data preservation through structured research data...
TRANSCRIPT
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Data Preservation Through Structured ResearchData Management
Nov 2015
Gylling Data Management, Inc.
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"Data" is Available Everywhere
Internet
Popular publications
Research journals
Historical experiments that exist in nearly every research organization
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Is this Useful Data?
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What About "Good Data"?
Well documented data
With a full description of assessment parameters
Includes detailed crop information
Complete trial site information:
Growing conditions (temperature, moisture)
Site, soil description and analyses
Trial maintenance activitiesNov 2015 4
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What About "Good Data"?
Stored electronically in a readily useable standard format
Indexed to quickly find relevant trials
Using standardized terminology
All values included defined units
Can be quickly combined with similar trials
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Study Management Tools
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Study Management Tools
Track progress of studies
Search current and historical trials
Extract information for mapping, etc.
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Trial Management Steps
1. Prepare treatment/entry list
2. Plan required number of replicates by either: best guess, consult statistician, or perform power analysis
3. Create randomization
4. Define plot size
5. Calculate treatment quantity to apply
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Trial Management Steps
6. Establish trial Plant Apply treatments Record site location and other information
7. Make assessments
8. Review and analyze assessments
9. Prepare key graphs
10.Print final reports
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Trial Management Steps
These steps are the same whether using:
Paper
Office/general purpose software
Project management software
ARM
Provides automations, and
Improves efficiency, quality, and consistency
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Overview of Trial ManagementSoftware Requirements
General Requirements:
Structure so trials are entered consistently
Dictionaries to standardize vocabulary
Enter information only once
Resulting Benefits:
Portability across languages and platforms
Automation of routine tasks
Efficiency and accuracy
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Protocol Components no. 1
Clearly-defined treatments with formulation and rate details
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Protocol Components no. 2
Description of required assessments
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Protocol Components no. 3
Define objectives
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Protocol Components no. 4
Study rules that clearly identify key information torecord in eachtrial createdfrom theprotocol
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Support for Typical Experimental Designs
Randomize and appropriately analyze
Completely Random Design
Randomized Complete Block (RCB)
Latin Square
Lattice Designs (Incomplete Block)
Multi-Factor Designs
RCB with Factorial Arrangement of Treatments
Split-Plot
Strip-Block (Criss-Cross)Nov 2015 19
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Randomize Treatments
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Power and Efficiency Planner,Plan Experiments to Have:
A reasonable chance of distinguishing anticipated treatment differences
The optimum number of replicates required to meet objectives
An efficient experimental design and randomization for desired precision
Cost-effective utilization of the available experimental area
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Why is Planning Critical?
Can reduce costs by selecting optimum number of replicates and samples
Expected treatment differences are typically < 10%, and frequently < 5%, so small precision gains can help to:
Distinguish an actual treatment difference(reject null hypothesis H0)
Strengthen evidence of no treatment diff.)(do not reject null hypothesis H0)
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Power and Efficiency Planner
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Power and Efficiency Planner
Help plan experiments that successfully detect expected treatment differences
Available in both protocols and trials so:
Protocol writers can more effectively plan experiments
Trialists can verify whether CV expectations are realistic based on local experience for specified crop(s)
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Power and Efficiency Planner
Calculates "power" based on:
Estimated CV of key assessment (e.g. yield)
Number of replicates
Power = Level of certainty to detect "real" treatment effects (80% or 90%)
Alpha Significance Level (e.g. 5%, 10%)
% Mean Diff = estimated treatment effect, expressed as percentage of overall (grand) mean across treatments of key assessment
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Power and Efficiency Planner
"Lock at" to keep 3-4 columns constant
Calculates table of possible values for "unlocked" columns (e.g. Rep or CV)
Values entered by protocol writer are carried into trials created from protocol, conveying protocol expectations
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Power and Efficiency Planner
Compare effect of significance level on minimum replicates for CV=6% vs. 10%
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Power and Efficiency Planner
Consider impact of Replicates on precision to detect treatment differences
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Click on column heading to sort
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Randomization Quality Review
Goal is to improve experiment precision:
1. Arrange replicates as squares, not strips
2. Equalize treatment distribution
a. Balance average distance from all other treatments
b. Balance "Edge effect" across treatments
3. Randomize all replicates
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Randomization Quality Tab
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Arrange Replicates as Squares not Strips
"Optimum" is smallest surface-to-area ratio
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Equalize Treatment Distribution
"Undesirable" layout of 7 treatments and 5 replicates in Randomized Complete Block:
Trt. 6 in middle 3columns of all reps
Trt. 5 in right 2 colsfor all but one plot
Example from Federer, "Experimental Design" 1955October 2015 32
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Uses "Average Distance of Treatment" Comparison (ADTC)
van Es and van Es, "Spatial Nature of Randomization and Its Effect on the Outcome of Field Experiments", Agronomy Journal, 85:420-428 (1993).
Comparison between treatments 1 and 2 is taken from 5 plots for each treatment.
Measure the plot-to-plot distance for each plot containing treatment 1 to the paired plot within replicate containing treatment 2, for a total of 5 distances.
ADTC for the treatment pair 1-2 is the average of the 5 distances.
