[Pastecs-commits] r11 - in pkg: . inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 2 12:48:45 CET 2014
Author: phgrosjean
Date: 2014-03-02 12:48:45 +0100 (Sun, 02 Mar 2014)
New Revision: 11
Added:
pkg/inst/pastecs-Ex.R
Removed:
pkg/pastecs-Ex.R
Modified:
pkg/DESCRIPTION
Log:
Further rework of Author/Authors at R fields
Moving pastecs-Ex.R to inst/pastecs-Ex.R
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2014-03-02 09:00:05 UTC (rev 10)
+++ pkg/DESCRIPTION 2014-03-02 11:48:45 UTC (rev 11)
@@ -1,13 +1,13 @@
Package: pastecs
Title: Package for Analysis of Space-Time Ecological Series
-Version: 1.3-16
+Version: 1.3-17
Date: 2014-03-02
Author: Philippe Grosjean [aut, cre],
- Frederic Ibanez [aut, cre],
+ Frederic Ibanez [aut],
Michele Etienne [ctb]
Authors at R: c(person("Philippe", "Grosjean", role = c("aut", "cre"),
email = "phgrosjean at sciviews.org"),
- person("Frederic", "Ibanez", role = c("aut", "cre"),
+ person("Frederic", "Ibanez", role = "aut",
email = "ibanez at obs-vlfr.fr"),
person("Michele", "Etienne", role = "ctb",
email = "etienne at obs-vlfr.fr"))
Added: pkg/inst/pastecs-Ex.R
===================================================================
--- pkg/inst/pastecs-Ex.R (rev 0)
+++ pkg/inst/pastecs-Ex.R 2014-03-02 11:48:45 UTC (rev 11)
@@ -0,0 +1,1013 @@
+pkgname <- "pastecs"
+source(file.path(R.home("share"), "R", "examples-header.R"))
+options(warn = 1)
+library('pastecs')
+
+assign(".oldSearch", search(), pos = 'CheckExEnv')
+cleanEx()
+nameEx("AutoD2")
+### * AutoD2
+
+flush(stderr()); flush(stdout())
+
+### Name: AutoD2
+### Title: AutoD2, CrossD2 or CenterD2 analysis of a multiple time-series
+### Aliases: AutoD2 CrossD2 CenterD2
+### Keywords: ts multivariate htest
+
+### ** Examples
+
+data(marphy)
+marphy.ts <- as.ts(as.matrix(marphy[, 1:3]))
+AutoD2(marphy.ts)
+marphy.ts2 <- as.ts(as.matrix(marphy[, c(1, 4, 3)]))
+CrossD2(marphy.ts, marphy.ts2)
+# This is not identical to:
+CrossD2(marphy.ts2, marphy.ts)
+marphy.d2 <- CenterD2(marphy.ts, window=16)
+lines(c(17, 17), c(-1, 15), col=4, lty=2)
+lines(c(25, 25), c(-1, 15), col=4, lty=2)
+lines(c(30, 30), c(-1, 15), col=4, lty=2)
+lines(c(41, 41), c(-1, 15), col=4, lty=2)
+lines(c(46, 46), c(-1, 15), col=4, lty=2)
+text(c(8.5, 21, 27.5, 35, 43.5, 57), 11, labels=c("Peripheral Zone", "D1",
+ "C", "Front", "D2", "Central Zone")) # Labels
+time(marphy.ts)[marphy.d2$D2 > marphy.d2$chisq]
+
+
+
+cleanEx()
+nameEx("GetUnitText")
+### * GetUnitText
+
+flush(stderr()); flush(stdout())
+
+### Name: GetUnitText
+### Title: Format a nice time units for labels in graphs
+### Aliases: GetUnitText
+### Keywords: ts
+
+### ** Examples
+
+timeser <- ts(1:24, frequency=12) # 12 observations per year
+if (exists("is.R") && is.function(is.R) && is.R()) { # We are in R
+attr(timeser, "units") <- "years" # time in years for 'ts' object
+} else { # We are in Splus
+attr(attr(timeser, "tspar"), "units") <- "years" # Idem for Splus 'rts' object
+}
+GetUnitText(timeser) # formats unit (1/12 year=months)
+
+
+
+cleanEx()
+nameEx("abund")
+### * abund
+
+flush(stderr()); flush(stdout())
+
+### Name: abund
+### Title: Sort variables by abundance
+### Aliases: abund extract.abund identify.abund lines.abund plot.abund
+### print.abund print.summary.abund summary.abund
+### Keywords: multivariate
+
+### ** Examples
+
+data(bnr)
+bnr.abd <- abund(bnr)
+summary(bnr.abd)
+plot(bnr.abd, dpos=c(105, 100))
+bnr.abd$n <- 26
+# To identify a point on the graph, use: bnr.abd$n <- identify(bnr.abd)
+lines(bnr.abd)
+bnr2 <- extract(bnr.abd)
+names(bnr2)
+
+
+
+cleanEx()
+nameEx("buysbal")
+### * buysbal
+
+flush(stderr()); flush(stdout())
+
+### Name: buysbal
+### Title: Buys-Ballot table
+### Aliases: buysbal
+### Keywords: ts
+
+### ** Examples
+
+data(releve)
+buysbal(releve$Day, releve$Melosul, frequency=4, units="days",
+ datemin="21/03/1989", dateformat="d/m/Y")
+buysbal(releve$Day, releve$Melosul, frequency=4, units="days",
+ datemin="21/03/1989", dateformat="d/m/Y", count=TRUE)
+
+
+
+cleanEx()
+nameEx("daystoyears")
+### * daystoyears
+
