeding CHEW Chlorosis - yellowing or bleaching CHLO Chlorotic (yellow or pale) spots CSPOT Cleistothecia (Ascocarp) - small, superficial, globose, closed fruiting body ACL Defoliation - leaf loss DEFOL Dieback DIEB Digitate (finger-like) leaf mine DIG Discoloration other than chlorosis DCOL Distortion DIST Emergence or exit hole EHOL Excrement (other than frass or honeydew) EXCR Exfoliation - excessive or abnormal peeling or flaking of bark EXFOL Failure - breakage or collapse of limbs, trunk or roots FAIL Frass - sawdust-like wood fragments mixed with excrement FRASS Gall - plant tissue overgrowth GALL Gall-detachable (easily removable) GDTCH Gall-integral (not easily removed without cutting or breaking) GINT Gouging or scoring GOUGE Hole leaf feeding HOLE Honeydew - clear, sticky liquid excreted from anus of some Homoptera HDEW Individual eggs or clusters, masses EGG Insect excrement other than frass or honeydew EXCR Larval cases/shelters CASE Larval or nymphal stage LARVA Leaf crinkling CRINK Leaf rolling ROLL Leaf tying with webbing or silk TIE Linear leaf mine LINE Mistletoe MTOE Mosaic - angular chlorotic patches intermingled with normal areas MOS Mycelium - fungal filaments MYCEL Necrosis - dead plant parts NECR Necrotic (dead) spots NSPOT Oviposition (egg-laying) slits or holes OVI Perithecia (Ascocarp) - small, subglobose or flask-like fruiting body APER Pileate basidiocarp - a conk-like fruiting body BPIL Pitting PIT Pocket rot - wood decay localized in discrete pockets PROT Powdery mildew - superficial, usually white fungal growth on leaves PM Punctures PUNC Pupa, cocoon, or pupal case PUPA Pycnidia - small globose or flask-like fruiting body PYC Reduced production REDUC Resupinate basidiocarp - sheet-like fruiting body BRES Rot, type unspecified ROT Roughened bark ROUGH Sap bleeding and ooze SAP Scale insects SCALE Serpentine (meandering) leaf mine SERP Shot-hole SHOT Silken mats or pads SILK Single boring into phloem and wood (e.g. cerambycids) BORE Skeletonizing - feeding that leaves major leaf veins only SKEL Sooty mold - black superficial mold associated with insect honeydew SOOT Spittle - frothy insect secretions SPIT Sporodochium - spores formed on a cushion-like mass of conidiophores SPRD Sporulation, type unspecified SPOR Stipitate basidiocarp - a mushroom-like fruiting body BSTP Stipple - fine spotting STIP Stromatic ascocarp - spores in cavities within mass of fungal tissue ASTR Stunting STUNT Target canker - regular, concentrically zonate perennial canker TCANK Tunnels or galleries in phloem or bark (e.g. bark beetles) TUN Vascular discoloration - darkening or streaking of conductive tissue VDCOL Wax WAX Web or tent-like shelters WEB White rot - light-colored decay; spongy, stringy, crumbly, or brittle WROT Wilt WILT Windowing - foliar feeding leaves one epidermal layer and major veins WNDW Witch's broom - proliferation of multiple shoots WBRM STATUS This field refers to the nature of the impact that the agent has on the tree. There are two parts to this field. The codes for the first part are: 1 Primary - Agent is capable of attacking healthy tissue 2 Secondary - Agent only attacks injured, stressed, or otherwise compromised tissues ? Unknown The second part of the field indicates whether the symptoms listed are a direct result of the agent, or an indirect effect, due to an damage to another part of the tree (e.g. wilting can be an indirect effect of root rot, stem boring, etc.) D Direct I Indirect AGENT DESCRIPTION CODES On all screens that show the agent name, the agent description field is found above the agent genus field. This field contains a series of codes that organizes the agents into hierarchical categories and gives information about the taxonomic position of the biotic agents. There are five levels of classification in this field. The first three levels are denoted by single-character fields and the last two levels are denoted by three-character fields. TIP: Remember, you can have these codes translated on screen from the main window by pressing (View codes). However, if you wish to conduct a filter search on any of the codes in the agent description field, you will need to use the codes listed below. Level 1 This code