Methods to display the outputs of an analysis performed with ade4
Description
S3 methods to display the outputs of an analysis performed with ade4
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115  ## S3 method for class 'foucart'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), pos = 1,
storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mcoa'
kplot(object, xax = 1, yax = 2, which.tab = 1:nrow(object$cov2),
option = c("points", "axis", "columns"), pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mfa'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), traject = FALSE,
permute = FALSE, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mbpcaiv'
kplot(object, xax = 1, yax = 2, which.tab =
1:length(object$blo), pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pta'
kplot(object, xax = 1, yax = 2, which.tab = 1:nrow(object$RV), which.graph = 1:4,
pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'sepan'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), permute = FALSE,
traject = FALSE, posieig = "bottomleft", pos = 1, storeData = TRUE, plot = TRUE, ...)
kplotsepan.coa(object, xax = 1, yax = 2, which.tab = 1:length(object$blo),
permute = FALSE, posieig = "bottomleft", pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'statis'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$tab.names), traject = FALSE,
arrow = TRUE, class = NULL, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'acm'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betcoi'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betdpcoa'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betwitdpcoa'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betrlq'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'between'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'coinertia'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'discrimin'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'dpcoa'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'fca'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'foucart'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE,
plot = TRUE, ...)
## S3 method for class 'krandboot'
plot(x, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'krandxval'
plot(x, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mcoa'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mfa'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE,
plot = TRUE, ...)
## S3 method for class 'multiblock'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'multispati'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'niche'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pcaiv'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pta'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'procuste'
plot(x, xax = 1, yax = 2, pos = 1, storeData =
TRUE, plot = TRUE, ...)
## S3 method for class 'randboot'
plot(x, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'randxval'
plot(x, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'rlq'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'sepan'
plot(x, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'statis'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'witcoi'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'witdpcoa'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'within'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'witrlq'
plot(x, xax = 1, yax = 2, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'dudi'
scatter(x, xax = 1, yax = 2, permute = FALSE, posieig = "topleft", prop = FALSE,
density.plot = ifelse(permute, ncol(x$tab) > 1000, nrow(x$tab) > 1000), plot = TRUE,
storeData = TRUE, pos = 1, ...)
## S3 method for class 'coa'
scatter(x, xax = 1, yax = 2, method = 1:3, posieig = "topleft", pos = 1,
storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pco'
scatter(x, xax = 1, yax = 2, posieig = "topleft", pos = 1, storeData = TRUE,
plot = TRUE, ...)
## S3 method for class 'nipals'
scatter(x, xax = 1, yax = 2, posieig = "topleft", pos = 1, storeData = TRUE,
plot = TRUE, ...)
## S3 method for class 'acm'
score(x, xax = 1, which.var = NULL, type = c("points", "boxplot"), pos = 1,
storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mix'
score(x, xax = 1, which.var = NULL, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pca'
score(x, xax = 1, which.var = NULL, pos = 1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'dudi'
screeplot(x, col.kept = "grey", col = "white", pos = 1, plot = TRUE, ...)
## S3 method for class 'dudi'
biplot(x, pos = 1, plot = TRUE, ...)

Arguments
object, x 
objects used to select a method 
xax 
an integer (or a vector) indicating which column(s) of object or 
yax 
an integer (or a vector) indicating which column(s) of object or 
which.tab 
a numeric vector (used in 
option 
a string of characters (only used in 
which.graph 
an integer between 1 and 4 (only used in 
permute 
a logical value (used in 
traject 
a logical value (used in 
posieig 
a character value or a twolength numeric vector (in normalized parent coordinates 
arrow 
a logical value (only used in 
class 
if not NULL, a factor of length equal to the number of the total columns of the Ktables (only used in 
prop 
a logical value (only used in 
density.plot 
a logical value (only used in 
method 
an integer between 1 and 3 (only used in 
which.var 
the numbers of the kept columns for the analysis, otherwise all columns (used in 
type 
a string of characters (only used in 
col.kept 
one color value to color the kept axes in the barchart (used in 
col 
one color value to color the axes in the barchart (used in 
plot 
a logical indicating if the graphics is displayed 
storeData 
a logical indicating if the data should be stored in
the returned object. If 
pos 
an integer indicating the position of the
environment where the data are stored, relative to the environment
where the function is called. Useful only if 
... 
additional graphical parameters (see

Value
Returns an ADEg
or an ADEgS
object.
The result is displayed if plot
is TRUE
.
Author(s)
Alice JulienLaferriere, Aurelie Siberchicot aurelie.siberchicot@univlyon1.fr and Stephane Dray
References
See ade4
website: <URL: http://pbil.univlyon1.fr/ADE4/>
Examples
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