Covers user guide.cdr
Contents
1. Quality of match 0 0459 EF 0 0862 Recommended value in each category Figure 11 Result from comparison between observations and predictions 12 SUMMARY D ge NS ei Install the software Configure system settings before using the program Check validity of data for analysis by DJPheno Specify the biological information to search E g from March 1 to 5 of the captures of a generation or from 5 to 50 of the captures Create the file corresponding to the biological information searched Check for error messages if any and take the necessary steps to correct the situation Estimate the base temperature using the files created and various methods of calculation consult the literature and decide on a base temperature and the best method of calculation Compare observations against predictions for the biological information and the previously determined base temperature and method of calculation Check that the results are plausible LIST OF ERROR MESSAGES AND THEIR MEANING The start date does not exist in weather file means that no weather data exists for the start date given The weather file cannot be found The weather file for the selected site cannot be found in the database You must add the missing file or select a site near to the site being studied and for which there is a weather file in the database 13 APPENDIX COMPARATIVE STATISTICS Reference Ya2. any short date format but be sure that DJPheno is closed before changing this setting It is also recommended that Microsoft Excel remain closed while DJPheno is in USE WEATHER STATIONS Properties Base temperatures Biological file format Path to database C Program Files D Phena stations mdb ie Station Folder acadie anselm arthab arunde assomp auteni beauce beaupo bradfo charic comptn Dente mu k L Acadie S EA nselme Arthabaska Arundel L Assomption Auteuil Beauceville Beauport Bradford Chateau Richer Compton Denheld enn rmh li lk L Acadie Arthabaska Arundel L Assomption Auteuil Beauport Bradford Chateau Richer Compton Denheld ra1 k iI ilk hM ereal uat uebe M s erealliuat L uebe M ereal uat uebe Ms erealluat L uebe M ereal uat uebe hM ereal uat maria GA ves sornementale M Sh ereal uat uebe h ereal uat Ontaria T kA kd ed es IaM 12 Cancel Figure 1 Properties in the File menu To view or edit the list of weather stations DJPheno can use select File then Properties Figure 1 On the Observation sites and weather stations tab you provide the path to the file containing the weather data You can add modify or delete weather stations W
3. 90 Agriculture and Agriculture et Agri Food Canada Agroalimentaire Canada DJPheno Degree days estimator to predict phenological stages Version 2 6 ivi Canada DJPheno Degree days estimator to predict phenological stages Version 2 6 Dominique Plouffe B Sc Ga tan Bourgeois Ph D Genevieve Gay B Sc Nathalie Beaudry D E C Agriculture and Agri Food Canada CRDH Saint Jean sur Richelieu QC Cat No A54 9 2004 5E PDF ISBN 0 662 38852 6 Cat No A54 9 2004 5E HTML ISBN 0 662 38853 4 Her Majesty the Queen in Right of Canada 2004 Acknowledgement The authors wish to sincerely thank the following people for their work and their implication in the development of the DJPheno software Helene Laurence Danielle Choquette Anne Marie Fortier Yves Malenfant and Marc Ecuyer DJPheno The Degree Days Estimator to Predict Phenological Stages DJPheno was developed by the bioclimatology and modelling team at the Horticulture Research and Development Centre of Agriculture and Agri Food Canada This software is used to determine the base temperature of a living organism for the purpose of modelling its development in relation to temperature The base temperature corresponds with the minimum temperature at which the organism in question develops The software also calculates the number of degree days required for certain biological processes to happen in the life of the organism plant or insect TAB
4. LE OF CONTENTS INSTALLATION eue 3 SYSTEM CONFIGURATION soanen e dagen 3 WEATHER SIATIONS a ea aaa 4 CREATING WEATHER HEE iieri de adv de eod E S 5 USING DJPHENO nhers A a 6 BIOLOGICAL DATA FILE S A 6 ANALYZING THE BIOLOGICAL DATA crcire a a 8 A ESEN 9 ESTIMATING THE BASE 10 COMPARING OBSERVATIONS AGAINST 11 Ille HO 13 LIST OF ERROR MESSAGES AND THEIR MEANING 13 APPENDIX COMPARATIVE 14 INSTALLATION To install DJPheno double click Setup exe The first time you open the software you may have a message indicating that the weather stations database cannot be found Click OK and select your database named Stations mdb which will be in the same folder as the program Also all meteorological data files must be in the same folder Note that you can select the language English or French in the File Fichier menu SYSTEM CONFIGURATION Before you use DJPheno you must configure a few items in your Windows operating system In the Start menu select Settings Control Panel Regional and Language Options Regional Options tab Customize button and Numbers tab Put a period next to Decimal symbol and a comma next to List separator On the Date tab you can select