+flush(stderr()); flush(stdout())
+
+### Name: daystoyears
+### Title: Convert time units from "days" to "years" or back
+### Aliases: daystoyears yearstodays
+### Keywords: ts
+
+### ** Examples
+
+# A vector with a "days" time-scale (25 values every 30 days)
+A <- (1:25)*30
+# Convert it to a "years" time-scale, using 23/05/2001 (d/m/Y) as first value
+B <- daystoyears(A, datemin="23/05/2001", dateformat="d/m/Y")
+B
+# Convert it back to "days" time-scale
+yearstodays(B, xmin=30)
+
+# Here is an example showing the shift introduced, and its consequence:
+C <- daystoyears(unclass(as.Date(c("1970-1-1","1971-1-1","1972-1-1","1973-1-1"),
+ format = "%Y-%m-%d")))
+C
+
+
+
+cleanEx()
+nameEx("decaverage")
+### * decaverage
+
+flush(stderr()); flush(stdout())
+
+### Name: decaverage
+### Title: Time series decomposition using a moving average
+### Aliases: decaverage
+### Keywords: ts smooth
+
+### ** Examples
+
+data(marbio)
+ClausoB.ts <- ts(log(marbio$ClausocalanusB + 1))
+ClausoB.dec <- decaverage(ClausoB.ts, order=2, times=10, sides=2, ends="fill")
+plot(ClausoB.dec, col=c(1, 3, 2), xlab="stations")
+# A stacked graph is more representative in this case
+plot(ClausoB.dec, col=c(1, 3), xlab="stations", stack=FALSE, resid=FALSE,
+ lpos=c(53, 4.3))
+
+
+
+cleanEx()
+nameEx("deccensus")
+### * deccensus
+
+flush(stderr()); flush(stdout())
+
+### Name: deccensus
+### Title: Time decomposition using the CENSUS II method
+### Aliases: deccensus
+### Keywords: ts smooth
+
+### ** Examples
+
+data(releve)
+# Get regulated time series with a 'years' time-scale
+rel.regy <- regul(releve$Day, releve[3:8], xmin=6, n=87, units="daystoyears",
+ frequency=24, tol=2.2, methods="linear", datemin="21/03/1989", dateformat="d/m/Y")
+rel.ts <- tseries(rel.regy)
+# We must have complete cycles to allow using deccensus()
+start(rel.ts)
+end(rel.ts)
+rel.ts2 <- window(rel.ts, end=c(1992,5))
+rel.dec2 <- deccensus(rel.ts2[, "Melosul"], trend=TRUE)
+plot(rel.dec2, col=c(1,4,3,2))
+
+
+
+cleanEx()
+nameEx("decdiff")
+### * decdiff
+
+flush(stderr()); flush(stdout())
+
+### Name: decdiff
+### Title: Time series decomposition using differences (trend elimination)
+### Aliases: decdiff
+### Keywords: ts smooth
+
+### ** Examples
+
+data(marbio)
+ClausoB.ts <- ts(log(marbio$ClausocalanusB + 1))
+ClausoB.dec <- decdiff(ClausoB.ts, lag=1, order=2, ends="fill")
+plot(ClausoB.dec, col=c(1, 4, 2), xlab="stations")
+
+
+
+cleanEx()
+nameEx("decevf")
+### * decevf
+
+flush(stderr()); flush(stdout())
+
+### Name: decevf
+### Title: Time series decomposition using eigenvector filtering (EVF)
+### Aliases: decevf
+### Keywords: ts smooth
+
+### ** Examples
+
+data(releve)
+melo.regy <- regul(releve$Day, releve$Melosul, xmin=9, n=87,
+ units="daystoyears", frequency=24, tol=2.2, methods="linear",
+ datemin="21/03/1989", dateformat="d/m/Y")
+melo.ts <- tseries(melo.regy)
+acf(melo.ts)
+# Autocorrelation is not significant after 0.16
+# That corresponds to a lag of 0.16*24=4 (frequency=24)
+melo.evf <- decevf(melo.ts, lag=4, axes=1)
+plot(melo.evf, col=c(1, 4, 2))
+# A superposed graph is better in the present case
+plot(melo.evf, col=c(1, 4), xlab="stations", stack=FALSE, resid=FALSE,
+ lpos=c(0, 60000))
+
+
+
+cleanEx()
+nameEx("decloess")
+### * decloess
+
+flush(stderr()); flush(stdout())
+
+### Name: decloess
+### Title: Time series decomposition by the LOESS method
+### Aliases: decloess
+### Keywords: ts smooth
+
+### ** Examples
+
+data(releve)
+melo.regy <- regul(releve$Day, releve$Melosul, xmin=9, n=87,
+ units="daystoyears", frequency=24, tol=2.2, methods="linear",
+ datemin="21/03/1989", dateformat="d/m/Y")
+melo.ts <- tseries(melo.regy)
+melo.dec <- decloess(melo.ts, s.window="periodic")
+plot(melo.dec, col=1:3)
+
+
+
+cleanEx()
+nameEx("decmedian")
+### * decmedian
+
+flush(stderr()); flush(stdout())
+
+### Name: decmedian
+### Title: Time series decomposition using a running median
+### Aliases: decmedian
+### Keywords: ts smooth
+
+### ** Examples
+
+data(marbio)
+ClausoB.ts <- ts(log(marbio$ClausocalanusB + 1))