separates agents into two categories: biotic and abiotic Abiotic (nonliving) agents A Biotic (biological) agents B Level 2 This code is used to separate the two categories of agents into broad, mostly non-taxonomic groups. Arthropods (insects, mites, and associates) A Chemical toxicity C Environmental conditions E Genetic factors (includes genetic diseases) G Mycorrhizae (symbiotic root colonizing fungi) M Pathogens (disease-causing organisms) P Saprophytes (organisms attacking only dead plant parts) S Level 3 This code further breaks down the level 2 groups. For the biotic agents, the level 3 codes separate major taxonomic groupings of organisms. Arachnids (includes mites) A Bacteria B Fungi F Inorganic chemicals G Insects I Mollicutes (spiroplasmas, mycoplasma-like organisms) M Nematodes N Organic compounds O Radiation-related (includes light and temperature effects) R Vascular Plants P Viruses and viroids V Water-related (includes flooding and drought effects) W The following lists contain the codes for levels 4 and 5. Level 5 codes are presented under the appropriate level 4 groups. Level 4 This three-letter code is primarily used to indicate the taxonomic order of the arthropods and other taxonomic levels for the remaining biotic agents. Level 5 The final three-letter code is used to indicates either the taxonomic class or family of biotic organisms. Acarina (Mites) ACA Eriophyidae (Gall and blister mites) ERI Tenuipalidae (False spider mites) TNU Tetranychidae (Spider mites) TTR Tydeidae TYD Aerial exposure (to abiotic agents) AIR Angiosperms (Flowering plants) ANG Dicotyledons (dicots) DIC Ascomycetes ASC Discomycetes (cup fungi) DIS Hemiascomycetes HEM Loculoascomycetes (Bitunicate ascomycetes) LOC Pyrenomycetes (Unitunicate perithecial ascomycetes) PYM Basidiomycetes BAS Agaricales (Agarics or gilled mushrooms) AGA Aphyllophorales APY Dacrymycetales DAC Exobasidiales EXO Polyporales (Polypores) POL Sclerodermatales (Puffballs and earthballs) SCL Septobasidiales SEP Tremellales (Jelly fungi) TRE Uredinales (Rusts) URE Coleoptera (Beetles) COL Anobiidae (Drugstore beetles) ANO Anthicidae (Antlike flower beetles) ANT Bostrichidae (Branch and twig borers) BOS Brentidae (Straight-snouted weevils) BRN Buprestidae (Metallic wood-boring beetles) BUP Byturidae (Fruitworm beetles) BYT Carabidae (Ground beetles) CRB Cerambycidae (Long-horned beetles) CER Chrysomelidae (Leaf beetles) CHR Cleridae (Checkered beetles) CLE Coccinellidae (Ladybird beetles) CNL Cucujidae (Flat bark beetles) CCJ Curculionidae (Snout beetles) CUR Dermestidae (Dermestid or skin beetles) DMS Elateridae ELA Eucnemidae EUC Histeridae (Hister beetles) HST Limnichidae (Minute marsh-loving beetles) LIM Lucanidae (Stag beetles) LUC Lyctidae (Powder-post beetles) LYC Melandryidae (False darkling beetles) MEL Nitidulidae (Sap beetles) NIT Ptinidae (Spider beetles) PTN Scarabaeidae (Scarab beetles) SCA Scolytidae (Bark or engraver beetles, ambrosia or timber beetles) SCO Tenebrionidae (Darkling beetles) TNB Dermaptera (Earwigs) DER Deuteromycetes (Imperfect fungi) DEU Coelomycetes (Pycnidial and acervular fungi) COE Hyphomycetes (Conidial fungi) HYP Diptera (Flies) DIP Agromyzidae (Leafminer flies) AGR Cecidomyiidae (Gall midges or gall gnats) CEC Drosophilidae (Pomace or small fruit flies) DRO Lauxaniidae LAU Scenopinidae (Window flies) SCE Syrphidae (Syrphid or flower flies) SYR Tephritidae (Fruit flies) TEP Therevidae (Stiletto flies) THE Dorylaimida DOR Trichodoridae TRI Embioptera (Webspinners) EMB Oligotomidae OLI Gram Negative Rod-Shaped Bacteria GNR Enterobacteriaceae ENT Hemiptera (Bugs) HEM Aradidae (Flat or fungus bugs) ARA Leptopodidae (Spiny shore bugs) LET Lygaeidae (Seed bugs) LYG Miridae (Plant or leaf bugs) MIR Pentatomidae (Stink bugs) PEN Tingidae (Lace bugs) TIN Homoptera (Aphids, scales, and allies) HOM Aleyrodidae (Whiteflies) ALE Aphididae (Aphids) APH Asterolecaniidae (Pit scales) AST Cercopidae (Spittlebugs or froghoppers) CCP Cerococcidae CCC Cicadellidae (Leafhoppers) CIC Cicadidae (Cicadas) CAD Coccidae (Soft, wax, and turtle scales) COC Diaspididae (Armored scales) DIA Eriococcidae (Mealybugs) ECC Kermidae (Gall-like coccids) KER Margarodidae (Giant coccids) MRG Membracidae (Treehoppers) MEM Phylloxeridae (Phylloxerans) PLL Pseudococcidae (Mealybugs) PSE Psyllidae PSL Hymenoptera (Bees, wasps, and allies) HYM Braconidae (Braconids) BRA Cimbicidae CIM Cynipidae (Gall wasps) CYN Diprionidae DIP Encyrtidae (Encyrtid wasps) ENC Eupelmidae EUP Eurytomidae (Seed chalcids) EUR Formicidae (Ants) FOR Ichneumonidae (Ichneumons) ICH Pteromalidae (Pteromalid wasps) PTE Siricidae (Horntails) SIR Tenthredinidae (Common sawflies) TEN Xyelidae (Xyleid sawflies) XYE Xylocopidae (Carpenter bees) XYL Isoptera (Termites) ISO Hodotermitidae (Dampwood termites) HOD Kalotermitidae (Drywood, dampwood, and powderpost termites) KAL Lepidoptera (Butterflies and moths) LEP Agonoxenidae AGO Arctiidae (Tiger and footman moths) ARC Blastobasidae (Blastobasid moths) BLA Bucculatrigidae BUC Carposinidae (Carposinid moths) CAR Cochylidae (Cochylid moths) CCH Coleophoridae (Casebearers) COL Cosmopterygidae (Cosmopterygid moths) COS Cossidae (Carpenter and leopard moths) CSS Dioptidae (Oakworms) DIO Eriocraniidae (Eriocraniid moths) ERO Gelechiidae (Gelechiid moths) GEL Geometridae (Measuringworms, geometers) GEO Gracilariidae (Leaf blotch miners) GRA Heliozelidae (Shield bearers) HEL Hesperiidae (Skippers) HES Incurvariidae (Yucca and fairy moths) INC Lasiocampidae (Tent caterpillars and lappet moths) LAS Liparidae LIP Lycaenidae (Hairstreaks, coppers, blues, metalmarks, harvesters) LCN Lymantriidae (Tussock moths) LYM Lyonetiidae (Lyonetiid moths) LYO Nepticulidae (Minute leaf miners) NEP Noctuidae (Millers, Owlet moths, Cutworms, Armyworms) NOC Nolidae NOL Notodontidae (Prominents) NOT Nymphalidae (Brush-footed butterflies) NYM Oecophoridae (Oecophorid moths) OEC Olethreutidae OLE Phycitidae PHY Plutellidae (Diamondback moths) PLU Psychidae (Bagworm moths) PSY Pyralidae (Snout and grass moths) PYR Saturniidae (Giant silkworm moths) SAT Sesiidae (Clear-winged moths) SES Sphingidae (Sphinx or hawk moths) SPH Stenomidae STE Tineidae (Clothes moths) TND Tischeriidae (Tischeriid moths) TIS Tortricidae (Tortricid moths) TOR Microcoryphia (Bristletails) MIC Meinertellidae (Rock bristletails) MEI Myxomycetes (Slime molds) MYX Oomycetes (Water molds) OOM Peronosporales PER Orthoptera (Grasshoppers and allies) ORT Acrididae (Short-horned grasshoppers) ACR Gryllidae GRY Tettigoniidae TET Phasmatodea (Walking sticks and timemas) PHS Timematidae (Timemas) TIM Psocoptera (Psocids or Barklice and Booklice) PSO Lachesillidae (Fateful barklice) LCH Mesopsocidae (Middle barklice) MES Peripsocidae PRI Philotarsidae PHI Pseudocaeciliidae PSD Psocidae (Common barklice) PSC Soil exposure (to abiotic agents) SOI Thysanoptera (Thrips) THY Aeolothripidae (Broad-winged or banded thrips) AEO Phlaeothripidae (Tubular thrips) PHT Thripidae (Common thrips) THR Tylenchida TYL Criconematidae CRI Heteroderidae (Root-knot nematodes) HET ADDITIONAL NOTES Agent genus & species notations Some of the insect records included in CODA are not completely identified. Determining species and even genera of some groups of organisms is time-consuming and may require a specialist in the taxonomy of a given group. In some cases, the insects may actually represent species that have not yet been described and named. We have decided to retain many of these incomplete or tentative identifications in the current release of CODA. These records are generally marked with the following notations: - (?) following a genus or species name indicates a tentative identification. - nr (short for near) is used to indicate that a specimen is similar to a described genus or species. - nov. sp. in the species field indicates that the agent is a new, undescribed species. Agent family field for fungal species Although the taxonomic family is a fairly stable and useful grouping for most vascular plants, insects, and some other groups, it is less useful in fungal taxonomy. While some groups of fungi can be grouped into coherent families, this is not the case for many other fungi. Where the family is not a useful grouping, other taxonomic groups, such as the class, may be listed under the "Family" field in the agent window. When the group listed in the "Family" field is other than a taxonomic family, it is enclosed in parentheses.