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EricMarconEricMarcon
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Merge pull request #3 from teunbrand/master
Compatibility with ggplot2 3.6.0
2 parents 104c5eb + b9740e3 commit 3caad62

16 files changed

+42
-42
lines changed

‎R/Accumulation.R

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@@ -237,9 +237,9 @@ autoplot.AccumCurve <-
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function(object, ..., main = NULL,
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xlab = "Sample Size", ylab = NULL,
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ShadeColor = "grey75", alpha = 0.3, BorderColor = "red",
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col = ggplot2::GeomLine$default_aes$colour,
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lty = ggplot2::GeomLine$default_aes$linetype,
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lwd = ggplot2::GeomLine$default_aes$size)
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col = "black",
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lty = 1,
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lwd = 0.5)
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{
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thePlot <- ggplot2::ggplot(as.data.frame.list(object), ggplot2::aes(x=.data$x, y=.data$y))
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if (!(is.null(object$high) | is.null(object$low))) {

‎R/CommunityProfile.R

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@@ -131,9 +131,9 @@ autoplot.CommunityProfile <-
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function(object, ..., main = NULL,
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xlab = "Order of Diversity", ylab = "Diversity",
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ShadeColor = "grey75", alpha = 0.3, BorderColor = "red",
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col = ggplot2::GeomLine$default_aes$colour,
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lty = ggplot2::GeomLine$default_aes$linetype,
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lwd = ggplot2::GeomLine$default_aes$size)
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col = "black",
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lty = 1,
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lwd = 0.5)
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{
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thePlot <- ggplot2::ggplot(as.data.frame.list(object), ggplot2::aes(x=.data$x, y=.data$y))
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if (!(is.null(object$high) | is.null(object$low))) {

‎R/DivPart.R

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@@ -93,8 +93,8 @@ function (x, ...)
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autoplot.DivPart <-
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function (object, col = ggplot2::GeomRect$default_aes$fill,
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border = ggplot2::GeomRect$default_aes$colour, ...)
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function (object, col = "grey35",
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border = NA, ...)
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{
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thePlot <- ggplot2::ggplot() +
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ggplot2::geom_rect(ggplot2::aes(xmin=.data$xmin, ymin=.data$ymin, xmax=.data$xmax, ymax=.data$ymax),

‎R/DivProfile.R

Lines changed: 3 additions & 3 deletions
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@@ -219,9 +219,9 @@ function (x, ..., main = NULL, xlab = "Order of Diversity", ylab = NULL, Which =
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autoplot.DivProfile <-
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function (object, ..., main = NULL, xlab = "Order of Diversity", ylab = NULL, Which = "All",
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ShadeColor = "grey75", alpha = 0.3, BorderColor = "red", labels = NULL, font.label = list(size=11, face="plain"),
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col = ggplot2::GeomLine$default_aes$colour,
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lty = ggplot2::GeomLine$default_aes$linetype,
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lwd = ggplot2::GeomLine$default_aes$size)
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col = "black",
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lty = 1,
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lwd = 0.5)
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{
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if (Which == "All" | (Which == "Alpha" & is.null(main))) main <- "Total Alpha Diversity"
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if (Which == "All" | (Which == "Alpha" & is.null(ylab))) ylab <- expression(paste(alpha, " diversity"))

‎R/MCdiversity.R

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@@ -20,8 +20,8 @@ function (x, ...)
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autoplot.MCdiversity <-
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function (object, col = ggplot2::GeomCol$default_aes$fill,
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border = ggplot2::GeomCol$default_aes$colour, ...)
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function (object, col = "grey35",
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border = NA, ...)
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{
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theData <- data.frame(x=c(names(object$Communities), "", "Metacommunity"), y=c(object$Communities, 0, object$Total))
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# Factors to keep the order of bars (avoid sort by name)

‎R/MCentropy.R

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@@ -19,8 +19,8 @@ function (x, ...)
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2020

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autoplot.MCentropy <-
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function (object, col = ggplot2::GeomCol$default_aes$fill,
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border = ggplot2::GeomCol$default_aes$colour, ...)
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function (object, col = "grey35",
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border = NA, ...)
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{
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theData <- data.frame(x=c(names(object$Communities), "", "Metacommunity"), y=c(object$Communities, 0, object$Total))
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# Factors to keep the order of bars (avoid sort by name)

‎R/PhyloValue.R

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -33,9 +33,9 @@ function (x, xlab = expression(italic("T")), ylab = NULL, main = NULL, ...)
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autoplot.PhyloValue <-
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function (object, xlab = expression(italic("T")), ylab = NULL, main = NULL,
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col = ggplot2::GeomLine$default_aes$colour,
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lty = ggplot2::GeomLine$default_aes$linetype,
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lwd = ggplot2::GeomLine$default_aes$size,
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col = "black",
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lty = 1,
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lwd = 0.5,
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...)
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{
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Entity <- ""

‎R/SpeciesDistribution.R

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Original file line numberDiff line numberDiff line change
@@ -371,9 +371,9 @@ function(x, ..., Distribution = NULL,
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autoplot.SpeciesDistribution <-
372372
function(object, ..., Distribution = NULL,
373373
ylog = TRUE, main = NULL, xlab = "Rank", ylab = NULL,
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pch = ggplot2::GeomPoint$default_aes$shape,
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col = ggplot2::GeomPoint$default_aes$colour,
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cex = ggplot2::GeomPoint$default_aes$size)
374+
pch = 19,
375+
col = "black",
376+
cex = 1.5)
377377
{
378378
# Eliminate zeros and sort
379379
Ns <- sort(object[object > 0], decreasing = TRUE)

