agridat {agridat} | R Documentation

## Datasets from agricultural experiments

### Description

This package contains datasets from publications relating to agriculture, including field crops, tree crops, animal studies, and a few others.

### Details

If you use these data, please cite both the agridat package and the original source of the data.

Abbreviations in the 'other' column include: xy = coordinates, pls = partial least squares, rsm = response surface methodology, row-col = row-column design, ts = time series,

Uniformity trials with a single genotype

name | dimensions | other | model
ansari.wheat.uniformity | 96 x 8 | xy |
baker.barley.uniformity | 3 x 19 | xy, 10 years |
baker.wheat.uniformity | 12 x 12 | xy |
bancroft.peanut.uniformity | 6 x 18 | xy, 2 blocks |
batchelor.apple.uniformity | 8 x 28 | xy |
batchelor.lemon.uniformity | 14 x 16 | xy |
batchelor.navel1.uniformity | 20 x 50 | xy |
batchelor.navel2.uniformity | 15 x 33 | xy |
batchelor.valencia.uniformity | 12 x 20 | xy |
batchelor.walnut.uniformity | 10 x 28 | xy |
bose.multi.uniformity | 15 x 26 | xy, 3 years |
bradley.multi.uniformity | 10 x 11 | xy |
christidis.cotton.uniformity | 16 x 16 | xy, 4 blocks |
christidis.wheat.uniformity | 12 x 24 | xy |
correa.soybean.uniformity | 24 x 48 | xy |
davies.pasture.uniformity | 19 x 40 | xy |
day.wheat.uniformity | 31 x 100 | xy |
draper.safflower.uniformity | 18 x 16 | xy, 2 expt | smith
eden.tea.uniformity | 12 x 12 | xy |
garber.multi.uniformity | 45 x 6 | xy, 2 years/crops |
gomez.rice.uniformity | 18 x 36 | xy | aov,smith
goulden.barley.uniformity | 20 x 20 | xy |
harris.multi.uniformity | 2 x 23 | xy, 23 crops | corrgram
holtsmark.timothy.uniformity | 6 x 40 | xy |
hutchinson.cotton.uniformity | 32 x 40 | xy |
igue.sugarcane.uniformity | 36 x 42 | xy |
immer.sugarbeet.uniformity | 10 x 60 | xy, 3 traits |
iyer.wheat.uniformity | 25 x 80 | xy |
kadam.millet.uniformity | 8 x 20 | xy, 2 expts |
kalamkar.potato.uniformity | 6 x 96 | xy |
kalamkar.wheat.uniformity | 16 x 80 | xy, 2 traits |
kempton.barley.uniformity | 7 x 28 | xy |
khin.rice.uniformity | 30 x 36 | xy |
kiesselbach.oats.uniformity | 3 x 69 | xy |
kristensen.barley.uniformity | 22 x 11 | xy |
kulkarni.sorghum.uniformity | 4 x 40 | xy, 3 years |
lander.multi.uniformity | 5 x 39 | xy, 4 years |
lessman.sorghum.uniformity | 46 x 60 | xy |
li.millet.uniformity | 6 x 100 | xy |
lord.rice.uniformity | 5 x 14 | xy, 8 fields |
love.cotton.uniformity | 16 x 10 | xy |
lyon.potato.uniformity | 34 x 6 | xy |
magistad.pineapple.uniformity | 5 x 5 | xy |
masood.rice.uniformity | 12 x 24 | xy |
mcclelland.corn.uniformity | 2 x 219 | xy |
mercer.mangold.uniformity | 10 x 20 | xy |
mercer.wheat.uniformity | 25 x 20 | xy, 2 traits | spplot
montgomery.wheat.uniformity | 14 x 16 | xy, 2 years | lm
moore.polebean.uniformity | 12 x 12 | xy |
moore.bushbean.uniformity | 24 x 24 | xy |
moore.sweetcorn.uniformity | 24 x 12 | xy |
moore.carrot.uniformity | 24 x 12 | xy |
moore.springcauliflower.uniformity | 12 x 20 | xy |
moore.fallcauliflower.uniformity | 12 x 20 | xy |
nagai.strawberry.uniformity | 18 x 24 \ tab xy |
narain.sorghum.uniformity | 10 x 16 | xy |
nonnecke.peas.uniformity | 15 x 18 | xy, 2 traits |
nonnecke.sweetcorn.uniformity | 32 x 18 | xy, 3 loc |
odland.soybean.uniformity | 25 x 42 | xy |
odland.soyhay.uniformity | 28 x 55 | xy |
parker.orange.uniformity | 10 x 27 | xy, 6 yr |
polson.safflower.uniformity | 52 x 33 | xy | smith
robinson.peanut.uniformity | 16 x 36 | xy |
sawyer.multi.uniformity | 8 x 6 | xy, 3 year |
sayer.sugarcane.uniformity | 8 x 136, 8 x 121 | xy, 2 year |
smith.beans.uniformity | 18 x 12, 16 x 15 | xy, 2 yr, 2 crops |
smith.corn.uniformity | 6 x 20 | xy, 3 years | rgl
stephens.sorghum.uniformity | 100 x 20 | xy |
stickler.sorghum.uniformity | 20 x 20 | xy, 4 expts, 2 years |
strickland.apple.uniformity | 11 x 18 | xy |
strickland.grape.uniformity | 5 x 31 | xy |
strickland.peach.uniformity | 8 x 18 | xy |
strickland.tomato.uniformity | 30 x 6 | xy |
wassom.brome.uniformity | 36 x 36 | xy, 3 expts |
wiebe.wheat.uniformity | 12 x 125 | xy | medianpolish, loess
wiedemann.safflower.uniformity | 54 x 33 | xy | smith
williams.barley.uniformity | 48 x 15 | xy | loess
williams.cotton.uniformity | 24 x 12 | xy | loess