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Distances, Treatments 1-2
Average distance = 3 plots = 24 feetfor 8 footwide plots
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Unequal Treatment Distribution
Average distance from 17.9 to 24.6 Ranges from 11.9(T3,T6) to 34(T2,T5) Error variances for treatments may not
be homogeneous
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Unbalanced "Edge effect"
Treatment 1 occurs at edge 4 times,T2 and T3 at edge only 2 times
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Balanced Treatment Distribution and Edge Effect
Average distance from 21.3 to 24.4 Distances range from 18.7 to 27.2 "Edge effect" is balanced
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Randomize All Replicates
This frame displays when a non-randomized replicate is defined in Settings
Select "Randomize All Replicates" tofollow recommended statistical practice
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Post-hoc Power Analysis
Optional descriptive statisticon AOV Means Table report
Lists, for each assessment column, the minimum number of replicates required to statistically separate treatment means based on Treatment P(F) and current significance level
Use for planning future trials
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Post-hoc Power Analysis
In example, LSD can distinguish 25% mean difference (largest existing difference is 18%)
Current AOV Trt P(F)is 0.2979, so use0.30+ significancelevel to separatetreatment means
Need 8+ replicates toreject null hypothesisat 0.05 significance
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Data Protection
Offer a protection that allows only trial owners to change assessment data
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Robust Data Collection Tools
Enter data only once to avoid transcription errors
Employ appropriate range checking for assessed values
Perform data quality checks before leaving trial site (analyze, graph)
Include photographs that illustrate or support measurements & observations
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ARM Tablet Data Collector
Win 8.1 Pro
tablet+
ARM+
specialARMtablet
features
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Tablet Data Collector Features
Tablet Data Entry
Tablet Image Capture
Tablet GPS
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Assessment - Linked Image
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Assessment Review Tools
Analysis of Data
Graph of Variability
Assessment Map (look for site effect)
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Analysis of Data
Duncan’sTest at 5%
Coefficientof Variation
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Variability Graph (Box-Whisker)
Duncan’s Test at 5%
Stableacrossreplicates
Morevariableacrossreplicates
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Assessment Map
Replicate 1valuesdarker(larger)than other replicates
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Site Information no. 1
Trial Location
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Site Information no. 2
People
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Site Information no. 3
Site and Design
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Site Information no. 4
Soil
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Site Information no. 5
Application
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Site Information no. 6
Application Equipment
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Site Information no. 7
Other site informationas appropriate
Trial objectives and conclusions
Crop and pest details
Rainfall and irrigation
Notes and deviations from protocol
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Management Reports
Trial Map
Applications: spray or seeding plan
Plot Signs
Site Information
Labels: container, plot, seed, harvest
Field Tour Sheet
List of Treatments
Statistical analysis of assessmentsNov 2015 57
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Label Reports
Labels for:
Pre-measured quantity ofproducts foreach application,placed in smallcontainers
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Label Reports
Labels for:
Identifying eachplot
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Label Reports
Labels for:
Identifyingpackets of seedto plant
Identifyingsmall sacks ofmaterial harvestedfrom each plot
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Applications Report
Spray/Seeding Plan
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Appl. no. 1
Appl. no. 2
Product quantity to measure for each application rate
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Data Analysis Reports
Choices of different statistical methods:
Assessment Data Summary
AOV Means Table
Factorial AOV
Correlations
Dose-Response
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Study Management Tools
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Study Management Tools
Track progress of studies
Search current and historical trials
Extract information for mapping, etc.
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Multi-Trial Summary
Tools to analyze experiments over locations and years
Easy selection of trials, treatments, and assessments to include
Automated statistical analysis
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ARM Summary Across Trials
Optional ARM add-in to summarizea trial series over locations and years
Summarize selected treatments/entriesacross a wide range of trials
View and arrange summary on a grid
Export the report to Word, Excel, PDF
Data graphs of across-trial means, trial clusters
Export raw data to other statistics software
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Windows Server with SQL Server
ATD Trial Database
ARM clients connect to ATDBackend database eitherdirectly over a local network,or remotely over VPN
Authorized ARM clientsexport trials to SQL ServerATD Backend database thatresides on the shared server
ATD Database
Stand-alone PC
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Using ATD with ARM
Authorized ARM users export trialsto ATD database using “DatabaseExport” button on ARM toolbar
All ARM users who install the ATDconnection can import trials fromATD using “Database Import” toselect 1 or more trials to importfrom Backend database (interfaceis similar to ARM study list)
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Using ATD with ARM
ARM trials imported from ATDBackend database can be usedin ARM like any standard trial:reviewing, graphing, and analyzing assessment data, or printing reports
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Using ATD with ST
ST criteria/query selection screen connects directly to ATD
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Using ATD with ST
ST is the query and multi-trial summary interface for ATD.
Select one or more fieldentries from drop-downlists showing unique fieldentries in ATD for thecurrent ARM entry field.
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Software Must Always “Grow”
As research methods and objectives change and improve, software must also adapt to support those new research objectives and methods.
“Unchanging” software:
Becomes less useful each year.
Can be costly by “losing” (not supporting) information gathered with new technology.
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