Merge branch 'startup-message'

DESCRIPTION

@@ -37,9 +37,9 @@ Authors@R: c(person("Jari", "Oksanen", role=c("aut","cre"),
 	   person("Adrian", "Stier", role="aut"),
 	   person("Cajo J.F.", "Ter Braak", role="aut"),
 	   person("James", "Weedon", role="aut"))
-Depends: permute (>= 0.9-0), lattice, R (>= 4.1.0)
+Depends: permute (>= 0.9-0), R (>= 4.1.0)
 Suggests: parallel, knitr, markdown, vegan3d (>= 1.3-0)
-Imports: MASS, cluster, mgcv
+Imports: MASS, cluster, lattice, mgcv
 VignetteBuilder: utils, knitr
 Description: Ordination methods, diversity analysis and other
   functions for community and vegetation ecologists.

man/adonis.Rd

@@ -160,9 +160,6 @@ dat
 Agropyron <- with(dat, as.numeric(field) + as.numeric(NO3)+2) +rnorm(12)/2
 Schizachyrium <- with(dat, as.numeric(field) - as.numeric(NO3)+2) +rnorm(12)/2
 total <- Agropyron + Schizachyrium
-dotplot(total ~ NO3, dat, jitter.x=TRUE, groups=field,
-        type=c('p','a'), xlab="NO3", auto.key=list(columns=3, lines=TRUE) )
-
 Y <- data.frame(Agropyron, Schizachyrium)
 mod <- metaMDS(Y, trace = FALSE)
 plot(mod)

man/oecosimu.Rd

@@ -245,8 +245,8 @@ out
 plot(as.ts(out))
 lag.plot(as.ts(out))
 acf(as.ts(out))
-## Density plot
-densityplot(permustats(out), as.table = TRUE, layout = c(1,4))
+## Density plot in lattice graphics
+lattice::densityplot(permustats(out), as.table = TRUE, layout = c(1,4))
 ## Use quantitative null models to compare
 ## mean Bray-Curtis dissimilarities
 data(dune)

man/ordixyplot.Rd

@@ -139,7 +139,7 @@ ordixyplot(ord, data=dune.env, form = CA1 ~ CA2 | Management,
 ## Choose a different scaling
 ordixyplot(ord, scaling = "symmetric")
 ## ... Slices of third axis
-ordixyplot(ord, form = CA1 ~ CA2 | equal.count(CA3, 4),
+ordixyplot(ord, form = CA1 ~ CA2 | lattice::equal.count(CA3, 4),
    type = c("g","p", "polygon"))
 ## Display environmental variables
 ordixyplot(ord, envfit = envfit(ord ~ Management + A1, dune.env, choices=1:3))

man/permustats.Rd

@@ -170,8 +170,9 @@ mod <- adonis2(dune ~ Management + A1, data = dune.env)
 ## use permustats
 perm <- permustats(mod)
 summary(perm)
-densityplot(perm)
-qqmath(perm)
+## lattice graphics
+lattice::densityplot(perm)
+lattice::qqmath(perm)
 boxplot(perm, scale=TRUE, lty=1, pch=16, cex=0.6, col="hotpink", ylab="SES")
 abline(h=0, col="skyblue")
 ## example of multiple types of statistic

man/permutest.betadisper.Rd

@@ -92,10 +92,10 @@ pmod <- permutest(mod, permutations = 99, pairwise = TRUE)
 (mod.HSD <- TukeyHSD(mod))
 plot(mod.HSD)
 
-## Has permustats() method
+## lattice graphics with permustats
 pstat <- permustats(pmod)
-densityplot(pstat, scales = list(x = list(relation = "free")))
-qqmath(pstat, scales = list(relation = "free"))
+lattice::densityplot(pstat, scales = list(x = list(relation = "free")))
+lattice::qqmath(pstat, scales = list(relation = "free"))
 }
 \keyword{methods}
 \keyword{multivariate}

tests/Examples/vegan-Ex.Rout.save

@@ -22,8 +22,6 @@ Type 'q()' to quit R.
 > options(warn = 1)
 > library('vegan')
 Loading required package: permute
-Loading required package: lattice
-This is vegan 2.7-0
 > 
 > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
 > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
@@ -811,9 +809,6 @@ Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’
 > Agropyron <- with(dat, as.numeric(field) + as.numeric(NO3)+2) +rnorm(12)/2
 > Schizachyrium <- with(dat, as.numeric(field) - as.numeric(NO3)+2) +rnorm(12)/2
 > total <- Agropyron + Schizachyrium
-> dotplot(total ~ NO3, dat, jitter.x=TRUE, groups=field,
-+         type=c('p','a'), xlab="NO3", auto.key=list(columns=3, lines=TRUE) )
-> 
 > Y <- data.frame(Agropyron, Schizachyrium)
 > mod <- metaMDS(Y, trace = FALSE)
 > plot(mod)
@@ -5038,8 +5033,8 @@ Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’
 > plot(as.ts(out))
 > lag.plot(as.ts(out))
 > acf(as.ts(out))
-> ## Density plot
-> densityplot(permustats(out), as.table = TRUE, layout = c(1,4))
+> ## Density plot in lattice graphics
+> lattice::densityplot(permustats(out), as.table = TRUE, layout = c(1,4))
 > ## Use quantitative null models to compare
 > ## mean Bray-Curtis dissimilarities
 > data(dune)
@@ -5850,7 +5845,7 @@ detaching ‘package:mgcv’, ‘package:nlme’
 > ## Choose a different scaling
 > ordixyplot(ord, scaling = "symmetric")
 > ## ... Slices of third axis
-> ordixyplot(ord, form = CA1 ~ CA2 | equal.count(CA3, 4),
+> ordixyplot(ord, form = CA1 ~ CA2 | lattice::equal.count(CA3, 4),
 +    type = c("g","p", "polygon"))
 > ## Display environmental variables
 > ordixyplot(ord, envfit = envfit(ord ~ Management + A1, dune.env, choices=1:3))
@@ -6177,8 +6172,9 @@ Model    2.9966 5.3815 1.0184       0.9625 1.6979    0.002 **
 Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
 
 (Interval (Upper - Lower) = 0.95)
-> densityplot(perm)
-> qqmath(perm)
+> ## lattice graphics
+> lattice::densityplot(perm)
+> lattice::qqmath(perm)
 > boxplot(perm, scale=TRUE, lty=1, pch=16, cex=0.6, col="hotpink", ylab="SES")
 > abline(h=0, col="skyblue")
 > ## example of multiple types of statistic
@@ -6271,10 +6267,10 @@ ungrazed-grazed -0.1219422 -0.2396552 -0.004229243 0.0429502
 
 > plot(mod.HSD)
 > 
-> ## Has permustats() method
+> ## lattice graphics with permustats
 > pstat <- permustats(pmod)
-> densityplot(pstat, scales = list(x = list(relation = "free")))
-> qqmath(pstat, scales = list(relation = "free"))
+> lattice::densityplot(pstat, scales = list(x = list(relation = "free")))
+> lattice::qqmath(pstat, scales = list(relation = "free"))
 > 
 > 
 > 
@@ -9146,7 +9142,7 @@ Procrustes sum of squares:
 > cleanEx()
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  8.741 0.323 9.079 0 0 
+Time elapsed:  8.748 0.349 9.109 0 0 
 > grDevices::dev.off()
 null device 
           1