Yield monitor

name | reps | years | trt | other | model
gartner.corn |  |  |  | xy,ym |
lasrosas.corn | 3 | 2 | 6 | xy,ym | lm

Animals

name | gen | years | trt | other | model
becker.chicken | 5,12 |  |  | heritability | lmer
crampton.pig |  |  | 5 | 2 cov | lm
brandt.switchback | 10 |  | 2 |  | aov
depalluel.sheep | 4 |  | 4 | latin |
diggle.cow |  |  | 4 | ts |
foulley.calving |  |  |  | ordinal | polr
goulden.eggs |  |  |  | controlchart |
harvey.lsmeans | 3,3 |  |  |  | lm
harville.lamb | 5 |  |  |  | lmer
henderson.milkfat |  |  |  |  | nls,lm,glm,gam
holland.arthropods | 5 |  |  |  |
ilri.sheep | 4 | 6 |  | diallel | lmer, asreml
kenward.cattle |  |  | 2 |  | asreml
lucas.switchback | 12 |  | 3 |  | aov
mead.lamb | 3 |  | 3 |  | glm
patterson.switchback | 12 |  | 4 |  | aov
urquhart.feedlot | 11 |  | 3 |  | lm
zuidhof.broiler |  |  |  | ts |

Trees

name | gen | loc | reps | years | trt | other | model
box.cork |  |  |  |  |  | repeated | radial, asreml
harris.wateruse | 2 |  |  |  | 2 | repeated | asreml,lme
hanover.whitepine | 7*4 |  | 4 |  |  | heritability | lmer
lavoranti.eucalyptus | 70 | 7 |  |  |  |  | svd
pearce.apple |  |  | 4 |  | 6 | cov | lm,lmer
williams.trees | 37 | 6 |  |  | 2 |  |