+ClausoB.dec <- decmedian(ClausoB.ts, order=2, times=10, ends="fill")
+plot(ClausoB.dec, col=c(1, 4, 2), xlab="stations")
+# This is a transect across a frontal zone:
+plot(ClausoB.dec, col=c(0, 2), xlab="stations", stack=FALSE, resid=FALSE)
+lines(c(17, 17), c(0, 10), col=4, lty=2)
+lines(c(25, 25), c(0, 10), col=4, lty=2)
+lines(c(30, 30), c(0, 10), col=4, lty=2)
+lines(c(41, 41), c(0, 10), col=4, lty=2)
+lines(c(46, 46), c(0, 10), col=4, lty=2)
+text(c(8.5, 21, 27.5, 35, 43.5, 57), 8.7, labels=c("Peripheral Zone", "D1",
+ "C", "Front", "D2", "Central Zone"))
+
+
+
+cleanEx()
+nameEx("decreg")
+### * decreg
+
+flush(stderr()); flush(stdout())
+
+### Name: decreg
+### Title: Time series decomposition using a regression model
+### Aliases: decreg
+### Keywords: ts smooth
+
+### ** Examples
+
+data(marphy)
+density <- ts(marphy[, "Density"])
+plot(density)
+Time <- time(density)
+
+# Linear model to represent trend
+density.lin <- lm(density ~ Time)
+summary(density.lin)
+xreg <- predict(density.lin)
+lines(xreg, col=3)
+density.dec <- decreg(density, xreg)
+plot(density.dec, col=c(1, 3, 2), xlab="stations")
+
+# Order 2 polynomial to represent trend
+density.poly <- lm(density ~ Time + I(Time^2))
+summary(density.poly)
+xreg2 <- predict(density.poly)
+plot(density)
+lines(xreg2, col=3)
+density.dec2 <- decreg(density, xreg2)
+plot(density.dec2, col=c(1, 3, 2), xlab="stations")
+
+# Fit a sinusoidal model on seasonal (artificial) data
+tser <- ts(sin((1:100)/12*pi)+rnorm(100, sd=0.3), start=c(1998, 4),
+ frequency=24)
+Time <- time(tser)
+tser.sin <- lm(tser ~ I(cos(2*pi*Time)) + I(sin(2*pi*Time)))
+summary(tser.sin)
+tser.reg <- predict(tser.sin)
+tser.dec <- decreg(tser, tser.reg)
+plot(tser.dec, col=c(1, 4), xlab="stations", stack=FALSE, resid=FALSE,
+ lpos=c(0, 4))
+plot(tser.dec, col=c(1, 4, 2), xlab="stations")
+
+# One can also use nonlinear models (see 'nls')
+# or autoregressive models (see 'ar' and others in 'ts' library)
+
+
+
+cleanEx()
+nameEx("disjoin")
+### * disjoin
+
+flush(stderr()); flush(stdout())
+
+### Name: disjoin
+### Title: Complete disjoined coded data (binary coding)
+### Aliases: disjoin
+### Keywords: manip
+
+### ** Examples
+
+# Artificial data with 1/5 of zeros
+Z <- c(abs(rnorm(8000)), rep(0, 2000))
+# Let the program chose cuts
+table(cut(Z, breaks=5))
+# Create one class for zeros, and 4 classes for the other observations
+Z2 <- Z[Z != 0]
+cuts <- c(-1e-10, 1e-10, quantile(Z2, 1:5/5, na.rm=TRUE))
+cuts
+table(cut(Z, breaks=cuts))
+# Binary coding of these data
+disjoin(cut(Z, breaks=cuts))[1:10, ]
+
+
+
+cleanEx()
+nameEx("disto")
+### * disto
+
+flush(stderr()); flush(stdout())
+
+### Name: disto
+### Title: Compute and plot a distogram
+### Aliases: disto
+### Keywords: multivariate ts
+
+### ** Examples
+
+data(bnr)
+disto(bnr)
+
+
+
+cleanEx()
+nameEx("escouf")
+### * escouf
+
+flush(stderr()); flush(stdout())
+
+### Name: escouf
+### Title: Choose variables using the Escoufier's equivalent vectors method
+### Aliases: escouf extract.escouf identify.escouf lines.escouf plot.escouf
+### print.escouf print.summary.escouf summary.escouf
+### Keywords: multivariate
+
+### ** Examples
+
+data(marbio)
+marbio.esc <- escouf(marbio)
+summary(marbio.esc)
+plot(marbio.esc)
+# The x-axis has short labels. For more info., enter:
+marbio.esc$vr
+# Define a level at which to extract most significant variables
+marbio.esc$level <- 0.90
+# Show it on the graph
+lines(marbio.esc)
+# This can also be done interactively on the plot using:
+# marbio.esc$level <- identify(marbio.esc)
+# Finally, extract most significant variables
+marbio2 <- extract(marbio.esc)
+names(marbio2)
+
+
+
+cleanEx()
+nameEx("first")
+### * first
+
+flush(stderr()); flush(stdout())
+
+### Name: first
+### Title: Get the first element of a vector
+### Aliases: first
+### Keywords: manip
+
+### ** Examples
+
+a <- c(NA, 1, 2, NA, 3, 4, NA)
+first(a)
+first(a, na.rm=TRUE)
+
+
+
+cleanEx()
+nameEx("is.tseries")
+### * is.tseries
+
+flush(stderr()); flush(stdout())
+
+### Name: is.tseries
+### Title: Is this object a time series?