5. biological event against its forecasted values To do so select File Open and Data file for processing Next select Compare observations against predictions In the dialogue box that appears specify the base temperature and select one of the six methods for calculating degree days If you want to obtain the average degree days required for the biological event and statistical information on the calculation method select Mean of Degree days If you want the predicted date when 11 number of degree days indicated is reached select DD and enter a value in related field Statistical results are calculated and shown on this form Details on these Statistics are provided at the end of this document Appendix Comparative Statistics Comparison 01 03 g n ration 5 Number of observations 2 Prediction calculations Base temperature E E Method Single sine Calculate Threshold for determining prediction dates f Use the mean of degree days for all observations Mean 263 4722 EE Diff EI pred A dif Squares of diff Farnham 1377 05 18 1377 05 25 Franklin 1377 05 17 1377 05 22 Frelighsburg 1377 05 18 1377 05 23 Hemmingford 1977 05 17 1977 05 24 Farnham 1975 05 31 1378 05 31 Magnitude of difference Probability of significant difference of absolute diff Paired t 0 2855 Sum of squares of diff MAE Direction of difference RMSE C Sum of differences RAMSE
6. ep Next select Estimate base temperatures In the dialogue box that appears select one of the six methods for calculating degree days single average and single sine are used most often one statistical criteria see Comparative Statistics at the end of this document RMSE Root Mean Square Error is recommended and specify the range of temperatures lowest and highest temperatures likely to contain the best base estimate A list of the 15 best base temperatures is then shown in a window and you can view a graph showing the chosen statistical criteria in relation to the various temperatures It is recommended that the results obtained using DJPheno be combined with information taken from the literature Theoretically the lowest RMSE would correspond with the best base temperature but this does not always coincide with what can be found in the literature Rather the base temperature is at the point where the RMSE curve starts to climb significantly In addition the Mean column gives the average degree days for the specified biological event at the indicated base temperature 10 L 1 1 L B Base temperatures Figure 10 Result from estimating base temperatures using RMSE as statistical criteria COMPARING OBSERVATIONS AGAINST PREDICTIONS Once you have determined the base temperature you can compare the observed values of a
7. hen adding a station be sure to provide a code up to 6 characters the full name of the site and the folder containing the weather observations Figure 2 If the site of your observations matches a weather station use the first option and provide the path by clicking the button to the right If your site does not match a station use the second option Use a different weather station and select the appropriate weather station in the drop down list 7 Add a weather station Code Bite Station Use the observation site as weather station Folder D t Use a different weather station Station ck Cancel Figure 2 Menu for adding a weather station CREATING A WEATHER FILE 2 3 4 5 7 8 E E City Province Code Latitude Longitude Altitude m Ciuebec 016294 4 000 1 3833 fu Year Month Day temp Mintemp Total rainfall 2004 1 1 2 1 13 8 0 2004 1 2 5 8 17 1 2004 1 J 11 5 20 0 2004 1 4 11 8 20 9 0 2004 1 5 5 1 14 4 0 Figure 3 Example of a weather file must be the site code in lowercase letters plus the year e g quebec2004 xls This file is then saved in a folder e g Quebec within the selected weather folder The content of the first three rows of the Excel file is shown above You can leave the identification code latitude longitude and elevation cells empty Six columns of data are required after that year month day maximum tempe
8. ile menu To analyze a file of observation data select File Open and Biological data file Navigate to the desired folder and click Open The available analysis options will then be shown Figure 8 You first choose the biological event to be forecasted under Observations You can preview the data by selecting the appropriate line under Site Next select a Prediction type For example if your study concerns phenology stages select Observed value and enter the stage code next to Prediction The default Start date for observations is March 1 You can change this date by clicking its button You can choose between a Specific date and Observation value or percentage The date is shown as day month if the regional setting is DD MM YYYY and as month day if the setting is YYYY MM DD Once you have made your selections click Create data file Note that the results are based on a linear interpolation among the events listed in the database file 44 Biological data Car 98 xls Observations g n ration n rationz z Compton Compton 1332 05 11 1332 05 18 1332 05 25 1992 06 01 1992 06 05 1992 06 15 1992 06 22 Start date Cumulative percentage it Cumulative value Prediction g n ration Observed value Figure 8 A biological data file before analysis If you get an error message open the Error message log which is in the same folder as the DJPheno program files The log file will
