---
title: "Additional sources of agricultural data"
author: "Kevin Wright"
date: "`r Sys.Date()`"
output:
  pdf_document: default
  html_document:
    highlight: tango
vignette: |
  % \VignetteIndexEntry{Additional agricultural data} 
  % \VignetteEncoding{UTF-8} 
  % \VignetteEngine{knitr::rmarkdown}
---

# Books

### Die Landwirtschaftlichen Versuchs-Stations
http://catalog.hathitrust.org/Record/000549685

Full view of research station reports 1859-1920. In German.


### S. J. Welham et al. (2015). _Statistical Methods In Biology_.
The online-supplements contain many small datasets for the examples and exercises.


### D. F. Andrews and A. M. Herzberg (1985). _Data_. 
http://www.stat.duke.edu/courses/Spring01/sta114/data/andrews.html
```
Table 2.1: agridat::darwin.maize 
Table 5.1: agridat::broadbalk.wheat 
Table 6.1: agridat::mercer.wheat.uniformity 
Table 6.2: agridat::wiebe.wheat.uniformity 
Table 58.1: agridat::caribbean.maize
```

### D. Bayisa (2010). _Application of Spatial Mixed Model in Agricultural Field Experiment_.
Master thesis. Department of Statistics, Addis Ababa University.
At least one dataset from wheat, RCB, with field coordinates.
See also http://www.ethstat.org.et/esa_publications.html, Volume 19


### M. N. Das & Narayan C. Giri (1987). _Design and Analysis of Experiments_.

```
31 Wool from 24 ewes, 6 cuttings
116 NPK factorial, 3 years
116 2^5 factorial, 1 rep
117 2^3 factorial, 3 rep
117 3^3 factorial
149 NPK split-plot, xy
150 nitro-variety split-plot
201 variety balanced lattice
279 covariate, yield & plant count
```

### Peter Diggle, Patrick Heagerty, Kung-Yee Liang, Scott Zeger. _Analysis of Longitudinal Data_.
http://faculty.washington.edu/heagerty/Books/AnalysisLongitudinal/datasets.html

Pig weight data is found in SemiPar::pig.weights

Sitka spruce data is found in: geepack::spruce

Milk protein data is found in: nlme::Milk.  A thorough description of this data can be found in Molenberghs & Kenward, /Missing Data in Clinical Studies/, p. 377.  Original source: A. P. Verbyla and B. R. Cullis, Modelling in Repeated Measures Experiments. http://www.jstor.org/stable/2347384 


### Federer, Walt (1955). _Experimental Design_.

```
192 3x3 factorial 
204 3x2 factorial 
236 2x2x2 factorial with confounding 
257 2x3x2 factorial with confounding 
276 split-plot with layout 
285 nested multi-loc (Also problems page 22) 
350 cubic lattice 
420 balanced inc block 
491 Latin square with covariate
```


### Finney 1972. _An Introduction to Statistical Science in Agriculture_.
Not reviewed.


### Galwey, N.W. (2014). _Introduction to Mixed Modelling_, 2nd ed.
http://www.wiley.com/WileyCDA/WileyTitle/productCd-1119945496.html
```
83 agridat::yates.oats
104 doubled-haploid barley
135 wheat/rye competition, heritability
190 chickpea flowering in families
250 canola oil gxe, sowing date, rainfall, oil Si & Walton
290 wheat anoxia, McDonald
291 wool fibers
370 alphalpha design (row-column inc block)
434 hollamby wheat trial, layout
```


### Kwanchai A. Gomez & Gomez (1984). _Statistical Procedures for Agricultural Research_.
Extensive collection of datasets from rice experiments.


