| NEWS | R Documentation |
CRAN checks (status ERROR). Changes in AMMI plot function, only biplot is considered.
CRAN checks (status NOTE), change name in documentation object ‘intervals.freq’ with ‘inter.freq’.
Improvements in the DAU.test function. Update the standard error.
Improvements in the audps function, includes when dates are not equidistant.
Improvements in the bar.err and group.plot functions, Update the standard error.
Improvements in the group.plot function, includes the 'decreasing' option for the decreasing order of the mean.
Improvements in the sp.plot and ssp.plot functions, include the p-value in the random factor block.
update PBIB.test when PBIB.test() is called from another function.
Improvements in the DAU.test function. controls can have different repetitions, at least two, do not use missing data.
Update design.graeco() by new version R-4.0 and higher
Improvements in the functions sp.plot, ssp.plot and strip.plot for the analysis of split plot and strip plot design, the mixed models with random blocks and fixed factors.
New function design.mat. Generate the design matrix from the fieldbook.
Update plot.group() by new version R-4.0
The examples were edited.
A control is set on the label limit for the functions order.group and orderPvalue.
The plot.AMMI function uses only type = 1 and type = 2 options.
Improvement in the formation of Duncan test groups and the confidence limits of Scheffe.test.
Shannon index on base log 2.
Update documentation on multiple comparison tests.
Improvement in the formation of Duncan test groups and the confidence limits of Scheffe.test.
Shannon index on base log 2.
Update documentation on multiple comparison tests.
The order.group function is again in agricolae.
It is equivalent to the orderPvalue function in functional terms.
In the post.hoc tests, the grouping of treatments are formed according to the probability of the difference between treatments and the alpha level.
The affected functions were BIB.test, DAU.test, duncan.test, durbin.test, friedman, HSD.test, kruskal, LSD.test, Median.test, PBIB.test, REGW.test, scheffe.test, SNK. Test, waller.test and waerden.test. Now there is good correspondence between the grouping and the pvalue.
A new function (plot.group) is included in agricolae for the graphs of treatment groups and their variation by range, interquartil range, Standard deviation and standard error.
The RANN package of suggestions was removed.
Updated documentation.
Documentation check.
Add model object in output PBIB.test function.
procedure duncan.test is better, the limitations in convergence were corrected.
The influence in AMMI (type=3) is relative neighbor graph as a sub-graph.
The post hoc nonparametrics tests (kruskal, friedman, durbin and waerden) are using the criterium Fisher's least significant difference (LSD)
Add suggests packages: RANN and rgeos to plot AMMI
Concordance index in correlation function(), additional arg (method="lin").
New function orderPvalue(). Grouping the treatments in a comparison with p.value minimum value (alpha)
Test LSD.test and kruskal the adjust P.value (holm, hommel, hochberg, bonferroni, BH, BY, fdr). The comparison in pairs and groups give similar results.
REGW.test(). New function for multiple comparisons of treatments. (Ryan, Einot and Gabriel and Welsch)
Concordance index in correlation function(), additional arg (method="lin").
New function orderPvalue(). Grouping the treatments in a comparison with p.value minimum value (alpha)
diffograph(). New function: Mean-mean scatter plot, test: Bonferroni, Fisher, Duncan, Student-Newman-Keul, Tukey, Kruskal-Wallis, Friedman and Waerden test.
Changes in all comparison means, add parameters to facility function diffograph.
Added randomization parameter (TRUE or FALSE) in all design function.
Update Tutorial.
Now in the frequency table shows the relative frequency as a percentage, the function is table.freq or summary( graph.freq or hist object)
The histogram class is added to graph.freq and it can use the package HistogramTools
The function design.bib create optimal design, use function optBlock(algDesign)
sketch option in design: rbcd, lsd, graeco, youden, bib.
Move packages from Suggests to Imports.
AUDPS. The Area Under the Disease Progress Stairs.
AMMI stability value (ASV) and Yield stability index (YSI)
Design youden.
Now the PBIB.test function uses missing values.
AMMI: aditional parameters PC=FALSE or TRUE, output principal components, check error equal cero.
plot.AMMI: graphic aditional parameters lwd = 1.8, length = 0.1 to arrow function.
simulation.model: aditional parameter console=FALSE or TRUE, output in console.
resampling.model: aditional parameter console=FALSE or TRUE, output in console.
stability.par: aditional parameter console=FALSE or TRUE, output in console.
stability.nonpar: aditional parameter console=FALSE or TRUE, output in console.
PBIB new parameter: group=TRUE. PBIB.test(block,trt,replication,y,k, method=c("REML","ML","VC"), test = c("lsd","tukey"), alpha=0.05, console=FALSE, group=TRUE). When you have many treatments to use group=FALSE.
design.rcbd(..., continue=FALSE). Continue=TRUE or FALSE, continuous numbering of plot.
Median.test. New function for multiple comparisons of treatments with Median.
Now, AMMI function checks the minimum number of environments and genotypes. Now use console=TRUE or FALSE to output in screen. the graphs are produced by the plot function.
plot.AMMI() or plot() functions generate plot of the AMMI with others principal components. type=1 (biplot), type=2 (triplot) and type=3 (influence genotype)
Changed parameters by default "first = TRUE" in designs: rcbd, ab, split and lsd.
Now vignettes in agricolae.
change name ogive.freq by ojiva.freq, the parameters are same.
AUDPC the evaluation parameter now can be numeric vector. To see help(audpc)
zigzag(outdesign). The new function applied to designs: rcbd, lsd, graeco, split, strip, ab, alpha, bib, cyclic, lattice, dau. The outdesign is the output book the function design.###(). The function zigzag change the order number plots in serpentine form.
Now, all design functions have two output objects: parameters and book, the parameters contain initial values that will allow reproduce the design and book contain field book.
Now, all design functions have two output objects: parameters and book, the parameters contain initial values that will allow reproduce the design and book contain field book.
The alpha and lattice designs have additionally two objects: statistics and field sketches.
BIB have the statistics