+### Aliases: is.tseries
+### Keywords: ts
+
+### ** Examples
+
+tser <- ts(sin((1:100)/6*pi)+rnorm(100, sd=0.5), start=c(1998, 4), frequency=12)
+is.tseries(tser) # TRUE
+not.a.ts <- c(1,2,3)
+is.tseries(not.a.ts) # FALSE
+
+
+
+cleanEx()
+nameEx("last")
+### * last
+
+flush(stderr()); flush(stdout())
+
+### Name: last
+### Title: Get the last element of a vector
+### Aliases: last
+### Keywords: manip
+
+### ** Examples
+
+a <- c(NA, 1, 2, NA, 3, 4, NA)
+last(a)
+last(a, na.rm=TRUE)
+
+
+
+cleanEx()
+nameEx("local.trend")
+### * local.trend
+
+flush(stderr()); flush(stdout())
+
+### Name: local.trend
+### Title: Calculate local trends using cumsum
+### Aliases: local.trend identify.local.trend
+### Keywords: ts
+
+### ** Examples
+
+data(bnr)
+# Calculate and plot cumsum for the 8th series
+bnr8.lt <- local.trend(bnr[,8])
+# To identify local trends, use:
+# identify(bnr8.lt)
+# and click points between which you want to compute local linear trends...
+
+
+
+cleanEx()
+nameEx("match.tol")
+### * match.tol
+
+flush(stderr()); flush(stdout())
+
+### Name: match.tol
+### Title: Determine matching observation with a tolerance in time-scale
+### Aliases: match.tol
+### Keywords: ts manip
+
+### ** Examples
+
+X <- 1:5
+Table <- c(1, 3.1, 3.8, 4.4, 5.1, 6)
+match.tol(X, Table)
+match.tol(X, Table, tol=0.2)
+match.tol(X, Table, tol=0.55)
+
+
+
+cleanEx()
+nameEx("pennington")
+### * pennington
+
+flush(stderr()); flush(stdout())
+
+### Name: pennington
+### Title: Calculate Pennington statistics
+### Aliases: pennington
+### Keywords: univar
+
+### ** Examples
+
+data(marbio)
+pennington(marbio[, "Copepodits2"])
+pennington(marbio[, "Copepodits2"], calc="mean", na.rm=TRUE)
+
+
+
+cleanEx()
+nameEx("pgleissberg")
+### * pgleissberg
+
+flush(stderr()); flush(stdout())
+
+### Name: pgleissberg
+### Title: Gleissberg distribution probability
+### Aliases: pgleissberg
+### Keywords: distribution
+
+### ** Examples
+
+# Until n=50, the exact probability is returned
+pgleissberg(20, 10, lower.tail=TRUE, two.tailed=FALSE)
+# For higher n values, it is approximated by a normal distribution
+pgleissberg(60, 33, lower.tail=TRUE, two.tailed=FALSE)
+
+
+
+cleanEx()
+nameEx("regarea")
+### * regarea
+
+flush(stderr()); flush(stdout())
+
+### Name: regarea
+### Title: Regulate a series using the area method
+### Aliases: regarea
+### Keywords: ts manip chron smooth
+
+### ** Examples
+
+data(releve)
+# The 'Melosul' series is regulated with a 25-days window
+reg <- regarea(releve$Day, releve$Melosul, window=25)
+# Then with a 50-days window
+reg2 <- regarea(releve$Day, releve$Melosul, window=50)
+# The initial and both regulated series are shown on the graph for comparison
+plot(releve$Day, releve$Melosul, type="l")
+lines(reg$x, reg$y, col=2)
+lines(reg2$x, reg2$y, col=4)
+
+
+
+cleanEx()
+nameEx("regconst")
+### * regconst
+
+flush(stderr()); flush(stdout())
+
+### Name: regconst
+### Title: Regulate a series using the constant value method
+### Aliases: regconst
+### Keywords: ts manip chron smooth
+
+### ** Examples
+
+data(releve)
+reg <- regconst(releve$Day, releve$Melosul)
+plot(releve$Day, releve$Melosul, type="l")
+lines(reg$x, reg$y, col=2)
+
+
+
+cleanEx()
+nameEx("reglin")
+### * reglin
+
+flush(stderr()); flush(stdout())
+
+### Name: reglin
+### Title: Regulation of a series using a linear interpolation
+### Aliases: reglin
+### Keywords: ts manip chron smooth
+
+### ** Examples
+
+data(releve)
+reg <- reglin(releve$Day, releve$Melosul)
+plot(releve$Day, releve$Melosul, type="l")
+lines(reg$x, reg$y, col=2)
+
+
+
+cleanEx()
+nameEx("regspline")
+### * regspline
+
+flush(stderr()); flush(stdout())
+
+### Name: regspline
+### Title: Regulation of a time series using splines
+### Aliases: regspline
+### Keywords: ts manip chron smooth
+
+### ** Examples
+
+data(releve)
+reg <- regspline(releve$Day, releve$Melosul)
+plot(releve$Day, releve$Melosul, type="l")
+lines(reg$x, reg$y, col=2)
+
+
+
+cleanEx()
+nameEx("regul")
+### * regul
+
+flush(stderr()); flush(stdout())
+
+### Name: regul
+### Title: Regulation of one or several time series using various methods
+### Aliases: regul extract.regul hist.regul identify.regul lines.regul
+### plot.regul print.regul print.specs.regul print.summary.regul
+### specs.regul summary.regul
+### Keywords: ts manip chron smooth
+
+### ** Examples
+
+data(releve)
+# The series in this data frame are very irregularly sampled in time:
+releve$Day
+length(releve$Day)
+intervals <- releve$Day[2:61]-releve$Day[1:60]
+intervals
+range(intervals)
+mean(intervals)
+# The series must be regulated to be converted in a 'rts' or 'ts object
+rel.reg <- regul(releve$Day, releve[3:8], xmin=9, n=63, deltat=21,