### Cyril H. Goulden, _Methods of Statistical Analysis_.
First edition: http://archive.org/details/methodsofstatist031744mbp 
```
18 Uniformity trial: agridat::goulden.barley.uniformity 
153 Split-split plot with factorial sub-plot treatment: agridat::goulden.splitsplit 
194 Incomplete block 
197 Inc block 
205 Latin square 
208 Inc block 255 Covariates in feeding trial: agridat::crampton.pig
```
Second edition: http://krishikosh.egranth.ac.in/handle/1/2034118
```
216 Latin square: agridat::goulden.latin 
423 Control chart with egg weights: agridat::goulden.eggs
```


### Harry Love (1936). _Applications of Statistical Methods to Agricultural Research_.

```
379 MET 4 year, 2 field, 5 block, 5 gen
```

### Kang, Manjit (2003). _Handbook of Formulas and Software for Plant Geneticists and Breeders_


### Kuehl, Robert. _Design of Experiments_, 2nd ed.

```
357 alfalfa quadruple lattice
358 alpha design
488 split-plot sorghum hybrid,density
516 alfalfa rcb, two-year
521 crossover design cattle feedstuff
```


### Erwin LeClerg, Warren Leonard, Andrew Clark (1962). _Field Plot Technique_
Many small datasets.
```
27 uniformity agridat::goulden.barley.uniformity
213 split-plot
234 immer multi-environment
260 lattice pinto-bean
276 triple lattice cotton
280 lattice sugar beet
289 balanced lattice
336 repeated wheat
```


### Thomas M Little & F. Jackson Hills (1978). _Agricultural Experimentation_.

```
79 Latin square 
89 Split-plot 
103 Split-split 
117 Split-block: agridat::little.splitblock 
126 Repeated harvests
```


### Roger Mead, Robert N. Curnow, Anne M. Hasted (2002). _Statistical Methods in Agriculture and Experimental Biology_, 3rd ed.

```
10 weekly milk yields
24 carrot weight
96 cabbage fertilizer
143 intercropping cowpea maize
177 honeybee repellent non-normal
251 cauliflower poisson agridat::mead.cauliflower
273 rhubarb RCB covariate
296 onion density
316 lambs
341 germination
350 germination factorial agridat::mead.germination
352 poppy
359 lamb loglinear agridat::mead.lambs
375 rats
386 intercrop
390 intercrop cowpea maize agridat::mead.cowpeamaize
404 apple characteristics (incomplete)
```


### Roger Mead (1988). _The Design of Experiments_
https://books.google.com/books?id=CaFZPbCllrMC&pg=PA323
```
323 Turnip spacing data
```


### Bernard Ostle (1963). _Statistics in Research_, 2nd ed.
https://archive.org/details/secondeditionsta001000mbp
```
455 2 factors, 1 covariate
458 1 factor, 2 covariates: agridat::crampton.pig
```


### D. D. Paterson (1939). _Statistical Technique in Agricultural Research_.
https://archive.org/details/statisticaltechn031729mbp
```
84 Distribution of purple/white starchy/sweet seeds from 11 ears
190 Sugar cane MET: 2 year, 5 block, 5 variety
199 Tea MET: 3 year, 2^2 factorial fertilizer
206 Grass: 4 rep, 2 gen, 4 cutting treatments
211 Cotton: 4 dates, 3 spacings, 3 irrigation, 2 nitro. agridat::gregory.cotton
```


### Arthur Asquith Rayner (1969). _A First Course In Biometry For Agriculture Students_.

```
19/456. 2x2x4 Factorial, 2 rep
19/466. 2x4 factorial, layout, plot size, kale (from Rothamsted)
19/466. 3x5 factorial, 3 rep, potato
20/494. 3x4 Split-plot with layout
21/505. 2x2x2 Factorial, 5 rep
21/515. 2x2x2x2 Factorial, 3 rep, with layout. (Evaluated, rejected as too variable)
22/537. 2x2x2 factorial, 6 rep, potato
22/537. 2x2x2x2 factorial, 2 rep, wheat, layout
```

### G. W. Snedecor & W. G. Cochran. _Statistical Methods_.


### Robert G. D. Steel & James Hiram Torrie. _Principles and Procedures of Statistics_, 2nd ed.

```
154 Mint plant growth, 2-way + pot + plant
244 Trivariate data
319 Regression with three predictors
384 Split-plot yield
387 Split-plot row spacing
400 Soybean 3 loc
423 Pig weight gain
429 Guinea pig weight gain
434 Soybean lodging
```

### Oliver Schabenberger and Francis J. Pierce. _Contemporary Statistical Models for the Plant and Soil Sciences_.
Many datasets