9. indicate where weather data is missing and where there are errors in the file to be analyzed See List of Error Messages and Their Meaning DATA FILE FOR PROCESSING Once DJPheno has analyzed the Biological data files for the selected biological events it produces a Data file for processing in Excel format xls This file contains the numbered observations the start and end dates of the calculations and the corresponding weather file name Figure 9 Using the data in this file you can estimate base temperatures or compare the model s forecast against data observed in field C D F G H From 01 03 day month ta g n ration 245 QObseration Month Start Day Start Month End Day End Weather File 26 MoMeteoQuat Quebeci Comptonicamptni 993 xL 5 17 M MeteoQuot Quebeci Comptontcomptn1 994 xL S 16 MoMeteoQuat Quebeci Comptontcomptn1995 xL S 18 Mo MeteoQuot Quebeci Comptontcomptn1 996 xL S 20 MoMeteoQuat Quebeci Comptonicamptni 99 x 5 30 McMeteoQuot Quebeci Comptonicamptn1 99s ALS 2 3 4 5 b ri B g Dm 0 to h OI CO CO CO CO C 07 0j 10 Figure 9 Example of a data file for processing ESTIMATING THE BASE TEMPERATURE This allows you to determine the minimum temperature at which an organism can develop To use DJPheno to obtain an estimated temperature select File Open and Data file for Processing which uses the file created in the previous st
10. mns For example you may wish to have an observation column for each generation of an insect These additional columns may have empty cells should there be no corresponding observation on the Julian day indicated You must also indicate the upper threshold temperature temperature at which development stops in File Properties and on the Base temperatures tab The default setting is 40 C When available it is recommended to use published developmental optimum temperature of the studied organism Before using DJPheno it is important to ensure the data is valid For example when studying an insect s development we suggest that you view graphs of population dynamics by site and year to see if the data properly represents the cycles and the generations required to build a model in line with reality The two following graphs show what is and is not acceptable Figure 5 Figure 6 Coding moth captured at Dunham in 1998 45 40 Jb 3t 25 20 15 1 of captures Representation of acceptable data insects Coding moth captures at St Joseph in 1998 1 2 i 1 c 08 Sel OO 43 A dw dh E X J i 0 160 170 180 190 200 Julian day Representation of unacceptable data insufficient number of insects captured ANALYZING THE BIOLOGICAL DATA DJPheno mI View Window Help 1 Properties Data File for Processing Language Exit Figure 7 Open in F
11. ng et al 2000 Statistical methods for evaluating a crop nitrogen simulation model N ABLE Agric Systems 64 37 53 Where vi are the observation dates are the forecasted dates n is the number of observation dates Y is the average of the observation dates 1 Sum of difference D Y vi xi 2 Sum of absolute difference Dabs vi Xi 3 Sum of squares of difference Dsqr Yi Xi 4 Mean error D n 5 Mean absolute error MAE Dabs n 6 Root mean square error RMSE 7 Forecasting efficiency Note similar to R in regression analysis EF 1 Dsqr S vi Y 14 8 Modified forecasting efficiency EF 1 Dabs Y vi Y 9 Coefficient error absolute or Relative mean absolute error C RMAE MAE Y ADDITIONAL STATISTICS FROM STICS Reference Brisson N M Bruno D Ripoche et al 1998 STICS A generic model for the simulation of crops and their water and nitrogen balances Theory and parameterization applied to wheat and corn Agronomie 18 311 346 10 Relative mean error E Y 11 Relative root mean square error RRMSE RMSE Y 12 Paired t bi Ef E n 1 Jn 15
12. rature of the day C minimum The weather files you build must be in Microsoft Excel format xls The file name temperature of the day C and precipitation mm USING DJPHENO BIOLOGICAL DATA FILES The biological data files contain observations on the evolution of the plants or insects These files must also be in Microsoft Excel format xls and follow the format shown on figure 4 Site Year Producer Plot Variety Julian Day Observation 1 FRANKM 1909 FRANK F VARI 109 0 FRANKM 1909 E VARI 115 0 FRANKM 18988 VARI 122 0 FRANKM 1909 F1 YAR 129 2 FRANKM 18988 FRANK F1 VARI 155 100 Figure 4 Example of a biological data file The first row contains the column header information You can create a template by selecting File Properties Biological file format tab and Create a template file button The columns named Site Year Julian Day and Observation must contain data before the program will do an analysis The Producer Plot and Variety columns may remain empty It is the first 4 columns Site Year Producer and Plot that identify a data set If there are several varieties you must identify the plots by recording the name of the variety in the Plot column To obtain the correct codes of the sites associated with the weather files click File Properties and the Weather stations tab Note that the year must be indicated with four digits You can also add additional observation colu
Download Pdf Manuals
Related Search