Field and horticulture crops

name | gen | loc | reps | years | trt | other | model
acorsi.grayleafspot | 36 | 9 | 2 | 5 |  | nonnormal | gnm,ammi
adugna.sorghum | 28 | 13 |  | 5 |  |  |
aastveit.barley | 15 |  |  | 9 |  | yr*gen~yr*trt | pls
allcroft.lodging | 32 | 7 |  |  |  | percent | tobit
archbold.apple | 2 |  | 5 |  | 24 | split-split | lmer
ars.earlywhitecorn96 | 60 | 9 |  |  |  | 6 traits | dotplot
australia.soybean | 58 | 4 |  | 2 |  | 4-way, 6 traits | biplot
battese.survey |  | 12 | 1-5 |  | 2 |  | lmer
beall.webworms |  |  | 15 |  | 2,2 | xy | glm poisson
beaven.barley | 8 |  | 20 |  |  | xy |
besag.bayesian | 75 |  | 3 |  |  | xy | asreml
besag.beans | 6 |  | 4*6 |  |  | xy | lm,competition
besag.elbatan | 50 |  | 3 |  |  | xy | lm, gam
besag.endive |  |  |  |  |  | xy,binary | autologistic
besag.met | 64 | 6 | 3 |  |  | xy, incblock | asreml, lme
besag.triticale | 3 |  |  |  | 2,2,3 | xy | lm, asreml
bliss.borers |  |  |  |  | 4 |  | glm
blackman.wheat | 12 | 7 |  |  | 2 |  | biplot
bond.diallel | 6*6 |  |  |  | 9 | diallel |
bridges.cucumber | 4 | 2 | 4 |  |  | xy, latin, hetero | asreml
brandle.rape | 5 | 9 | 4 | 3 |  |  | lmer
burgueno.alpha | 15 |  | 3 |  |  | xy, alpha | asreml,lmer
burgueno.rowcol | 64 |  | 2 |  |  | xy, row-col | asreml,lmer
burgueno.unreplicated | 280 |  |  |  |  | xy | asreml
butron.maize | 49 | 3 |  | 2 |  | diallel,pedigree | biplot,asreml
caribbean.maize |  | 17 | 4 |  | 3 |  |
carmer.density | 8 |  |  |  | 4 |  | nls,nlme
carlson.germination | 15 |  |  |  | 8 |  | glm
chinloy.fractionalfactorial |  |  | 9 |  | 1/3 3^5 | xy | aov
christidis.competition | 9 |  | 5 |  |  | xy |
cochran.beets |  |  | 6 |  | 7 |  |
cochran.bib | 13 | 13 |  |  |  | bib | aov, lme
cochran.crd |  |  |  |  | 7 | xy, crd | aov
cochran.factorial |  |  | 2 |  | 4^2 | factorial | aov
cochran.latin |  |  | 6 |  | 6 | xy, latin | aov
cochran.lattice |  |  | 5 |  | 16 | xy, latin | lmer
cochran.wireworms |  |  | 5 |  | 5 | xy, latin | glm
cochran.eelworms |  |  | 4 |  | 5 | xy | aov
connolly.potato | 20 |  | 4 |  |  | xy, competition | lm
cornelius.maize | 9 | 20 |  |  |  |  | svd
corsten.interaction | 20 | 7 |  |  |  |  |
cramer.cucumber |  |  | 8 |  |  |  | pathcoef
crossa.wheat | 18 | 25 |  |  |  |  | ammi
crowder.seeds | 2 |  | 21 |  | 2 |  | glm,jags
cox.stripsplit |  |  | 4 |  | 3,4,2 | split-block | aov
cullis.earlygen | 532 |  |  |  |  | xy | asreml
dasilva.maize | 55 | 9 | 3 |  |  |  |
darwin.maize |  |  | 12 |  | 2 |  | t.test
denis.missing | 5 | 26 |  |  |  |  | lme
denis.ryegrass | 21 | 7 |  |  |  |  | aov
digby.jointregression | 10 | 17 |  |  | 4 |  | lm
durban.competition | 36 |  | 3 |  |  | xy, competition | lm
durban.rowcol | 272 |  | 2 |  |  | xy | lm, gam, asreml
durban.splitplot | 70 |  | 4 |  | 2 | xy | lm, gam, asreml
eden.potato |  |  | 4 | 3 | 4-12 | xy, rcb, latin | aov
eden.nonnormal |  |  | 4 |  | 4 |  | aov
engelstad.nitro |  | 2 |  | 5 | 6 | rsm1 | nls quadratic plateau
fan.stability | 13 | 10 |  | 2 |  | 3-way | stability
federer.diagcheck | 122 |  |  |  |  | xy | lm, lmer, asreml