### Pesticides in the Nation's Streams and Ground Water, 1992-2001
Extensive data for detection of pesticides in water samples.  See Appendix 5 and Appendix 6 of the supporting info.
https://water.usgs.gov/nawqa/pnsp/pubs/circ1291/supporting_info.php


# Journals - Data


### Ag Data Commons
https://data.nal.usda.gov/about-ag-data-commons


### CyVerse Data Commons

http://datacommons.cyverse.org/

http://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated


### CyVerse: Genomes by environment dataset now publicly accessible

http://www.cyverse.org/news/genomes-environment-dataset-now-publicly-accessible

http://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/Carolyn_Lawrence_Dill_G2F_Nov_2016

Very large GxE data here. Currently 2014, but more years planned. Hybrid & inbred phenotype data, weather data, genomic data.  Very nice.


### DataDryad
http://datadryad.org/


### Data In Brief
http://www.sciencedirect.com/science/journal/23523409


### Nature Scientific Data
http://www.nature.com/sdata/


### Open Data Journal for Agricultural Research
http://library.wur.nl/ojs/index.php/odjar/


### Plant Genomics and Phenomics Research Data Repository
http://edal.ipk-gatersleben.de/repos/pgp/


# Journals - Bulletins

### Iowa State Agricultural Research Bulletins
http://lib.dr.iastate.edu/ag_researchbulletins/
```
Vol 26/ 281. Cox: Analysis of Lattice and Triple Lattice.
Page 11: Lattice, 81 hybs, 4 reps 
Page 24: Triple lattice, 81 hybs, 6 reps

Vol 29/347. Homeyer. Punched Card and Calculating Machine Methods for Analyzing 
  Lattice Experiments Including Lattice Squares and the Cubic Lattice.
Page 37: Triple lattice (9 blocks * 9 hybrids) with 6 reps.
Page 60: Simple lattice, 8 blocks * 8 hybrids, 4 reps.
Page 76: Balanced lattice, 25 hybrids 
Page 87: Lattice square with (k+1)/2 reps, 121 hybrids, 6 rep 
Page 109: Lattice square with k+1 reps, 7 blocks * 7 hyb, 8 reps 
Page 126: Cubic lattice, 16 blocks * 4 plots = 64 varieties, 9 reps, cotton

Vol 32/396. Wassom. Bromegrass Uniformity Trial: agridat::wassom.bromegrass.uniformity

Vol 33/424. Heady. Crop Response Surfaces and Economic Optima in 
  Fertilizer agridat::heady.fertilizer

Vol 34/358. Schwab. Research on Irrigation of Corn and Soybeans At Conesville.
Page 257. 2 year, 2 loc, 4 rep, 2 nitro. Stand & yield.  
  Nice graph of soil moisture deficit (fig 9)

Vol. 34/463. Doll. Fertilizer Production Functions for Corn and Oats.
Table 1, 1954 Clarion Loam.  N,P,K.
Table 14, 1955 McPaul Silt Loam.  N,P.
Table 25, 1955 corn.  K,P,N.
Table 31, 1956 oats, K,P,N.  Trends difficult to establish.

Vol 34/472. Pesek. Production Surfaces and Economic Optima For Corn Yields.  
  Same data published in SSA journal?

Vol 34/488. Walker. Application of Game Theory Models to Decisions.

Vol 35/494. North Central Regional Potassium Studies with Alfalfa.
Page 176. Two years, several locs per state, multiple states, multiple fertilizer 
  levels, multiple cuttings. Soil test attributes.
Page 183. Yield and %K.

Vol 35/503. North Central Regional Potassium Studies with Corn.
```


# Papers

**Barrero, Ivan D. et al**. (2013).
A multi-environment trial analysis shows slight grain yield improvement in Texas commercial maize.
Field Crops Research, 149, Pages 167-176.
http://doi.org/10.1016/j.fcr.2013.04.017

Note: This is a large (14500 records), multi-year, multi-location, 10-trait data. Sent a note encouraging the authors to formally publish the data.
Source: http://maizeandgenetics.tamu.edu/CTP/CTP.html


**Cleveland, M.A. and John M. Hickey, Selma Forni** (2012).
A Common Dataset for Genomic Analysis of Livestock Populations.
G3, 2, 429-435.
http://doi.org/10.1534/g3.111.001453

Note: The supplemental information for this paper contains data for 3534 pigs with high-density genotypes (50000 SNPs), and a pedigree including parents and grandparents of the animals.


