Comprehensive information on Nitrogen Use Efficiency for cereal crop production, N use Efficiency  Research Methods in Agriculture
 email: bill.raun@okstate.edu

Research Methods in Plant and Soil Sciences
SOIL 5112

spring, odd years

ASK the Right Questions, Right Order, Right Product Research Methods 2015  (WEB of SCIENCE)
Puzzle Research Methods 2013
Stay focused INTERVIEW
Unrelenting effort DELIVER a PRODUCT

(Global WarmingNASA, Scientific Consensus

LIVE SITE:  Atmospheric CO2


NASA Long Term Soil Science Fertilizer Experiments

Last update: May 08, 2017

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.

Monthly Activity Routine, Monthly Activity, By Day Records,

 Experiment 502 data

 Experiment 502 plot plan 

 Wheat Growth Stages

Experiment 502, looking east
 
 Looking Back


FINAL 2017 Spring
Friday May 5, 7:30 am Room 463
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
  1. Use the following LINK

    https://it.sp.okstate.edu/itservices/4help/entry.aspx?entry=F78H445168

SED = square root (2*MSE/reps)   = square root (2*s2/reps) Suggestions.  fill our work order on http://pss.okstate.edu/forms/pass-it-work-order 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 463
"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 Non-estimatable Contrasts
Assumptions of analysis of variance

1.  Experimental error is random independent and normally distributed about a zero mean with a common variance.
2.  Treatment and environmental effects are additive.

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  
T Table from Steel and TorrieMean 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)
2017 Reading

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

Relationship between Mean Square Errors and Wheat Grain Yields in Long-term Experiments.  J. Plant Nutr.

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

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.


HOMEWORK #1 Calorie consumption) ABSTRACT, ASA

HOMEWORK #2
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)

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 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.




SAS Programs (wide range, includes Regression)


TOOL BOX outline

2017 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, 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



7. 
Proc iml and interaction contrasts

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

9. Covariance, Autocorrelation

10. Contrast EXAMPLE ( Eva )  (PLOT PLANS)
11. When should I block, How should I block?

12. Cate-Nelson 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

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

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 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 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
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)

Topics:

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)

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 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

Mixed vs GLM (popular press)

Mixed example, Sulu

Mixed EXAMPLE (for 2015 Class)

2011 Final Exam

FINAL 2013 KEY

FINAL 2015 KEY

Syllabus

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