notes_agridat.md
In kwstat/agridat: Agricultural Datasets

License note

Substantial effort has been made to contact authors of papers published within the past few decades to secure permission to use data in this package.

In the U.S., raw data are not generally subject to copyright. See \url{http://www.lib.umich.edu/copyright-office-mpublishing/copyrightability-charts-tables-and-graphs} and \url{http://sciencecommons.org/about/towards} for some discussion.

Data produced from work of the United States government (including the U.S. Department of Agriculture) are not subject to copyright. \url{http://en.wikipedia.org/wiki/Copyright_status_of_work_by_the_U.S._government}

Creative Commons licenses can apply to the \emph{structure} of a database, but not to the factual data. \url{https://wiki.creativecommons.org/wiki/Data}

Cochran uniformity done

evans.sugarcane.uniformity goulden.barley.uniformity ducker.groundnut.uniformity immer.sugarbeet.uniformity (1931) mckinstry.cotton.uniformity saunders.maize.uniformity smith.wheat.uniformity

This data was made available with special help from the staff at Rothamsted Research Library.

\source{ Rothamsted Research Library, Box STATS17 WG Cochran, Folder 5. }

Murray, E. K. S. (1934). The value of a uniformity trial in field experimentation with rubber. The Journal of Agricultural Science, 24(2), 177-184. https://doi.org/10.1017/s0021859600006572 Reviewed. Not used. Has 2 years of 5x5 grid from rubber trees. Based on data archived at Rothamsted, so not used at this time.

101 # 1925-1934 single rows, series E/F 102 # 1925-1934 single rows, series G 103_goulden_barley # done Grown at Dominion, 1931 104_beckett_coconut # 1919-1928, 22 plots, nuts per plot. Cochran paper #17 105_panse_cotton # done (see also 509) 106_mckinstry_cotton # done Gatooma 480 plots 107_saunders_maize # done Maize, Potchefstroom 1929-30 108 # Field B2a, B5b 109_saunders_maize # done Maize, Potchefstroom 1928-1929 110_immer_sugarbeet # done U of Minn 1931 111_evans_sugarcane # done Squared values 112_sayer_sugarcane # done At Harpr Jhili 113_christidis_wheat # done 114_smith_wheat # done Fairfield Smith data

201 # cotton Wad Medani, Sudan 202 # Wad Medani, Cotton 24x8=192 203 # 3x20, 1935-1936, weight in rotl 204 # Letter from Parish to Fisher, 205 # Oats 1923, Sudan Grass 1923, Wheat 1922 (10x26=260 plots) 206 # done hutchinson.cotton 207 # done Letter from Finney to Kilby 1943 208_ducker_groundnut # done Letter from Killby to Fisher, Ducker groundnut data 209 # 1938 Summerby to Cochran, Oats, 1921 3x33, Wheat todo. Data. Have pdf. 210 # 1937 Letter from Summerby to Cochran, Cochran to Summerby 211 # 1943 Letter Finney to Wadley. Thanks for the data. 212 # 1934 Letter Wadley to Finney. Ribes data. 213 # ignore China, 1x16 214 # omit - clove trees 600, 5 years, no coordinates, East Africa 215 # omit - clove tree part 2 216 # omit - wireworm traps, not a plant trial 217 # LeClerg field expt 1937-1938 sugar beet U Minn 218 # LeClerg greenhouse 1933 219 # 1939 letter LeClerg to Cochran, Narain to Cochran, Cochran to Westover, Eden to Cochran

301_day_table # done No data.