**Daillant-Spinnler** (1996). Relationships between perceived sensory properties and major preference directions of 12 variaties of apples from the southern hemisphere.
Food Quality and Preference, 7(2), 113-126.
http://dx.doi.org/10.1016/0950-3293(95)00043-7

Note: The data are available in ClustVarLV package.


**Gregory, Crowther & Lambert** (1932). The interrelation of factors controlling the production of cotton under irrigation in the Sudan.
Jour Agric Sci, 22, p. 617.


**Hedrick** (1920).
Twenty years of fertilizers in an apple orchard.
https://books.google.com/books?hl=en&lr=&id=SqlJAAAAMAAJ&oi=fnd&pg=PA446
Note: No significant differences between fertilizer treatments.


**Kayad et al**. (2016).
Assessing the Spatial Variability of Alfalfa Yield Using Satellite Imagery and Ground-Based Data. 
\emph{PLOS One}.
https://doi.org/10.1371/journal.pone.0157166
Supporting information contains yield monitor data for 4 hay harvests on a center-pivot field.


**Roger W. Hexem, Earl O.Heady, Metin Caglar** (1974)
A compendium of experimental data for corn, wheat, cotton and sugar beets grown at selected sites in the western United States and alternative production functions fitted to these data.
Technical report: Center for Agricultural and Rural Development, Iowa State University.
https://babel.hathitrust.org/cgi/pt?id=wu.89031116783;view=1up;seq=3

The technical report provides data from experiments on corn, wheat, cotton & sugar beets, each crop tested at several locations over two years, with a factorial structure on irrigation and nitrogen treatments, with replications.  Three polynomial functions were fit to the data for each location (quadratic, square root, three-halves).


**Kenward, Michael G.** (1987).
A Method for Comparing Profiles of Repeated Measurements.
Applied Statistics, 36, 296-308.

Note: An ante-dependence model is fit to repeated measures of cattle weight.  Data available here: https://faculty.biostat.ucla.edu/robweiss/filedepot_download/87/495


**Klumper & Qaim** (2015).
A Meta-Analysis of the Impacts of Genetically Modified Crops.
http://doi.org/10.1371/journal.pone.0111629

Note: Nice meta-analysis dataset.  Published data only include differences, not standard-errors.
See the comments on PLOS article for some peculiarities in the data.


**Lado, B. et al.** (2013). 
*Increased Genomic Prediction Accuracy in Wheat Breeding Through Spatial Adjustment of Field Trial Data*.  G3, 3, 2105-2114.
http://doi.org/10.1534/g3.113.007807

Note: Has a large haplotype data (83 MB) and two-year phenotype data with multiple traits.


**Payne, Roger** (2015). 
The Design and Analysis of Long-Term Rotation Experiments.
Agronomy Journal, 107, 772-784.
http://doi.org/10.2134/agronj2012.0411

Note: The data and R code appeared in the paper. Free access, but closed copyright.


**Snedecor, George and E. S. Haber** (1946).
Statistical Methods For an Incomplete Experiment on a Perennial Crop.
Biometrics Bulletin, 2, 61-67.
http://doi.org/10.2307/3001959

Harvest of asparagus over 10 years, three cutting dates per year, 6 blocks.


**Technow, Frank, et al.** (2014).
Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize.
August 1, 2014 vol. 197 no. 4 1343-1355.
http://doi.org/10.1534/genetics.114.165860

Note: Genotype and phenotype data appears in the sommer package.


**Tian, Ting** (2015).
Application of Multiple Imputation for Missing Values in Three-Way Three-Mode Multi-Environment Trial Data.
http://doi.org/10.1371/journal.pone.0144370

Note: Uses agridat::australia.soybean data and one other real dataset with 4 traits that are not identified.  All data and code available.