federer.tobacco |  |  | 8 |  | 7 | xy | lm
fisher.barley | 5 | 6 |  | 2 |  |  |
fisher.latin |  |  | 5 |  | 5 | xy,latin | lm
fox.wheat | 22 | 14 |  |  |  |  | lm
gathmann.bt | 2 |  | 8 |  |  |  | tost
gauch.soy | 7 | 7 | 4 | 12 |  |  | ammi
giles.wheat | 19 |  |  | 13 |  | 2 traits | gnm
gilmour.serpentine | 108 |  | 3 |  |  | xy, serpentine | asreml
gilmour.slatehall | 25 |  | 6 |  |  | xy | asreml
gomez.fractionalfactorial |  |  | 2 |  | 1/2 2^6 | xy | lm
gomez.groupsplit | 45 |  | 3 |  | 2 | xy, 3 gen groups | aov
gomez.heteroskedastic | 35 |  | 3 |  |  | hetero |
gomez.multilocsplitplot | 2 | 3 | 3 |  |  | rsm1,nitro | aov, lmer
gomez.nitrogen |  |  | 4 |  | 8 |  | aov, contrasts
gomez.nonnormal1 |  |  | 4 |  | 9 | log10 | lm
gomez.nonnormal2 | 14 |  | 3 |  |  | sqrt | lm
gomez.nonnormal3 | 12 |  | 3 |  |  | arcsin | lm
gomez.seedrate |  |  | 4 |  | 6 | rate | lm
gomez.splitplot.subsample |  |  | 3 |  | 8,4 | subsample | aov
gomez.splitsplit | 3 |  | 3 |  |  | xy, nitro, mgmt | aov, lmer
gomez.stripplot | 6 |  | 3 |  |  | xy, nitro | aov
gomez.stripsplitplot | 6 |  | 3 |  |  | xy, nitro | aov
gomez.wetdry |  |  | 3 | 2 | 5 | nitro | lmer
gotway.hessianfly | 16 |  | 4 |  |  | xy | lmer
goulden.latin |  |  | 5 |  | 5 | xy, latin | lm
goulden.splitsplit | 2 |  | 4 |  | 2*5 | xy, split | aov
graybill.heteroskedastic | 4 | 13 |  |  |  | hetero |
gregory.cotton |  |  |  | 2 | 4*3*2*2 | polar |
gumpertz.pepper |  |  |  |  |  | xy | glm
hanks.sprinkler | 3 |  | 3 |  |  | xy | asreml
hayman.tobacco | 8 |  | 2 | 2 |  | diallel | asreml
hazell.vegetables | 4 |  |  | 6 |  |  | linprog
heady.fertilizer |  |  | 2 |  | 9*9 | rsm2 | lm,rgl
hernandez.nitrogen |  | 5 | 4 |  |  | rsm1 | lm, nls
hildebrand.systems |  | 14 |  |  | 4 |  | asreml
holshouser.splitstrip | 4 |  | 4 |  | 2*4 | rsm1,pop | lmer
huehn.wheat | 20 | 10 |  |  |  |  | huehn
hughes.grapes |  |  | 3 |  | 6 | binomial | lmer, aod, glmm
hunter.corn |  | 12 |  | 3 | 1 | rsm1 | xyplot
ivins.herbs | 13 |  | 6 |  |  | 2 traits | lm, friedman
jansen.apple | 3 |  | 4 |  | 3 | binomial | glmer
jansen.carrot | 16 |  | 3 |  | 2 | binomial | glmer
jansen.strawberry | 12 |  | 4 |  |  | ordinal | mosaicplot
jenkyn.mildew |  |  | 9 |  | 4 |  | lm
john.alpha | 24 |  | 3 |  |  | alpha | lm, lmer
johnson.blight |  |  |  | 2 |  |  | logistic
kang.maize | 17 | 4 |  | 3 | 2,4 |  |
kang.peanut | 10 | 15 | 4 |  |  |  | gge
karcher.turfgrass |  |  | 4 |  | 2,4 | ordinal | polr
keen.potatodamage | 6 |  | 4 |  | 2,3,8 | ordinal | mosaicplot
kempton.competition | 36 |  | 3 |  |  | xy, competition | lme AR1
kempton.rowcol | 35 |  | 2 |  |  | xy, row-col | lmer
kempton.slatehall | 25 |  | 6 |  |  | xy | asreml, lmer
lee.potatoblight | 337 |  | 4 | 11 |  | xy, ordinal, repeated |
lehner.soybeanmold |  | 35 |  | 4 | 11 |  | metafor, lmer
lillemo.wheat | 24 | 13 |  | 7 |  | qq | medpolish, huehn
lin.superiority | 33 | 12 |  |  |  |  | superiority
lin.unbalanced | 33 | 18 |  |  |  |  | superiority
little.splitblock |  |  | 4 |  | 4,5 | xy, split-block | aov
