Last update: March 30, 2021
Research Methods in Plant and Soil Sciences


Research Ethics, $700 for the Chimaltenango
Women's Clinic, or one Brain Cancer Surgery? 

(OSU Global
Warming)
NASA, Scientific
Consensus Anthropegenic (pollutants originating from human activity) Relationship between mean square errors and wheat grain yields in longterm experiments LIVE SITE: Atmospheric CO2 Jorge Hirsch (2005, Hindex) How to improve your Hindex 

Academic Calendar Spring 2021
Finals Week, May 37: Graduate Commencement, Friday May 7 CLASS FINAL, 2021 (Friday April 29, 8:00 am) 

STUDENT EVALUATIONS (https://online.okstate.edu/) by clicking the link labeled "Course Evaluations 

Assumptions Underlying the Analysis of Variance (Churchill Eisenhart)  
** (Link, W.G. Cochran, 1947) **  
The Arrangement of Field Experiments, R.A. Fisher, 1923  
The Research Problem . . . . Or you try to internalize it in such a way that it really becomes intuitive. Working on the right problem is only part of what it takes to succeed. Perseverance is another essential ingredient." Steven Chu 

Last update: March 30, 2021 

Experiment 502 DATA, Plot Plan  
SAS Programs MANY Regression  
Covariance Surface Response Models (Regression Page) 

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 

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 T Table OFTMisused Mean Separation Procedures 
"Good Researchers aren't characterized by being smart, but by those who ask the right questions"  
Lecture Tuesday/Thursday 8:00 am, Ag Hall 401 

Class Goal: Identify problem, formulate hypothesis, implement treatment structure/experiment and generate observations that prove or disprove X hypothesis 
When is Research in a specific
field justified?
The applied versus basic quagmire. Basic Research (defined) Applied Research (defined) (Borlaug Borlaug2) Academic butterflies Philosophical understanding of what we are doing 


2019 Reading Assignments Use of the impact factor in agriculture. CSA News, Am. Soc. Agron. July issue, Madison, WI Relationship between mean square errors and wheat grain yields in longterm experiments. J. Plant Nutr. Taylor & Francis Swallow, Willima H. 1984. Those overworked and oftmisused mean separation procedures  Duncan's, LSD, etc. American Phytopathological Society. October, 919921. 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. Washington Post: Too much of too little (November 2013) Independence of Biological Processes in Agriculture 2019 Supply of food under threat due to biodiversity loss across the globe: UN report Southern Corn Leaf Blight 

T Table F Computation Contrast Coefficients Duncans Table 5% Duncans Table 1% Checklist for Troubleshooting Nonestimatable Contrasts 
Assumptions of analysis of
variance (Proc Univariate Example) Proc Rank
1.
Experimental error is random, independent and normally distributed about a
zero mean with a
common variance. Relationship between mean square errors and wheat grain yields in longterm experiments. J. Plant Nutr. Taylor & Francis 

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 CIMMYT  
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) Tyler Lynch SAS Program (variability about each treatment mean) outliers 

* * RCBD versus CRD, computing df * * EFFICIENT DESIGN STABILITY ANALYSIS 

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). Do the "combined" treatment means make sense? Or have we removed treatment differences that were present when analyzed "bysite"? b. treatment means (by year and combined) Does this change your conclusions (use the treatment structure) given for 502 HOMEWORK #3 What is a salient question that has not been answered in your scientific discipline? Please cite relevant literature documenting the need Biodegradable Plastics (Mexico)
•300
million tons of plastics manufactured/year
•10
percent recycled
•Great
Pacific garbage patch
•Lignin
plastics (Univ. Minnesota), adding Achilles heel to plastic
manufacturing that soil microbiology can take advantage of and later
degrade
By 2050, there will be more plastic than fish in the world’s oceans Experiment 502 (data) Data for Class (2/21/2019) HOMEWORK #4 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 values were for each relationship. What percent of the variability in y (yield) was explained by x (NDVI)? HOMEWORK #5 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 #5.5 (READ all of the Covariance Page) Homework # 5.6 (Read Churchill Eisenhart Article) Homework # 5.7 (Find a data set that used/employed qualitative data/scores). Run proc univariate to see if the data was normal. Then run Proc Rank to normalize the data. Homework #6 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 #7 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 PROC PRINT: "Hello SAS, What do you think I sent you" 1. Combining sites (SAS 502 DATA, 2012, 2013, 2014, 2015, 2016) 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. ( start by going over the treatment structure ) Contrast EXAMPLE ( Eva ) (PLOT PLANS) 9. Covariance, Autocorrelation 10. ByPlant Corn Studies (go to byplant studies) 

11. CateNelson Procedure, Linear Plateau (middle of entry page) Link to CateNelson SSSAJ 35: 658:661 Best example we have is BRUNO/MG, NDVI data (combined program) (as txt file) what is the Critical Level LinearLinear (bottom of Regression Page) Linear Plateau (Dennis Wallin) 12. When should I block, How should I block? (go to bottom of covariance page) 13. Difference between two independent Regression Equations 14. Stability Analysis 15. Output Means to a New Data SET CV corn versus CV wheat Weather Patterns, 502 Similarities in Environment 16. CV over time (pdf article) best time to treat variability abstract ADVANCED: Output treatment means and output "statistics" abstract As usable energy is irretrievably lost, disorganization, randomness and chaos increase (https://www.allaboutscience.org/secondlawofthermodynamics.htm, visited June 19, 2018). This is aligned with the second law of thermodynamics that embeds knowledge that the total entropy of an isolated system can never decrease over time, where entropy is the degree of disorder or randomness in the system (Costa et al., 2002). 17. Testing for a Normal Distribution 18. 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
Jana Disease Data
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) 

Syllabus 