**Randall J. Wisser et al.** (2011). 
Multivariate analysis of maize disease resistances suggests a pleiotropic genetic basis and implicates a GST gene. PNAS.  http://doi.org/10.1073/pnas.1011739108

Note: Supplement contains genotype data, but no phenotype data.


**Yan, Weikei** (2002).
Singular value partitioning in biplots.  Agron Journal.

Note: Winter wheat, 31 gen in 8 loc. This data is different from Yan's earlier papers. Unfortunately, the data given in the paper are missing two rows. 


# Papers - Uniformity trials


**Baker, G.A.** (1953).
Strawberry uniformity yield trials.
Biometrics, Vol. 9, No. 3, pp. 412-421.
http://doi.org/10.2307/3001713 

Note: Two small uniformity trials with yield per plant for 200, 500 plants.  CVs fairly high and correlation between neighboring plants very low.


**Niels Anton Hansen**, 1914.
Prøvedyrkning paa Forsøgsstationen ved Aarslev.
_Tidsskrift for landbrugets planteavl_.
http://dca.au.dk/publikationer/historiske/planteavl/ 
Bind 21, page 553. In Danish.

See comments by Eden & Maskell found here:
https://archive.org/stream/in.ernet.dli.2015.25895/2015.25895.Journal-Of-Agricultural-Science-Vol-xviii-1928#page/n175
Page 165: "One of the trials, comprising 35 plots, extended over the years 1907-11 and included oats, rye, barley, roots, barley."
Oats and rye 1907 and 1908 show marked positive correlation.
rye and barley 1908 and 1909 no correlation of significance.
barley and roots 1909 and 1910 no correlation.
roots and barley 1910 and 1911 a significant correlation.
rye and roots 1908 and 1910 satisfactory.


**Edmund B. Lambert** (1934).
Size and arrangement of plots for yield tests with cultivated mushrooms.
Journal of Agricultural Research, Vol 48, 971-980.

Note: Uniformity trial at three locations for mushrooms in growth houses.
https://naldc.nal.usda.gov/naldc/download.xhtml?id=IND43968493


**Moore, John Francis** (1952).
A study of field plot technique with sprouting broccoli.  Proc Amer Soc Hort Sci: 1-474.

Note: This paper is not available, but a summary can be found here: http://eurekamag.com/research/013/624/013624967.php


# R packages


### aml - Adaptive Mixed LASSO
Has 'wheat' data with genetic and phenotypic data for wheat.


### agricolae 
Has assorted data and functions for analysis of agricultural data.


### BGLR - Bayesian Generalized Linear Regression.
Has an A matrix (but no pedigree) for 499 genotypes at 4 locations.


### BLR - Bayesian Linear Regression.
Has an A matrix (but no pedigree) for 499 genotypes at 4 locations.


### BSagri
Safety assessment in agriculture trials


### ClustVarLV
The apples_sh data has sensory attributes and preference scores for 12 apple varieties.


### cropcc - Climate change on crops
https://r-forge.r-project.org/projects/cropcc/


### drc - Dose response curves
Has nice herbicide dose response curves and germination data for mungbean, rice, wheat.


### FW - Finlay-Wilkinson regression
https://github.com/lian0090/FW/ Has phenotype data and marker data for 599 wheat lines in 4 environments.


### lmtest
Data lmtest::ChickEgg is a time series of annual chicken and egg production in the United States 1930-1983.


### missMDA 
The referenced source for 'geno' data does NOT contain the data.


### NADA
The 'Atra' and 'Recon' datasets contain measurements of Atrazine in water samples.


### nlraa
Miguez. Non-linear models in agriculture.
http://r-forge.r-project.org/R/?group_id=1599

   
### nlme
Datasets for growth of Orange trees and Soybean plants.  Soybean data is from the book "Nonlinear Models for Repeated Measurement Data".


### plantbreeding
https://r-forge.r-project.org/projects/plantbreeding/
```
Data: fulldial
Data: linetester
Data: peanut same as agridat::kang.peanut
```

### SDaA - Survey Data and Analysis
This package has county-level data from the United States Census of Agriculture, along with a vignette to illustrate survey sampling analyses.