+ tol=1.05, methods=c("s","c","l","a","s","a"), window=21)
+rel.reg
+plot(rel.reg, 5)
+specs(rel.reg)
+# Now we can extract one or several regular time series
+melo.ts <- extract(rel.reg, series="Melosul")
+is.tseries(melo.ts)
+
+# One can convert time-scale from "days" to "years" during regulation
+# This is most useful for analyzing seasonal cycles in a second step
+melo.regy <- regul(releve$Day, releve$Melosul, xmin=6, n=87,
+ units="daystoyears", frequency=24, tol=2.2, methods="linear",
+ datemin="21/03/1989", dateformat="d/m/Y")
+melo.regy
+plot(melo.regy, main="Regulation of Melosul")
+# In this case, we have only one series in 'melo.regy'
+# We can use also 'tseries()' instead of 'extract()'
+melo.tsy <- tseries(melo.regy)
+is.tseries(melo.tsy)
+
+
+
+cleanEx()
+nameEx("regul.adj")
+### * regul.adj
+
+flush(stderr()); flush(stdout())
+
+### Name: regul.adj
+### Title: Adjust regulation parameters
+### Aliases: regul.adj
+### Keywords: ts chron
+
+### ** Examples
+
+# This example follows the example for regul.screen()
+# where we determined that xmin=9, deltat=21, n=63, with tol=1.05
+# is a good choice to regulate the irregular time series in 'releve'
+data(releve)
+regul.adj(releve$Day, xmin=9, deltat=21)
+# The histogram indicates that it is not useful to increase tol
+# more than 1.05, because few observations will be added
+# except if we increase it to 5-7, but this value could be
+# considered to be too large in comparison with deltat=22
+# On the other hand, with tol <= 1, the number of matching
+# observations will be almost divided by two!
+
+
+
+cleanEx()
+nameEx("regul.screen")
+### * regul.screen
+
+flush(stderr()); flush(stdout())
+
+### Name: regul.screen
+### Title: Test various regulation parameters
+### Aliases: regul.screen
+### Keywords: ts chron
+
+### ** Examples
+
+data(releve)
+# This series is very irregular, and it is difficult
+# to choose the best regular time-scale
+releve$Day
+length(releve$Day)
+intervals <- releve$Day[2:61]-releve$Day[1:60]
+intervals
+range(intervals)
+mean(intervals)
+# A combination of xmin=1, deltat=22 and n=61 seems correct
+# But is it the best one?
+regul.screen(releve$Day, xmin=0:11, deltat=16:27, tol=1.05)
+# Now we can tell that xmin=9, deltat=21, n=63, with tol=1.05
+# is a much better choice!
+
+
+
+cleanEx()
+nameEx("stat.desc")
+### * stat.desc
+
+flush(stderr()); flush(stdout())
+
+### Name: stat.desc
+### Title: Descriptive statistics on a data frame or time series
+### Aliases: stat.desc
+### Keywords: ts
+
+### ** Examples
+
+data(marbio)
+stat.desc(marbio[,13:16], basic=TRUE, desc=TRUE, norm=TRUE, p=0.95)
+
+
+
+cleanEx()
+nameEx("stat.pen")
+### * stat.pen
+
+flush(stderr()); flush(stdout())
+
+### Name: stat.pen
+### Title: Pennington statistics on a data frame or time series
+### Aliases: stat.pen
+### Keywords: ts
+
+### ** Examples
+
+data(marbio)
+stat.pen(marbio[,c(4, 14:16)], basic=TRUE, desc=TRUE)
+
+
+
+cleanEx()
+nameEx("stat.slide")
+### * stat.slide
+
+flush(stderr()); flush(stdout())
+
+### Name: stat.slide
+### Title: Sliding statistics
+### Aliases: stat.slide lines.stat.slide plot.stat.slide print.stat.slide
+### Keywords: ts
+
+### ** Examples
+
+data(marbio)
+# Sliding statistics with fixed-length blocs
+statsl <- stat.slide(1:68, marbio[, "ClausocalanusA"], xmin=0, n=7, deltat=10)
+statsl
+plot(statsl, stat="mean", leg=TRUE, lpos=c(55, 2500), xlab="Station",
+ ylab="ClausocalanusA")
+
+# More information on the series, with predefined blocs
+statsl2 <- stat.slide(1:68, marbio[, "ClausocalanusA"],
+ xcut=c(0, 17, 25, 30, 41, 46, 70), basic=TRUE, desc=TRUE, norm=TRUE,
+ pen=TRUE, p=0.95)
+statsl2
+plot(statsl2, stat="median", xlab="Stations", ylab="Counts",
+ main="Clausocalanus A") # Median
+lines(statsl2, stat="min") # Minimum
+lines(statsl2, stat="max") # Maximum
+lines(c(17, 17), c(-50, 2600), col=4, lty=2) # Cuts
+lines(c(25, 25), c(-50, 2600), col=4, lty=2)
+lines(c(30, 30), c(-50, 2600), col=4, lty=2)
+lines(c(41, 41), c(-50, 2600), col=4, lty=2)
+lines(c(46, 46), c(-50, 2600), col=4, lty=2)
+text(c(8.5, 21, 27.5, 35, 43.5, 57), 2300, labels=c("Peripheral Zone", "D1",
+ "C", "Front", "D2", "Central Zone")) # Labels
+legend(0, 1900, c("series", "median", "range"), col=1:3, lty=1)
+# Get cuts back from the object
+statsl2$xcut
+
+
+
+cleanEx()
+nameEx("trend.test")
+### * trend.test
+
+flush(stderr()); flush(stdout())
+
+### Name: trend.test
+### Title: Test if an increasing or decreasing trend exists in a time
+### series
+### Aliases: trend.test
+### Keywords: ts htest
+
+### ** Examples
+
+data(marbio)
+trend.test(marbio[, 8])
+# Run a bootstrap test on the same series
+marbio8.trend.test <- trend.test(marbio[, 8], R=99)
+# R=999 is a better value... but it is very slow!