lonnquist.maize | 11 |  |  |  |  | diallel | asreml
lyons.wheat |  | 12 |  | 4 |  |  |
lu.stability | 5 | 6 |  |  |  |  | huehn
mcconway.turnip | 2 |  | 4 |  | 2,4 | hetero | aov, lme
mcleod.barley |  | 8 |  |  | 6 |  | aggregate
mead.cauliflower |  |  |  | 2 |  | poisson | glm
mead.cowpeamaize | 3,2 |  | 3 |  | 4 | intercrop |
mead.germination |  |  | 4 |  | 4,4 | binomial | glm
mead.strawberry | 8 |  | 4 |  |  |  |
mead.turnip |  |  | 3 |  | 5,4 |  | aov
minnesota.barley.weather |  | 6 |  | 10 |  |  |
minnesota.barley.yield | 22 | 6 |  | 10 |  |  | dotplot
omer.sorghum | 18 | 2 | 4 | 3 |  |  | jags
onofri.winterwheat | 8 |  | 3 | 7 |  |  | ammi
ortiz.tomato | 15 | 18 |  |  | 16 | env*gen~env*cov | pls
pacheco.soybean | 18 | 11 |  |  |  |  | ammi
perry.springwheat | 28 | 5 |  | 4 |  | gain | lm,lmer,asreml
piepho.cocksfoot | 25 |  |  | 7 |  |  | lmer
ratkowsky.onions |  |  |  |  |  |  | lm
reid.grasses | 4 |  |  | 3 | 21 |  | nlme SSfpl
ridout.appleshoots |  |  | 30 |  | 2,4 | zip | zeroinfl
rothamsted.brussels |  |  | 4 |  | 6 |  |
ryder.groundnut | 5 |  | 4 |  |  | xy, rcb | lm
salmon.bunt | 10 |  | 2 |  | 20 |  | betareg
senshu.rice |  | 40 |  |  |  |  | lm,Fieller
shafii.rapeseed | 6 | 14 | 3 | 3 |  |  | biplot
silva.cotton |  |  | 5 |  | 5 | 5 traits | glm,poisson
sinclair.clover |  |  |  |  | 5,5 | rsm2,mitzerlich | nls,rgl
snedecor.asparagus |  |  | 4 | 4 | 4 |  | split-plot, antedependence
snijders.fusarium | 17 |  |  | 3 | 4 | percent | glm/gnm,gammi
steptoe.morex.pheno | 152 | 16 |  |  |  | 10 traits |
steptoe.morex.geno | 150 |  |  |  |  | 223 markers, qtl |
streibig.competition | 2 |  | 3 |  |  |  | glm
stroup.nin | 56 |  | 4 |  |  | xy | asreml
stroup.splitplot |  |  | 4 |  |  |  | asreml, MCMCglmm
student.barley | 2 | 51 |  | 6 |  |  | lmer
tai.potato | 8 | 3 |  | 2 |  |  | tai
talbot.potato | 9 | 12 |  |  |  | gen*env~gen*trt | pls
theobald.barley | 3 | 5 |  | 2 | 5 | rsm1 |
theobald.covariate | 10 | 7 | 5 |  |  | cov | jags
thompson.cornsoy |  | 5 |  | 33 |  | repeated measures | aov
vaneeuwijk.fusarium | 20 |  |  | 4 | 7 | 3-way | aov
vaneeuwijk.drymatter | 6 | 4 |  | 7 |  | 3-way | aov,lmer
vaneeuwijk.nematodes | 11 |  |  |  |  | nonnormal,poisson | gnm, gammi
vargas.wheat1 | 7 |  |  | 6 |  | gen*yr~gen*trt, yr*gen~yr*cov | pls
vargas.wheat2 | 8 | 7 |  |  |  | env*gen~env*cov | pls
vargas.txe |  |  |  | 10 | 24 | yr*trt~yr*cov | pls
verbyla.lupin | 9 | 8 | 2-3 | 2 |  | rsm1, xy, density | asreml
vold.longterm |  |  |  | 19 | 4 | rsm1 | nls,nlme
vsn.lupin3 | 336 | 3 |  |  |  | xy | asreml
wedderburn.barley | 10 | 9 |  |  |  | percent | glm/gnm
weiss.incblock | 31 |  | 6 |  |  | xy,incblock | asreml
weiss.lattice | 49 |  | 4 |  |  | xy,lattice | lm,asreml
welch.bermudagrass |  |  |  |  | 4,4,4 | rsm3, factorial | lm, jags
wheatley.carrot |  |  | 3 |  | 11 |  | glm-binomial
yan.winterwheat | 18 | 9 |  |  |  |  | gge,biplot
yang.barley | 6 | 18 |  |  |  |  | biplot
yates.missing |  |  | 10 |  | 3^2 | factorial | lm, pca
yates.oats | 3 |  | 6 |  |  | xy,split,nitro | lmer

