Research Methods in Plant and Soil Sciences


(Global
Warming)
NASA, Scientific
Consensus LIVE SITE: Atmospheric CO2 Jorge Hirsch (2005, Hindex) 

Academic Calendar Spring 2019 Finals, May610: Graduation Friday May 10  
Last update: January 17, 2019 

SAS Programs (wide range,
includes Regression) 

Statistics Care Package (.pdf many articles)  


Routine, Monthly Activity, By Day Records, Experiment 502 data (to 2018) Experiment 502 plot plan Wheat Growth Stages Looking Back 

FINAL 2019 Spring 7:30am Room 401 
OFF Campus: You will need to go to
it.okstate.edu. You can download SAS 9.4 from the software
distribution center. Use your OKSTATE email and password. Depending on
your operating system (32 or 64 bit) download the appropriate version. VIRTUAL SAS


SED =
square root (2*MSE/reps) = square root
(2*s^{2}/reps) LSD = t,dfe,alpha 0.05 *SED 
Suggestions. fill our work order on http://pss.okstate.edu/forms/passitworkorder You can also download and install the software yourself from the Software Distribution Center website at https://app.it.okstate.edu/sdc/. You will also get new license files from Software Distribution Center.  
Lecture Tuesday/Thursday 8:00 am, Ag Hall 401 
"Good Researchers aren't characterized by being smart, but by those who ask the right questions"  
Class Goal: Identify problem, formulate hypothesis, implement treatment structure/experiment and generate observations that prove or disprove hypothesis. 
When is Research in a specific
field justified? The applied versus basic quagmire. Basic Research (defined) Applied Research (defined) (Borlaug) 

T Table F Computation Duncans Table 5% Duncans Table 1% Contrast Coefficients Checklist for Troubleshooting Nonestimatable Contrasts 
Assumptions of analysis of
variance
1.
Experimental error is random independent and normally distributed about a
zero mean with a
common variance. 

Ian: Your scientists were so preoccupied with whether or not they could, they didn’t stop to think if they should. Jurassic Park  THE WALL, Dr. Borlaug  
Mean Separation: Calculation of the SED 
Experimental Method should
attempt to remove all sources of variability other than the effects being
evaluated within the treatment structure. (Everything other than the variables being evaluated should be held constant) PROC PRINT: "Hello SAS, What do you think I sent you" 

2019 Reading Swallow, Willima H. 1984. Those overworked and oftmisused mean separation procedures  Duncan's, LSD, etc. American Phytopathological Society. October, 919921. Relationship between Mean Square Errors and Wheat Grain Yields in Longterm Experiments. J. Plant Nutr. Washington Post: Too much of too little (November 2013) Frozen versus NonFrozen Sample Preparation for Plant Tissue Phosphorus Analysis. Commun. Soil Sci. Plant Anal. 20:197211. Emergence of Corn as Affected by Source and Rate of Solution Fertilizers Applied with the Seed. J. Fert. Issues. 3:1824. (PDF) Economic and Agronomic Impacts of Varied Philosophies of Soil Testing. 1982. Agron J. 74:492499. 

HOMEWORK #1
Calorie consumption)
ABSTRACT, ASA HOMEWORK #2 a. compute the FTest for combining any two years (not covered in class), need SAS printout. Run glm analysis by year and over years (combined). 3 sets of treatment means (year 1, year 2, combined) b. treatment means (by year and combined) Does this change your conclusions (use the treatment structure) given for 502 HOMEWORK #3 From experiment 502, generate a linear model of NDVI versus grain yield for 3 different year periods. The SAS printout will do. Provide a written interpretation of what you found, and what the R2 were for each relationship. What percent of the variability in y (yield) was explained by x (NDVI)? HOMEWORK #4 Using the SAS program provided in class, generate a functional surface response model using two random sources of data plotted against a dependent variable that you measured. Example, NDVI, at Feekes 4 and NDVI at Feekes 5, versus grain yield or "buac" in Experiment 502. Homework #5 For the data set included, decipher whether or not the covariate was significant in removing variability in maize grain yield. Output needs to include GLM results, and significant levels of main effects using the appropriate error term to test the effect. Tillage is "split" in this trial, so you need to have 2 error terms. You should also include: 1. treatment means, and standard deviation, 2. least square adjusted means . The Covariate is "preP" or preplant soil test phosphorus. data one; input rep nrate tillage yield preP; cards; 1 0 0 20 16 1 50 0 25 13 1 100 0 29 13 1 150 0 35 14 1 0 1 35 18 1 50 1 35 16 1 100 1 38 11 1 150 1 39 19 2 0 0 20 22 2 50 0 26 23 2 100 0 30 21 2 150 0 32 25 2 0 1 36 19 2 50 1 36 11 2 100 1 37 18 2 150 1 40 16 3 0 0 17 18 3 50 0 22 19 3 100 0 25 28 3 150 0 29 22 3 0 1 29 13 3 50 1 34 25 3 100 1 38 24 3 150 1 40 18 Homework #6 Please editassemble and run a linearplateau model (nonlinear regression) for data of your own, or data from one of your fellow students. Output and data used are required. 