+marbio8.trend.test
+plot(marbio8.trend.test)
+marbio8.trend.test$p.value
+
+
+
+cleanEx()
+nameEx("tsd")
+### * tsd
+
+flush(stderr()); flush(stdout())
+
+### Name: tsd
+### Title: Decomposition of one or several regular time series using
+### various methods
+### Aliases: tsd extract.tsd plot.tsd print.specs.tsd print.summary.tsd
+### print.tsd specs.tsd summary.tsd
+### Keywords: ts smooth loess nonparametric
+
+### ** Examples
+
+data(releve)
+# Regulate the series and extract them as a time series object
+rel.regy <- regul(releve$Day, releve[3:8], xmin=6, n=87, units="daystoyears",
+ frequency=24, tol=2.2, methods="linear", datemin="21/03/1989",
+ dateformat="d/m/Y")
+rel.ts <- tseries(rel.regy)
+
+# Decompose all series in the set with the "loess" method
+rel.dec <- tsd(rel.ts, method="loess", s.window=13, trend=FALSE)
+rel.dec
+plot(rel.dec, series=5, col=1:3) # An plot series 5
+
+# Extract "deseasoned" components
+rel.des <- extract(rel.dec, series=3:6, components="deseasoned")
+rel.des[1:10,]
+
+# Further decompose these components with a moving average
+rel.des.dec <- tsd(rel.des, method="average", order=2, times=10)
+plot(rel.des.dec, series=3, col=c(2, 4, 6))
+# In this case, a superposed graph is more appropriate:
+plot(rel.des.dec, series=3, col=c(2,4), stack=FALSE, resid=FALSE,
+ labels=c("without season cycle", "trend"), lpos=c(0, 55000))
+# Extract residuals from the latter decomposition
+rel.res2 <- extract(rel.des.dec, components="residuals")
+
+
+
+cleanEx()
+nameEx("tseries")
+### * tseries
+
+flush(stderr()); flush(stdout())
+
+### Name: tseries
+### Title: Convert a 'regul' or a 'tsd' object into a time series
+### Aliases: tseries
+### Keywords: ts manip
+
+### ** Examples
+
+data(releve)
+rel.regy <- regul(releve$Day, releve[3:8], xmin=6, n=87, units="daystoyears",
+ frequency=24, tol=2.2, methods="linear", datemin="21/03/1989",
+ dateformat="d/m/Y")
+# This object is not a time series
+is.tseries(rel.regy) # FALSE
+# Extract all time series contained in the 'regul' object
+rel.ts <- tseries(rel.regy)
+# Now this is a time series
+is.tseries(rel.ts) # TRUE
+
+
+
+cleanEx()
+nameEx("turnogram")
+### * turnogram
+
+flush(stderr()); flush(stdout())
+
+### Name: turnogram
+### Title: Calculate and plot a turnogram for a regular time series
+### Aliases: turnogram extract.turnogram identify.turnogram plot.turnogram
+### print.summary.turnogram print.turnogram summary.turnogram
+### Keywords: ts htest
+
+### ** Examples
+
+data(bnr)
+# Let's transform series 4 into a time series (supposing it is regular)
+bnr4 <- as.ts(bnr[, 4])
+plot(bnr4, type="l", main="bnr4: raw data", xlab="Time")
+# A simple turnogram is calculated
+bnr4.turno <- turnogram(bnr4)
+summary(bnr4.turno)
+# A complete turnogram confirms that "level=3" is a good value:
+turnogram(bnr4, complete=TRUE)
+# Data with maximum info. are extracted (thus taking 1 every 3 observations)
+bnr4.interv3 <- extract(bnr4.turno)
+plot(bnr4, type="l", lty=2, xlab="Time")
+lines(bnr4.interv3, col=2)
+title("Original bnr4 (dotted) versus max. info. curve (plain)")
+# Choose another level (for instance, 6) and extract the corresponding series
+bnr4.turno$level <- 6
+bnr4.interv6 <- extract(bnr4.turno)
+# plot both extracted series on top of the original one
+plot(bnr4, type="l", lty=2, xlab="Time")
+lines(bnr4.interv3, col=2)
+lines(bnr4.interv6, col=3)
+legend(70, 580, c("original", "interval=3", "interval=6"), col=1:3, lty=c(2, 1, 1))
+# It is hard to tell on the graph which series contains more information
+# The turnogram shows us that it is the "interval=3" one!
