Changes in new version

Version agricolae 1-3.7 (Oct 22, 2023)
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- CRAN checks (status ERROR). Changes in AMMI plot function, only biplot is considered.

Version agricolae 1-3.6 (Jun 30, 2023)
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- 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.

Version agricolae 1-3.5 (Jun 5, 2021)
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- Improvements in the DAU.test function. Control treatments can have different repetitions, eliminate missing data.
- The design.graeco function has been updated for its functionality for new versions 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.

Version agricolae 1-3.3 (June 5, 2020)
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- New function design.mat. Generate the design matrix from the fieldbook. 
- Update plot.group() by new version R-4.0

Version agricolae 1-3.2 (January 18, 2020)
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- 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.

Version agricolae 1-3.1 (April 4, 2019)
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- 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.

Version agricolae 1-2.9 (January 4, 2019)
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Plot.group function include argument label size with cex=NULL
HSD.test include parameter unbalanced, equal TRUE is not equal replication

Version agricolae 1-2.8 (September 12, 2017)
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The order.group function  is again in agricolae. 
It is equivalent to the orderPvalue function in functional terms.

Version agricolae 1-2.7 (August 30, 2017)
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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. 

Version agricolae 1-2.6 (August 4, 2017)
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Documentation check.

Version agricolae 1-2.5 (July 20, 2017)
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1. Add model object in output PBIB.test function.
2. procedure duncan.test is better, the limitations in convergence were corrected.
3. The influence in AMMI (type=3) is relative neighbor graph as a sub-graph.
4. The post hoc nonparametrics tests (kruskal, friedman, durbin and waerden) 
are using the criterium Fisher's least significant difference (LSD)

Version agricolae 1-2.4 (June 12, 2016)
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1. Add suggests packages: RANN and rgeos to plot AMMI
2. Concordance index in correlation function(), additional arg (method="lin").
3. New function orderPvalue(). Grouping the treatments in a comparison with p.value minimum value (alpha)
4. 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.

Version agricolae 1-2.3 (October 6, 2015)
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1. REGW.test(). New function for multiple comparisons of treatments. 
(Ryan, Einot and Gabriel and Welsch)
2. diffograph(). New function: Mean-mean scatter plot, test: Bonferroni, Fisher, Duncan, Student-Newman-Keul 
Tukey, Kruskal-Wallis, Friedman and Waerden test.
3. Changes in all comparison means, add parameters to facility function diffograph.
4. Added randomization parameter (TRUE or FALSE) in all design function.
5. Update Tutorial

Version agricolae 1-2.2 (August 12, 2015)
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1. Now in the frequency table shows the relative frequency as a percentage, the function is table.freq or 
summary( graph.freq or hist object)
2. The histogram class is added to graph.freq and it can use the package HistogramTools
3. The function design.bib create optimal design, use function optBlock(algDesign)
4. sketch option in design: rbcd, lsd, graeco, youden, bib

Version agricolae 1-2.1 (August 25, 2014)
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1. Move packages from Suggests to Imports
2. AUDPS. The Area Under the Disease Progress Stairs.
3. AMMI stability value (ASV) and Yield stability index (YSI)
4. Design youden
5. Now the PBIB.test function uses missing values.

Version agricolae 1-2.0 (June 30, 2014)
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1. AMMI: aditional parameters PC=FALSE or TRUE, output principal components, check error equal cero.
2. plot.AMMI: graphic aditional parameters lwd = 1.8, length = 0.1 to arrow function 
3. simulation.model: aditional parameter console=FALSE or TRUE, output in console
4. resampling.model: aditional parameter console=FALSE or TRUE, output in console
5. stability.par: aditional parameter console=FALSE or TRUE, output in console
6. stability.nonpar: aditional parameter console=FALSE or TRUE, output in console

Version agricolae 1-1.9 (June 17, 2014)
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1. 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.
2. design.rcbd(..., continue=FALSE) 
continue=TRUE or FALSE, continuous numbering of plot.
3. Median.test. New function for multiple comparisons of treatments with Median.
4. 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.
5. 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)
6. Changed parameters by default "first = TRUE" in designs: rcbd, ab, split and lsd.
7. Now vignettes in agricolae.
8. change name ogive.freq by ojiva.freq, the parameters are same.
9. AUDPC the evaluation parameter  now can be numeric vector. To see help(audpc)  

Version agricolae 1-1.8 (February 21, 2014)
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* 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.
# Randomized complete design.
trt<-LETTERS[1:5]
outdesign<-design.rcbd(trt,r=4, serie=2)
book<-outdesign$book
> t(matrix(book[,1],5))
     [,1] [,2] [,3] [,4] [,5]
[1,]  101  102  103  104  105
[2,]  201  202  203  204  205
[3,]  301  302  303  304  305
[4,]  401  402  403  404  405
fieldbook <- zigzag(outdesign)
> t(matrix(fieldbook[,1],5))
     [,1] [,2] [,3] [,4] [,5]
[1,]  101  102  103  104  105
[2,]  205  204  203  202  201
[3,]  301  302  303  304  305
[4,]  405  404  403  402  401

* 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 with parameters and field book.
* Cyclic have the stetches with parameters and field book.


