Comprehensive information on Nitrogen Use Efficiency for cereal crop production, N use Efficiency  Research Methods in Agriculture

Last update: March 30, 2021

Research Methods in Plant and Soil Sciences
SOIL 5112,
spring, odd years
Class Survey Results, 2019

ASK the Right Questions, Right Order, Right Product Deliver a Product
Puzzle Research Methods 2013
Stay focused  
Unrelenting effort  

Research Ethics, $700 for the Chimaltenango Women's Clinic, or one Brain Cancer Surgery?
Guatemala Women's Clinic 
(OSU Global WarmingNASA, Scientific Consensus

Anthropegenic (pollutants originating from human activity)
Relationship between mean square errors and wheat grain yields in long-term experiments

LIVE SITE:  Atmospheric CO2

NASA Long Term Soil Science Fertilizer Experiments

Jorge Hirsch (2005, H-index)
  How to improve your H-index
Academic Calendar Spring 2021 Finals Week, May 3-7: 
Graduate Commencement, Friday May 7
CLASS FINAL, 2021 (Friday April 29, 8:00 am)
( 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

Surface Response Models (Regression Page)
Statistics Care Package (.pdf many articles)
Student Name  2021 SOIL 5112  
Abit, Ma Gweneth M.
Akin, Samuel G.
Alserae, Hussein A.
Carpenter, Jonathan T.
Cox, Connor R.
Gerhardt, Alayna L.
Harris, Stephen C.
Hassani, Kianoosh
Lovewell, Hunter R.
Monteza, Reynilda M.
Ogden, Grace K.
Singh, Ravinder
Terry, Keren E.
Thomas, Matthew O.
Tucker, Abigail M.
Zander, Anna D.
Monthly Activity Routine, Monthly Activity, By Day Records,

 Experiment 502 data (to 2018)

 Experiment 502 plot plan 

 Wheat Growth Stages

Experiment 502, looking east
 Looking Back
OFF Campus:  You will need to go to  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.

  1. Use the following LINK

SED = square root (2*MSE/reps)   = square root (2*s2/reps)

LSD = t,dfe,alpha 0.05 *SED

T Table

OFT-Misused Mean Separation Procedures
"Good Researchers aren't characterized by being smart, but by those who ask the right questions"
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  Borlaug-2)
Academic butterflies

Philosophical understanding of what we are doing

Professor Robert A. OlsonRobert L. Westerman
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 long-term experiments. J. Plant Nutr.  Taylor & Francis

Swallow, Willima H.  1984. Those overworked and oft-misused mean separation procedures - Duncan's, LSD, etc.  American Phytopathological Society. October, 919-921.

Frozen versus Non-Frozen Sample Preparation for Plant Tissue Phosphorus Analysis. Commun. Soil Sci. Plant Anal. 20:197-211.

Emergence of Corn as Affected by Source and Rate of Solution Fertilizers Applied with the Seed. J. Fert. Issues. 3:18-24. (PDF)

Economic and Agronomic Impacts of Varied Philosophies of Soil Testing.  1982. Agron J. 74:492-499.

Washington Post: Too much of too little (November 2013)

Independence of Biological Processes in Agriculture 2019

CNN 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 Non-estimatable 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.
2.  Treatment and environmental effects are additive.
** (Link, W.G. Cochran, 1947) **

Relationship between mean square errors and wheat grain yields in long-term 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 CIMMYT, Dr. Borlaug's Wall  THE WALL, Dr. Borlaug     CIMMYT
T_TableMean 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 * *



HOMEWORK #1 Calorie consumption) ABSTRACT, ASA

a. compute the F-Test 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 "by-site"?

b. treatment means (by year and combined) Does this change your conclusions (use the treatment structure) given for 502

What is a salient question that has not been answered in your scientific discipline?  Please cite relevant literature documenting the need

Great Pacific Garbage Patch 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

Eradicate Plastic - join the fight against single-use plastics

Experiment 502 (data) 

Data for Class (2/21/2019)

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)?

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;
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 edit-assemble and run a linear-plateau model (non-linear 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, by-year, 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/non-orthogonal contrasts, over lapping of sums of squares

Proc iml and interaction contrasts

8. ( start by going over the treatment structure )
Contrast EXAMPLE ( Eva )  (PLOT PLANS)

9. Covariance, Autocorrelation

By-Plant Corn Studies (go to by-plant studies) 

11. Cate-Nelson Procedure, Linear Plateau (middle of entry page)
Link to

Cate-Nelson SSSAJ 35: 658:661

Best example we have is BRUNO/MG, NDVI data  (combined program) (as txt file)
what is the Critical Level

Linear-Linear (bottom of Regression Page)

Linear Plateau (Dennis Wallin)

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

Stillwater 222, Temperature, Rainfall, 1969-2016  Lahoma 502, 1993-2016

16. CV over time (pdf article) best time to treat variability abstract

ADVANCED:  Output treatment means and output "statistics"

Grain yields over time Experiment 502  Experimental Error, with time, Experiment 502 abstract

As usable energy is irretrievably lost, disorganization, randomness and chaos increase (, 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, PUE

"One shot to the head, or 5 in the chest and bleed to deathTime we all do not have

Accounting for all sources of "error" (rep*trt*year is the error term)

START: Finishing writing, importance, skills

suggests indicates tended 
suggested indicated tended to show
showed documented provided
revealed provided illustrated
quantified evidenced illuminated
communicated estimated proved 

TEXT from SOIL 5813 Book 
Class Publications (1999-2017)
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

Output, Log, and Editor Screens (how are they used)
Error messages, Log messages

creating data sets (excel)
 (see program below on combining sites)
 (cut and paste data) 
  to excell CTL-alt-V (will paste your line text into columns)

data set structure
character variables, use of $  ( input rep trt loc $ )
missing data (use GLM)
rep-trt in the same cell (101, 102, 103)


Physical Design, Plot Plans

Experiment 502, looking east Experiment 222, Stillwater, OK, Long-term-Experiment Magruder Plots, 2017

Experiment 502, Lahoma, Oklahoma Experiment 222, Plot Plan Magruder Plots, Plot Plan

RCBD vs CRD, and Contrasts (link goes to RCBD and CRD examples)

Checklist for Troubleshooting Non-estimatable 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. By-Plant Corn Studies

Collecting Added Data:  When is this useful? 
Why collect Added Data?
Who is the expert on your particular study?

Discussion (Testing) (Forage N Uptake/Calibration, excel file), go to Sheet 3

Univariate, Testing for a Normal Distribution

              Jana Disease Data
              New Algorithm 2007

8. Applied Statistical Procedures
       -regression versus ANOVA
       -Cate-Nelson and Linear-Plateau

Mean Separation: Calculation of the SED

SED = square root (2*MSE/reps)   = square root (2*s2/reps)

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 Long-Term Soil Fertility Experiments.  Agron J. 85:159-167)

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)

“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)

2011 Final Exam





Soil Plant Nutrient Cycling and Environmental Quality, Soil 5813
Soil Plant Nutrient Cycling and Environmental Quality

Precision Agriculture
Precision Agriculture

Soil Nutrient Management
Soil Nutrient Management