+
+
+
+cleanEx()
+nameEx("turnpoints")
+### * turnpoints
+
+flush(stderr()); flush(stdout())
+
+### Name: turnpoints
+### Title: Analyze turning points (peaks or pits)
+### Aliases: turnpoints extract.turnpoints lines.turnpoints plot.turnpoints
+### print.summary.turnpoints print.turnpoints summary.turnpoints
+### Keywords: ts
+
+### ** Examples
+
+data(marbio)
+plot(marbio[, "Nauplii"], type="l")
+# Calculate turning points for this series
+Nauplii.tp <- turnpoints(marbio[, "Nauplii"])
+summary(Nauplii.tp)
+plot(Nauplii.tp)
+# Add envelope and median line to original data
+plot(marbio[, "Nauplii"], type="l")
+lines(Nauplii.tp)
+# Note that lines() applies to the graph of original dataset!!!
+title("Raw data, envelope maxi., mini. and median line")
+
+
+
+cleanEx()
+nameEx("vario")
+### * vario
+
+flush(stderr()); flush(stdout())
+
+### Name: vario
+### Title: Compute and plot a semi-variogram
+### Aliases: vario
+### Keywords: ts
+
+### ** Examples
+
+data(bnr)
+vario(bnr[, 4])
+
+
+
+### * <FOOTER>
+###
+cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
+grDevices::dev.off()
+###
+### Local variables: ***
+### mode: outline-minor ***
+### outline-regexp: "\\(> \\)?### [*]+" ***
+### End: ***
+quit('no')
Deleted: pkg/pastecs-Ex.R
===================================================================
--- pkg/pastecs-Ex.R 2014-03-02 09:00:05 UTC (rev 10)
+++ pkg/pastecs-Ex.R 2014-03-02 11:48:45 UTC (rev 11)
@@ -1,1013 +0,0 @@
-pkgname <- "pastecs"
-source(file.path(R.home("share"), "R", "examples-header.R"))
-options(warn = 1)
-library('pastecs')
-
-assign(".oldSearch", search(), pos = 'CheckExEnv')
-cleanEx()
-nameEx("AutoD2")
-### * AutoD2
-
-flush(stderr()); flush(stdout())
-
-### Name: AutoD2
-### Title: AutoD2, CrossD2 or CenterD2 analysis of a multiple time-series
-### Aliases: AutoD2 CrossD2 CenterD2
-### Keywords: ts multivariate htest
-
-### ** Examples
-
-data(marphy)
-marphy.ts <- as.ts(as.matrix(marphy[, 1:3]))
-AutoD2(marphy.ts)
-marphy.ts2 <- as.ts(as.matrix(marphy[, c(1, 4, 3)]))
-CrossD2(marphy.ts, marphy.ts2)
-# This is not identical to:
-CrossD2(marphy.ts2, marphy.ts)
-marphy.d2 <- CenterD2(marphy.ts, window=16)
-lines(c(17, 17), c(-1, 15), col=4, lty=2)
-lines(c(25, 25), c(-1, 15), col=4, lty=2)
-lines(c(30, 30), c(-1, 15), col=4, lty=2)
-lines(c(41, 41), c(-1, 15), col=4, lty=2)
-lines(c(46, 46), c(-1, 15), col=4, lty=2)
-text(c(8.5, 21, 27.5, 35, 43.5, 57), 11, labels=c("Peripheral Zone", "D1",
- "C", "Front", "D2", "Central Zone")) # Labels
-time(marphy.ts)[marphy.d2$D2 > marphy.d2$chisq]
-
-
-
-cleanEx()
-nameEx("GetUnitText")
-### * GetUnitText
-
-flush(stderr()); flush(stdout())
-
-### Name: GetUnitText
-### Title: Format a nice time units for labels in graphs
-### Aliases: GetUnitText
-### Keywords: ts
-
-### ** Examples
-
-timeser <- ts(1:24, frequency=12) # 12 observations per year
-if (exists("is.R") && is.function(is.R) && is.R()) { # We are in R
-attr(timeser, "units") <- "years" # time in years for 'ts' object
-} else { # We are in Splus
-attr(attr(timeser, "tspar"), "units") <- "years" # Idem for Splus 'rts' object
-}
-GetUnitText(timeser) # formats unit (1/12 year=months)
-
-
-
-cleanEx()
-nameEx("abund")
-### * abund
-
-flush(stderr()); flush(stdout())
-
-### Name: abund
-### Title: Sort variables by abundance
-### Aliases: abund extract.abund identify.abund lines.abund plot.abund
-### print.abund print.summary.abund summary.abund
-### Keywords: multivariate
-
-### ** Examples
-
-data(bnr)
-bnr.abd <- abund(bnr)
-summary(bnr.abd)
-plot(bnr.abd, dpos=c(105, 100))
-bnr.abd$n <- 26
-# To identify a point on the graph, use: bnr.abd$n <- identify(bnr.abd)
-lines(bnr.abd)
-bnr2 <- extract(bnr.abd)
-names(bnr2)
-
-
-
-cleanEx()
-nameEx("buysbal")
-### * buysbal
-
-flush(stderr()); flush(stdout())
-
-### Name: buysbal
-### Title: Buys-Ballot table
-### Aliases: buysbal
-### Keywords: ts
-
-### ** Examples
-
-data(releve)
-buysbal(releve$Day, releve$Melosul, frequency=4, units="days",
- datemin="21/03/1989", dateformat="d/m/Y")
-buysbal(releve$Day, releve$Melosul, frequency=4, units="days",
- datemin="21/03/1989", dateformat="d/m/Y", count=TRUE)
-
-
-
-cleanEx()
-nameEx("daystoyears")
-### * daystoyears
-
-flush(stderr()); flush(stdout())
-
-### Name: daystoyears
-### Title: Convert time units from "days" to "years" or back
