kwstat/agridat

Agricultural datasets

agridat's Issues

john.alpha with rows and cols

Hi, since I am using it in teaching and in combination with desplot(), I made the effort to get row and col info for john.alpha from the source. In case you would like to update this to agridat::john.alpha - below is a tribble and here is a link to it as a csv file:
https://raw.githubusercontent.com/SchmidtPaul/DSFAIR/master/data/John%26Williams1995.csv

head(agridat::john.alpha)
#>   plot rep block gen  yield
#> 1    1  R1    B1 G11 4.1172
#> 2    2  R1    B1 G04 4.4461
#> 3    3  R1    B1 G05 5.8757
#> 4    4  R1    B1 G22 4.5784
#> 5    5  R1    B2 G21 4.6540
#> 6    6  R1    B2 G10 4.1736
john.alpha2 <- tibble::tribble(
  ~plot,   ~rep, ~block,  ~gen, ~yield, ~row, ~col,
  1, "R1",       "B1", "G11", 4.1172,    4,    1,
  2, "R1",       "B1", "G04", 4.4461,    3,    1,
  3, "R1",       "B1", "G05", 5.8757,    2,    1,
  4, "R1",       "B1", "G22", 4.5784,    1,    1,
  5, "R1",       "B2", "G21",  4.654,    4,    2,
  6, "R1",       "B2", "G10", 4.1736,    3,    2,
  7, "R1",       "B2", "G20", 4.0141,    2,    2,
  8, "R1",       "B2", "G02",  4.335,    1,    2,
  9, "R1",       "B3", "G23", 4.2323,    4,    3,
  10, "R1",       "B3", "G14", 4.7572,    3,    3,
  11, "R1",       "B3", "G16", 4.4906,    2,    3,
  12, "R1",       "B3", "G18", 3.9737,    1,    3,
  13, "R1",       "B4", "G13",  4.253,    4,    4,
  14, "R1",       "B4", "G03",  3.342,    3,    4,
  15, "R1",       "B4", "G19", 4.7269,    2,    4,
  16, "R1",       "B4", "G08", 4.9989,    1,    4,
  17, "R1",       "B5", "G17", 4.7876,    4,    5,
  18, "R1",       "B5", "G15", 5.0902,    3,    5,
  19, "R1",       "B5", "G07", 4.1505,    2,    5,
  20, "R1",       "B5", "G01", 5.1202,    1,    5,
  21, "R1",       "B6", "G06", 4.7085,    4,    6,
  22, "R1",       "B6", "G12",  5.256,    3,    6,
  23, "R1",       "B6", "G24", 4.9577,    2,    6,
  24, "R1",       "B6", "G09", 3.3986,    1,    6,
  25, "R2",       "B1", "G08", 3.9926,    4,    7,
  26, "R2",       "B1", "G20", 3.6056,    3,    7,
  27, "R2",       "B1", "G14", 4.5294,    2,    7,
  28, "R2",       "B1", "G04", 4.3599,    1,    7,
  29, "R2",       "B2", "G24", 3.9039,    4,    8,
  30, "R2",       "B2", "G15", 4.9114,    3,    8,
  31, "R2",       "B2", "G03", 3.7999,    2,    8,
  32, "R2",       "B2", "G23", 4.3042,    1,    8,
  33, "R2",       "B3", "G12", 5.3127,    4,    9,
  34, "R2",       "B3", "G11", 5.1163,    3,    9,
  35, "R2",       "B3", "G21", 5.3802,    2,    9,
  36, "R2",       "B3", "G17", 5.0744,    1,    9,
  37, "R2",       "B4", "G05", 5.1202,    4,   10,
  38, "R2",       "B4", "G09", 4.2955,    3,   10,
  39, "R2",       "B4", "G10", 4.9057,    2,   10,
  40, "R2",       "B4", "G01", 5.7161,    1,   10,
  41, "R2",       "B5", "G02", 5.1566,    4,   11,
  42, "R2",       "B5", "G18", 5.0988,    3,   11,
  43, "R2",       "B5", "G13",  5.484,    2,   11,
  44, "R2",       "B5", "G22", 5.0969,    1,   11,
  45, "R2",       "B6", "G19", 5.3148,    4,   12,
  46, "R2",       "B6", "G07", 4.6297,    3,   12,
  47, "R2",       "B6", "G06", 5.1751,    2,   12,
  48, "R2",       "B6", "G16", 5.3024,    1,   12,
  49, "R3",       "B1", "G11", 3.9205,    4,   13,
  50, "R3",       "B1", "G01", 4.6512,    3,   13,
  51, "R3",       "B1", "G14", 4.3887,    2,   13,
  52, "R3",       "B1", "G19", 4.5552,    1,   13,
  53, "R3",       "B2", "G02",  4.051,    4,   14,
  54, "R3",       "B2", "G15", 4.6783,    3,   14,
  55, "R3",       "B2", "G09", 3.1407,    2,   14,
  56, "R3",       "B2", "G08", 3.9821,    1,   14,
  57, "R3",       "B3", "G17", 4.3234,    4,   15,
  58, "R3",       "B3", "G18", 4.2486,    3,   15,
  59, "R3",       "B3", "G04",  4.396,    2,   15,
  60, "R3",       "B3", "G06", 4.2474,    1,   15,
  61, "R3",       "B4", "G12", 4.1746,    4,   16,
  62, "R3",       "B4", "G13", 4.7512,    3,   16,
  63, "R3",       "B4", "G10", 4.0875,    2,   16,
  64, "R3",       "B4", "G23", 3.8721,    1,   16,
  65, "R3",       "B5", "G21",  4.413,    4,   17,
  66, "R3",       "B5", "G22", 4.2397,    3,   17,
  67, "R3",       "B5", "G16", 4.3852,    2,   17,
  68, "R3",       "B5", "G24", 3.5655,    1,   17,
  69, "R3",       "B6", "G03", 2.8873,    4,   18,
  70, "R3",       "B6", "G05", 4.1972,    3,   18,
  71, "R3",       "B6", "G20", 3.7349,    2,   18,
  72, "R3",       "B6", "G07", 3.6096,    1,   18
)