This folder contains correspondence

401 402_pound 403 cheesman christidis collinson collison 404 405_day # Done. demandt vandyk 406 407 408 posthumus 409_konigsberger about the demandt trials 410_demandt $ done 411 hutchinson immer look for parnell 412 413 kirk parnell macdonald 414 metzger parker pound 415 pound reynolds(cotton) richardson 416_saunders # done 417_saunders sayer swanson 418_swanson thompson 419 thompson notes 420 day westover wilcox

501_metzger # multi-year series 502_kansas 503 504_goulden_barley # done goulden.barley.uniformity 505_beckett_coconut # multi-year, Cochran #17 506 507_coffee # coffee 1934-1939, Cochran #18 508_mckinstry_cotton # done mckinstry.cotton.uniformity (correspondence, hand-written) 509_panse_cotton # done panse.cotton.uniformity (see also 109) 510_christidis_wheat # done christidis.wheat.uniformity 511_sayer_sugarcane # done sayer.sugarcane.uniformity 1932, 48 rows, 20 columns 513_hastings_oats_1911 # 514_immer_sugarbeet # done. 60 row, 10 col, 2nd year of data 515_sugarcane # barbados sugarcane 516_macdonald_cotton # field B2a B5b. See folder 1, file 8 517_rothamsted 518_saunders_maize_28_29 # done potchefstroom 519_saunders_maize_29_30 # done potchefstroom

Decided not to use this data.

There were 2 cut dates. The data for dry matter is highly variable. The field notes are a bit cryptic and suggest that there was some lack of uniformity in how the plants were handled (cut in morning, afternoon, etc).

601 7/1 pt 2, copy 1, row 1-84, col k-u 602 7/1 pt 2, copy 2, row 1-84, col k-u 603 4/2 pt 1, copy2, row 1-84, col a-k 604 4/2 pt 1, copy1, row 1-84, col a-k 605 4/2 pt 2, copy2, row 1-84, col l-v 606 7/1 pt 1, copy 2, row 1-84, col za-j 607 experiment details 608 7/1 pt 1, copy 1, row 1-84, col za-j 609 4/2 pt 2, copy1, row 1-84, col l-v

701_smith_correspondence # done 702_smith_reference # done 703_smith_ears_copy_B # done 704_smith_grain_copy_B # done 705_smith_grain_copy_A # done 707_smith_ears_copy_A # done

801_cochran_notes_1 802_cochran_notes_2 803_cochran_notes_3 804_cochran_notes_4 800_cochran_notes_0 805_evans_sugarcane_letter # done evans.sugarcane.uniformity 806_evans_sugarcane_data # done evans.sugarcane.uniformity

Decided not to use this data.

There is very little contextual information about these data.

901_demandt_diagram 902_demandt_data

change theobald.covariate from JAGS to brms?
brms examples for crowder.seeds
Figure out best way to use jags
JAGS code for edwards.oats
JAGS code for lee.potatoblight
JAGS code for theobald.barley
JAGS code for besag.elbatan
Note: R_MAX_NUM_DLLS=150
Rcmd check --run-dontrun before release devtools::run_examples(run=FALSE, start="butron.maize") build_site(lazy=TRUE, run=TRUE)

Do NOT use Roxygen to document data, because it will complain about data/*.txt files with error messages like: Error: 'uscrime' is not an exported object from 'namespace:agridat'

This document lists notes about data sources searched and additional sources of agricultural data. Although this is an .md file, the formatting is best viewed in plain text mode.

Henry Wallace archive at Univ Iowa Library http://www.lib.uiowa.edu/sc/location-and-hours/ Henry Wallace research papers http://aspace.lib.uiowa.edu/repositories/2/archival_objects/400608 500 Ear experiment. Might be the data for "What is in the corn judge's mind" paper http://aspace.lib.uiowa.edu/repositories/2/archival_objects/400615

wanted

Yield-monitor data for a split-planter field
Yield-monitor data for a strip trial.