-### Aliases: daystoyears yearstodays
-### Keywords: ts
-
-### ** Examples
-
-# A vector with a "days" time-scale (25 values every 30 days)
-A <- (1:25)*30
-# Convert it to a "years" time-scale, using 23/05/2001 (d/m/Y) as first value
-B <- daystoyears(A, datemin="23/05/2001", dateformat="d/m/Y")
-B
-# Convert it back to "days" time-scale
-yearstodays(B, xmin=30)
-
-# Here is an example showing the shift introduced, and its consequence:
-C <- daystoyears(unclass(as.Date(c("1970-1-1","1971-1-1","1972-1-1","1973-1-1"),
- format = "%Y-%m-%d")))
-C
-
-
-
-cleanEx()
-nameEx("decaverage")
-### * decaverage
-
-flush(stderr()); flush(stdout())
-
-### Name: decaverage
-### Title: Time series decomposition using a moving average
-### Aliases: decaverage
-### Keywords: ts smooth
-
-### ** Examples
-
-data(marbio)
-ClausoB.ts <- ts(log(marbio$ClausocalanusB + 1))
-ClausoB.dec <- decaverage(ClausoB.ts, order=2, times=10, sides=2, ends="fill")
-plot(ClausoB.dec, col=c(1, 3, 2), xlab="stations")
-# A stacked graph is more representative in this case
-plot(ClausoB.dec, col=c(1, 3), xlab="stations", stack=FALSE, resid=FALSE,
- lpos=c(53, 4.3))
-
-
-
-cleanEx()
-nameEx("deccensus")
-### * deccensus
-
-flush(stderr()); flush(stdout())
-
-### Name: deccensus
-### Title: Time decomposition using the CENSUS II method
-### Aliases: deccensus
-### Keywords: ts smooth
-
-### ** Examples
-
-data(releve)
-# Get regulated time series with a 'years' time-scale
-rel.regy <- regul(releve$Day, releve[3:8], xmin=6, n=87, units="daystoyears",
- frequency=24, tol=2.2, methods="linear", datemin="21/03/1989", dateformat="d/m/Y")
-rel.ts <- tseries(rel.regy)
-# We must have complete cycles to allow using deccensus()
-start(rel.ts)
-end(rel.ts)
-rel.ts2 <- window(rel.ts, end=c(1992,5))
-rel.dec2 <- deccensus(rel.ts2[, "Melosul"], trend=TRUE)
-plot(rel.dec2, col=c(1,4,3,2))
-
-
-
-cleanEx()
-nameEx("decdiff")
-### * decdiff
-
-flush(stderr()); flush(stdout())
-
-### Name: decdiff
-### Title: Time series decomposition using differences (trend elimination)
-### Aliases: decdiff
-### Keywords: ts smooth
-
-### ** Examples
-
-data(marbio)
-ClausoB.ts <- ts(log(marbio$ClausocalanusB + 1))
-ClausoB.dec <- decdiff(ClausoB.ts, lag=1, order=2, ends="fill")
-plot(ClausoB.dec, col=c(1, 4, 2), xlab="stations")
-
-
-
-cleanEx()
-nameEx("decevf")
-### * decevf
-
-flush(stderr()); flush(stdout())
-
-### Name: decevf
-### Title: Time series decomposition using eigenvector filtering (EVF)
-### Aliases: decevf
-### Keywords: ts smooth
-
-### ** Examples
-
-data(releve)
-melo.regy <- regul(releve$Day, releve$Melosul, xmin=9, n=87,
- units="daystoyears", frequency=24, tol=2.2, methods="linear",
- datemin="21/03/1989", dateformat="d/m/Y")
-melo.ts <- tseries(melo.regy)
-acf(melo.ts)
-# Autocorrelation is not significant after 0.16
-# That corresponds to a lag of 0.16*24=4 (frequency=24)
-melo.evf <- decevf(melo.ts, lag=4, axes=1)
-plot(melo.evf, col=c(1, 4, 2))
-# A superposed graph is better in the present case
-plot(melo.evf, col=c(1, 4), xlab="stations", stack=FALSE, resid=FALSE,
- lpos=c(0, 60000))
-
-
-
-cleanEx()
-nameEx("decloess")
-### * decloess
-
-flush(stderr()); flush(stdout())
-
-### Name: decloess
-### Title: Time series decomposition by the LOESS method
-### Aliases: decloess
-### Keywords: ts smooth
-
-### ** Examples
-
-data(releve)
-melo.regy <- regul(releve$Day, releve$Melosul, xmin=9, n=87,
- units="daystoyears", frequency=24, tol=2.2, methods="linear",
- datemin="21/03/1989", dateformat="d/m/Y")
-melo.ts <- tseries(melo.regy)
-melo.dec <- decloess(melo.ts, s.window="periodic")
-plot(melo.dec, col=1:3)
-
-
-
-cleanEx()
-nameEx("decmedian")
-### * decmedian
-
-flush(stderr()); flush(stdout())
-
-### Name: decmedian
-### Title: Time series decomposition using a running median
-### Aliases: decmedian
-### Keywords: ts smooth
-
-### ** Examples
-
-data(marbio)
-ClausoB.ts <- ts(log(marbio$ClausocalanusB + 1))
-ClausoB.dec <- decmedian(ClausoB.ts, order=2, times=10, ends="fill")
-plot(ClausoB.dec, col=c(1, 4, 2), xlab="stations")
-# This is a transect across a frontal zone:
-plot(ClausoB.dec, col=c(0, 2), xlab="stations", stack=FALSE, resid=FALSE)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pastecs -r 11
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