Time series

name | years | trt | other | model
byers.apple |  |  |  | lme
broadbalk.wheat | 74 | 17 |  |
hessling.argentina | 30 |  | temp,precip |
kreusler.maize | 4 | 5 | plant growth |
lambert.soiltemp | 1 | 7 |  |
nass.barley | 146 |  |  |
nass.corn | 146 |  |  |
nass.cotton | 146 |  |  |
nass.hay | 104 |  |  |
nass.sorghum | 93 |  |  |
nass.wheat | 146 |  |  |
nass.rice | 117 |  |  |
nass.soybean | 88 |  |  |
walsh.cottonprice | 34 |  |  | cor

Other

name | model
cate.potassium | cate-nelson
cleveland.soil | loess 2D
harrison.priors | nls, prior
nebraska.farmincome | choropleth
pearl.kernels | chisq
stirret.borers | lm, 4 trt
turner.herbicide | glm, 4 trt
usgs.herbicides | non-detect
wallace.iowaland | lm, choropleth
waynick.soil | spatial, nitro/carbon

Comments of the package purpose

Box (1957) said, "I had hoped that we had seen the end of the obscene tribal habit practiced by statisticians of continually exhuming and massaging dead data sets after their purpose in life has long since been forgotten and there was no possibility of doing anything useful as a result of this treatment."

Massaging these dead data sets will not lead to any of the genetics being released for commercial use. The value of this package is: 1. Validating published analyses. 2. Providing data for testing new analysis methods. 3. Illustrating (and validating) the use of R.

White and van Evert (2008) present some guidelines for publication of data.

Some of the examples use the `asreml` package since it is the _only_ R tool for fitting mixed models with complex variance structures to large datasets, and the best option for modelling AR1xAR1 residual variance structures. Commercial use of `asreml` requires a license: http://www.vsni.co.uk/downloads/asreml.

Comments on the package structure

A large portion of these datasets appear in electronic form here for the first time.

A tremendous amount of effort has been given to the curating process of identifying datasets, extracting the data from source materials, checking data values, and documenting the data. In effect, to make the data somewhat 'computable' (Wolfram 2017).

The original sources for these data use several different words to refer to genotypes including accession, breed, cultivar, genotype, hybrid, line, progeny, stock, type, and variety. For consistency, these datasets mostly use `gen` (genotype).

Also for consistency `row` and `col` are usually used for the field coordinates.

In dataframes, 'block', 'rep', and similar terms are almost always coded like B1, B2, B3 instead of 1, 2, 3. This causes R to treat the data as a factor instead of a numeric covariate (which is a good thing).

Almost all of the data are presented as 'tidy' dataframes with 'observations' in rows and 'variables' in columns.

Although using `data()` is not necessary to access the data files, the example sections do include the use of `data()` because `devtools::run_examples()` needs it.

Please report any bugs to the package author or at the package github site.

### Author(s)

Kevin Wright

The author is grateful to the many people who granted permission to include their data in this package.

### References

G. E. P. Box (1957), Integration of Techniques in Process Development, Transactions of the American Society for Quality Control.

J. White and Frits van Evert. (2008). Publishing Agronomic Data. Agron J. 100, 1396-1400. http://doi.org/10.2134/agronj2008.0080F

Stephen Wolfram (2017). Launching the Wolfram Data Repository: Data Publishing that Really Works. http://blog.stephenwolfram.com/2017/04/launching-the-wolfram-data-repository-data-publishing-that-really-works/

[Package agridat version 1.16 Index]