Jose Crossa papers http://repository.cimmyt.org/xmlui/handle/10883/1/browse?value=Crossa,%20J.&type=author Meta-r http://repository.cimmyt.org/xmlui/handle/10883/4130 Data http://repository.cimmyt.org/xmlui/handle/10883/4036 http://repository.cimmyt.org/xmlui/handle/10883/2976 http://repository.cimmyt.org/xmlui/handle/10883/1380 http://repository.cimmyt.org/xmlui/handle/10883/4128 http://repository.cimmyt.org/xmlui/handle/10883/4290

Review of meta-analyses in agronomy http://www6.versailles-grignon.inra.fr/agronomie/Meta-analysis-in-agronomy/References

Papers

Biplot/StdErr/ VanEeuwijk 1993 - Incorporating env info Biplot Bartkowiak GxE table GE folder: Crossa 1997

F2 data. Folder: GE http://www.frontiersin.org/Plant_Physiology/10.3389/fphys.2013.00044/abstract CC license:

Comparison Between Linear and Non-parametric Regression Models for Genome-Enabled Prediction in Wheat https://www.scienceopen.com/document/vid/4017fb51-381c-4374-93aa-608423df4004;jsessionid=0TLjjSbaooSUk1y3JKd4nUeb.master:so-app1-prd Data: http://www.g3journal.org/content/suppl/2012/12/05/2.12.1595.DC1 All content has CC license

Extension

https://plant-breeding-genomics.extension.org/plant-breeding-and-genomics-learning-lessons

https://plant-breeding-genomics.extension.org/estimating-heritability-and-blups-for-traits-using-tomato-phenotypic-data/

https://plant-breeding-genomics.extension.org/genomic-relationships-and-gblup <--- todo review this

https://plant-breeding-genomics.extension.org/rrblup-package-in-r-for-genomewide-selection/

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Items below have been reviewed for data sources

Journals

Skimmed Vol 1

Vol 1-13

http://www.jstor.org/action/showPublication?journalCode=biometrics

http://archive.org Vol 3-5, 23-24 26

http://www.sciencedirect.com/science/journal/03784290/157 Vol 1-40

http://www.iasri.res.in/NewsLetters/nl.HTM

Vol 1.
Vol 2.
Vol 3. https://archive.org/details/in.ernet.dli.2015.271738/page/n653/mode/2up
  544 5 varieties, 2 blocks, 4 reps/block
Vol 4. 
Vol 5.
  579. agridat::bose.multi.uniformity
Vol 6. 
https://archive.org/details/in.ernet.dli.2015.271737
  34. 4-way factorial (3 gen, 5 date, 3 spacing, 3 pop) non-contiguous sub-plots. agridat::chakravertti.factorial
  460. agridat::kulkarni.sorghum.uniformity
  917. agridat::sayer.sugarcane.uniformity
Vol 9.
Vol 10.
Vol 11. 
Vol 12. 
  240. Wheat uniformity trial. agridat::iyer.wheat.uniformity
Vol 14.
Vol 16.
Vol 17.
Vol 19.

Vol 6.

Vol 23.

http://www.isas.org.in/jsp/onlinejournal.jsp Skimmed: Vol 50-56

http://www.jstor.org/action/showPublication?journalCode=jroyastatsocise4 Datasets 1998-2015 http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1467-9868/homepage/seriesb_datasets.htm http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291467-985X/homepage/datasets_all_series.htm

http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291467-985X/homepage/datasets_all_series.htm 1998-2015

http://dca.au.dk/publikationer/historiske/planteavl/

Books

Vol 19-24, 1906-1911 https://books.google.com/books?id=HBlJAAAAMAAJ Vol 25, 1912 https://books.google.com/books?id=M-5BAQAAMAAJ

Helen Elizabeth Conners (1951). Field plot techniques for sweet potatoes obtained from uniformity trial data. Master's Thesis. No data given.

Robert LeRoy Plaisted (1954). Field plot techniques for estimating onion yields. Master's Thesis. No data given.

Michael Holle. 1960. Plot technique for field evaluation of three characters in the lima bean. Master's Thesis. No data given.

Howard Lewis Taylor (1951). The effect of plot shape on experimental error. Master's Thesis. No data given. Used data from a corn uniformity trial, oats uniformity, and the data of Fairfield Smith. Smaller experimental errors were found for long narrow plots.