### SemiPar
Data: SemiPar::onions is same as agridat::ratkowski.onions


### sommer - Solving mixed model equations in R
Data: h2. Modest-sized GxE experiment in potato Data: cornHybrid. Yield/PLTHT for 100 hybrids from 20 inbred * 20 inbred, 4 locs. Phenotype and relationship matrix.

Data: wheatLines  CIMMYT wheat data for 599 lines. Phenotype and relationship data.

Data: RICE

Data: FDdata taken from agridat::bond.diallel

Data: Technow_data. AF=Additive Flint. AD=Additive Dent. MF=Marker Flint. MD=Marker Dent. pheno=phenotype data for 1254 hybrids (GY=yield, GM=moisture).  This data is from Technow et al:
http://www.genetics.org/content/197/4/1343.supplemental


### spdep
Has a vignette 'The Problem of Spatial Autocorrelation: forty years on' that examines agriculture in Irish counties.
See also the data ade4::irishdata.


### spuRs
Data: spuRs::trees has data for 107 trees that were cut into cross sections with the volume calculated at roughly 10-year increments.  This is a subset of the much-larger original data from Guttenberg: 
https://archive.org/stream/wachstumundertra00gutt


### SoyNAM - Soybean nested association mapping 
Dataset with phenotype data 3 yr, 9 locations, 18 environments, 60 thousand observations for height, maturity,
lodging, moisture, protein, oil, fiber, seed size. There are 5000+ strains, 40 families.


### st4gi - Stat for genetic improvement
https://github.com/reyzaguirre/st4gi


# Web sites


### ARS oat trials
http://www.ars.usda.gov/Main/docs.htm?docid=8419&page=4


### Rothamsted Electronic Archive
http://www.era.rothamsted.ac.uk/index.php
Data from Broadbalk and other long-term experiments.


### Rothamsted Documents Archive
http://www.era.rothamsted.ac.uk/eradoc/collections.php
Annual reports from Rothamsted 1908-1987. Many have data, especially in the 
early years (before WWII) there are data given for the 'Classical Experiments'.
```
Year, page
1908-1926 
1926-1927 agridat::sawyer.multi.uniformity 
1927-1928 agridat::sawyer.multi.uniformity
1929-1930
1931,143 agridat::yates.oats
1932
1933
1934,215-222 Sugar beet multi-environment trial with 3^3 fertilizer 
  treatments at each site Roots, SugarPercent, SugarWeight, PlantNumber, Tops, Purity.
1935
1936,241 Similar to the 1934 experiment, but only gives the main effects, 
  not the actual data.
1937-1939
1946-1953
```

### Germplasm Enhancement of Maize (ISU)
http://www.public.iastate.edu/~usda-gem/index.htm
Data from trials at multiple locations. Yield, mst, pltht, lodging. No field plans.


### Google datasets search engine
https://cse.google.com/cse/publicurl?cx=002720237717066476899:v2wv26idk7m


### Illinois Corn Hybrid Variety Trials
http://vt.cropsci.illinois.edu/corn.html


### ILRI International Livestock Research Institute
http://www.ilri.org/biometrics/CS/
Case study 4 is a nice dialel example with sheep data.
Available as agridat::ilri.sheep


### IRRI Biometrics and Breeding Informatics
http://bbi.irri.org/products
STAR, PBTools, CropStat.
The STAR user guide has well-documented data (even using 2 from agridat), but
the PBTools user guide does not document the data.


### SolCAP Solanaceae Coordinated Agricultural Project
http://www.solcap.msu.edu/
Potato and Tomato genotype and phenotype data.


### Statistical Analysis of Agricultural Experiments with R
http://rstats4ag.org/
Datasets for mixed models, ancova, dose response curves, competition.


### USDA National Agricultural Statistics Service
http://www.nass.usda.gov
http://quickstats.nass.usda.gov/
Group:       Field Crops
Commodity:   Corn
Category:    Area Harvested, Yield
Data Item:   Corn grain Acres Harvested, Yield Bu/Ac
Domain:      Total
Geography:   State
See agridat::nass.corn, nass.wheat, etc.