‎man/Accumulation.Rd

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -27,9 +27,9 @@ DivAC(Ns, q = 0, n.seq = seq_len(sum(Ns)), PCorrection="Chao2015", Unveiling="ge
2727
\method{autoplot}{AccumCurve}(object, ..., main = NULL,
2828
xlab = "Sample Size", ylab = NULL,
2929
ShadeColor = "grey75", alpha = 0.3, BorderColor = "red",
30-
col = ggplot2::GeomLine$default_aes$colour,
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lty = ggplot2::GeomLine$default_aes$linetype,
32-
lwd = ggplot2::GeomLine$default_aes$size)
30+
col = "black",
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lty = 1,
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lwd = 0.5)
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}
3434
\arguments{
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\item{x}{

‎man/CommunityProfile.Rd

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -23,9 +23,9 @@ is.CommunityProfile(x)
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\method{autoplot}{CommunityProfile}(object, \dots, main = NULL,
2424
xlab = "Order of Diversity", ylab = "Diversity",
2525
ShadeColor = "grey75", alpha = 0.3, BorderColor = "red",
26-
col = ggplot2::GeomLine$default_aes$colour,
27-
lty = ggplot2::GeomLine$default_aes$linetype,
28-
lwd = ggplot2::GeomLine$default_aes$size)
26+
col = "black",
27+
lty = 1,
28+
lwd = 0.5)
2929
CEnvelope(Profile, LineWidth = 2, ShadeColor = "grey75", BorderColor = "red", \dots)
3030
}
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\arguments{

‎man/DivPart.Rd

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,8 +15,8 @@ DivPart(q = 1, MC, Biased = TRUE, Correction = "Best", Tree = NULL,
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Normalize = TRUE, Z = NULL, CheckArguments = TRUE)
1616
is.DivPart(x)
1717
\method{plot}{DivPart}(x, \dots)
18-
\method{autoplot}{DivPart}(object, col = ggplot2::GeomRect$default_aes$fill,
19-
border = ggplot2::GeomRect$default_aes$colour, \dots)
18+
\method{autoplot}{DivPart}(object, col = "grey35",
19+
border = NA, \dots)
2020
\method{summary}{DivPart}(object, \dots)
2121
}
2222
\arguments{

‎man/DivProfile.Rd

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -22,9 +22,9 @@ is.DivProfile(x)
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\method{autoplot}{DivProfile}(object, \dots, main = NULL, xlab = "Order of Diversity",
2323
ylab = NULL, Which = "All", ShadeColor = "grey75", alpha = 0.3, BorderColor = "red",
2424
labels = NULL, font.label = list(size=11, face="plain"),
25-
col = ggplot2::GeomLine$default_aes$colour,
26-
lty = ggplot2::GeomLine$default_aes$linetype,
27-
lwd = ggplot2::GeomLine$default_aes$size)
25+
col = "black",
26+
lty = 1,
27+
lwd = 0.5)
2828
\method{summary}{DivProfile}(object, \dots)
2929
}
3030
\arguments{

‎man/MCdiversity.Rd

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
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\usage{
1414
is.MCdiversity(x)
1515
\method{plot}{MCdiversity}(x, \dots)
16-
\method{autoplot}{MCdiversity}(object, col = ggplot2::GeomCol$default_aes$fill,
17-
border = ggplot2::GeomCol$default_aes$colour, \dots)
16+
\method{autoplot}{MCdiversity}(object, col = "grey35",
17+
border = NA, \dots)
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\method{summary}{MCdiversity}(object, \dots)
1919
}
2020
\arguments{

‎man/MCentropy.Rd

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
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\usage{
1414
is.MCentropy(x)
1515
\method{plot}{MCentropy}(x, \dots)
16-
\method{autoplot}{MCentropy}(object, col = ggplot2::GeomCol$default_aes$fill,
17-
border = ggplot2::GeomCol$default_aes$colour, \dots)
16+
\method{autoplot}{MCentropy}(object, col = "grey35",
17+
border = NA, \dots)
1818
\method{summary}{MCentropy}(object, \dots)
1919
}
2020
\arguments{

‎man/PhyloValue.Rd

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -13,9 +13,9 @@
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\usage{
1414
is.PhyloValue(x)
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\method{autoplot}{PhyloValue}(object, xlab = expression(italic("T")), ylab = NULL, main = NULL,
16-
col = ggplot2::GeomLine$default_aes$colour,
17-
lty = ggplot2::GeomLine$default_aes$linetype,
18-
lwd = ggplot2::GeomLine$default_aes$size,
16+
col = "black",
17+
lty = 1,
18+
lwd = 0.5,
1919
\dots)
2020
\method{plot}{PhyloValue}(x, xlab = expression(italic("T")), ylab = NULL, main = NULL, \dots)
2121
\method{summary}{PhyloValue}(object, \dots)

‎man/SpeciesDistribution.Rd

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -32,9 +32,9 @@ as.SpeciesDistribution(x, \dots)
3232
\method{as.SpeciesDistribution}{numeric}(x, \dots)
3333
\method{autoplot}{SpeciesDistribution}(object, \dots, Distribution = NULL,
3434
ylog = TRUE, main = NULL, xlab = "Rank", ylab = NULL,
35-
pch = ggplot2::GeomPoint$default_aes$shape,
36-
col = ggplot2::GeomPoint$default_aes$colour,
37-
cex = ggplot2::GeomPoint$default_aes$size)
35+
pch = 19,
36+
col = "black",
37+
cex = 1.5)
3838
\method{plot}{SpeciesDistribution}(x, \dots, Distribution = NULL,
3939
type = "b", log = "y", main = NULL, xlab = "Rank", ylab = NULL)
4040
is.SpeciesDistribution(x)

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