desplot::desplot(
  data = john.alpha2,
  flip = TRUE,
  form = gen ~ col + row | rep,
  text = gen,
  cex = 1,
  shorten = "no",
  out1 = rep,
  out2 = block,
  show.key = F
)

^{Created on 2021-10-21 by the reprex package (v2.0.1)}

3D yield response to fertilizers missing example

In the vignette the text states:

The blue dots are observed data, and the tan surface is the fitted surface drawn by the rgl package).

However, there is no associated R code in the RMD file and rgl is not listed in the "Setup" section.

AMMI biplots fail with latest agricolae

Temporarily fixed by B. Ripley.

pcaMethods

I find it a bit odd that agridat imports a package (pcaMethods) that is not available from CRAN. I realized this when my students failed to do their homework (analyzing a data example from agridat) because they weren't able to install the package as they didn't figure out that they had to download pcaMethods from Bioconductor. If this import is really necessary, I think it could be helpful to point it out explicitly.

Apart from this, great package! Keep it up!

Philip

Piepho's data

One funny typo: Dactylis glomerata is called cock's foot and not cook's foot. And yes, it's also misspelt in Piepho's original publication.

CRAN check failure

I get this:

checking examples ... ERROR
Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: archbold.apple
> ### Title: Split-split plot experiment on apple trees
> ### Aliases: archbold.apple
> ### Keywords: datasets
> 
> ### ** Examples
> 
> dat <- archbold.apple
> 
> # Define main plot and subplot
> dat <- transform(dat, rep=factor(rep), spacing=factor(spacing), trt=factor(trt),
+                  mp = factor(paste(row,spacing,sep="")),
+                  sp = factor(paste(row,spacing,stock,sep="")))
> 
> # Due to 'spacing', the plots are different sizes, but the following layout
> # shows the relative position of the plots and treatments. Note that the
> # 'spacing' treatments are not contiguous in some reps.
> desplot(spacing~row*pos, dat, col=stock, cex=1, num=gen,
+         main="archbold.apple")
> 
> if(require("lme4")){
+ 
+ m1 <- lmer(yield ~ -1 + trt + (1|rep/mp/sp), dat)
+ 
+ require(lucid)
+ vc(m1)  # Variances/means on page 59
+ ##         grp        var1 var2   vcov sdcor
+ ## sp:(mp:rep) (Intercept) <NA>  193.3 13.9
+ ##      mp:rep (Intercept) <NA>  203.8 14.28
+ ##         rep (Intercept) <NA>  197.3 14.05
+ ##    Residual        <NA> <NA> 1015   31.86
+ 
+ }
Loading required package: lme4
Loading required package: Matrix
Loading required package: Rcpp
Loading required package: lucid
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘lucid’
Error: could not find function "vc"
Execution halted

possibly because of

checking package dependencies ... NOTE
Packages suggested but not available for checking:
  ‘agricolae’ ‘equivalence’ ‘FrF2’ ‘gstat’ ‘lucid’ ‘MCMCglmm’ ‘pscl’

But examples should work even without suggested packages.

lsmeans is leaving

Kevin,

I’m writing because your R package agridat still suggests the lsmeans package. For almost a year, the new package emmeans has been available, and I am planning to ask the CRAN team to deprecate it in the next few months. It is quite easy to make the transition to emmeans. There is a vignette providing some tips for how to do this at https://cran.r-project.org/web/packages/emmeans/vignettes/transition-from-lsmeans.html, and there is even a script for converting old R sources, vignettes, and workspaces.

Please let me know if you have any questions. I will keep in touch on this matter as is necessary.

Sincerely,

Russ Lenth

ANOVA table for Alpha lattice design of spring oats, wrong d.f.

anova(m1)
Analysis of Variance Table

Response: yield
Df Sum Sq Mean Sq F value Pr(>F)
gen 24 1458.83 60.785 728.2829 < 2.2e-16 ***
rep 2 6.14 3.068 36.7557 6.593e-09 ***
rep:block 15 3.60 0.240 2.8784 0.006255 **
Residuals 31 2.59 0.083

The degrees of freedom in the anova table for gen is 24 instead of 23, one less than number of levels. The df is wrong.

str(dat)
'data.frame': 72 obs. of 5 variables:
$ plot : int 1 2 3 4 5 6 7 8 9 10 ...
$ rep : Factor w/ 3 levels "R1","R2","R3": 1 1 1 1 1 1 1 1 1 1 ...
$ block: Factor w/ 6 levels "B1","B2","B3",..: 1 1 1 1 2 2 2 2 3 3 ...
** gen : Factor w/ 24 levels **G01","G02","G03",..: 11 4 5 22 21 10 20 2 23 14 ...
$ yield: num 4.12 4.45 5.88 4.58 4.65 ...