2019
SAS Programs 1. Combining sites (SAS 502 DATA, 2012, 2013, 2014, 2015, 2016) RCBD versus CRD, computing df 2. SAS: 502, 2015 and 2016 data, glm, by site, over sites, means, plots 3. NDVI various Stages versus Yield (2/21 and 2/23, 2017) 4. Exp. 502, byyear, SED example, 2008, 2009, 2010 (kg/ha conv. to bu/ac) 5. Blake Farrow Program (no differences in locations) 6. 502_surface response model (diamond/pyramid shapes) Orthogonal/nonorthogonal contrasts, over lapping of sums of squares 7. Proc iml and interaction contrasts 8. ByPlant Corn Studies (go to byplant studies) 9. Covariance, Autocorrelation 10. Contrast EXAMPLE ( Eva ) (PLOT PLANS) 

11.
When should I block,
How should I block? 12. CateNelson Procedure, Linear Plateau (middle of entry page) best example we have is Melissa, NDVI data (combined program) (as txt file) Linear Plateau (Dennis Wallin) 13. Difference between two independent Regression Equations 14. Stability Analysis CV corn versus CV wheat Weather Patterns, 502 CV over time Combining Experiments Saif 15. Testing for a Normal Distribution 16. Split Plot in Space and Time 

Abstract YIELD GOAL Abstract, PUE "One shot to the head, or 5 in the chest and bleed to death" Time we all do not have 

Accounting for all sources of "error" (rep*trt*year is the error term) START: Finishing writing, importance, skills


TEXT from SOIL 5813 Book  
Spring Semester Academic Calendar  
Can society justify basic research when 33,000 people die each day due to starvation? Who is "society?"  
Combining sites (SAS Program) SAS 502 DATA, 2012, 2013, 2014, 2015, 2016 Environment (Location, Year, Experiment #, Greenhouse, etc.) 1. Homogeneity of error variance? 2. Did conclusions change after sites were combined? (Could I have homogeneity of error variance, and still see different treatment responses at 2 different sites/years?) 3. How to identify outliers (SD about a mean) rules associated with removing outliers
MISC 

Topics: Physical Design, Plot Plans RCBD vs CRD, and Contrasts (link goes to RCBD and CRD examples) Checklist for Troubleshooting Nonestimatable Contrasts 1. The "Experimental Method" (defined) 2. The "Scientific Method" 3. Formulation of hypotheses a. 15 Steps to Good Research (Georgetown) b. Advice on Research and Writing (ASA abstract) 4. ByPlant Corn Studies
Collecting Added Data: When is this useful?
Discussion
(Testing) (Forage N Uptake/Calibration, excel file), go
to Sheet 3
8. Applied Statistical Procedures Mean Separation: Calculation of the SED SED = square root (2*MSE/reps) = square root (2*s^{2}/reps) 

STABILITY  
1.
Sarah Stability
Analysis (Genotype by Environment interactions, plant Breeding) 2. Stability Analysis (excel) (Treatment by environment interactions, N Rate Example) (example for agronomic experiments, Use of Stability Analysis for LongTerm Soil Fertility Experiments. Agron J. 85:159167) 3. Magruder excel file 

2011 Class
Programs 1. Apurba Trial (depth) 2. Sarah, Genotype by Environment Interaction (class sas program) 3. Jeremiah (complete factorial) (class sas program) Discuss treatment 13 vs rest 'contrast' 4. Lecture, 2/15 5. Lecture, 2/17 

Research Methods 2017 (on line, see below)
http://dasnr.adobeconnect.com/soil5112 “Enter as a Guest”, enter your name, click “Enter Room”, Can enter questions/comments in the chat window. 

Mixed vs GLM (popular press) Mixed example, Sulu Mixed EXAMPLE (for 2015 Class) 

FINAL 2015 KEY 
Syllabus 
