Climate Change with Proxies

Description

This program implements and improves upon the Wilkinson and Ivany approach to climate time series modeling. The jackknife is used to estimate the 95 percent confidence bounds for the modeled estimates. dx should be chosen to be approximately half a cycle or more.

Author(s)

Jonathan M. Lees

Maintainer: Jonathan M. Lees<jonathan.lees@unc.edu>

References

Wilkinson, B. H. and Ivany, L. C., Paleoclimatic inference from stable isotope profiles of accretionary biogenic hardparts; a quantitative approach to the evaluation of incomplete data, Palaeogeography, Palaeoclimatology, Palaeoecology, vol. 185, no. 1-2, pp.95-114, 01 Sep 2002.

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

Examples

## Not run: 
data(CLAM1)
x = CLAM1$x
y = CLAM1$y

dx = 3.392

gout = proxyJK(x, y, dx)

plotproxy1(x, y, gout)

par(mfrow=c(2,1))

plotproxy.error(x, y, gout, type = 1)
plotproxy.error(x, y, gout, type = 2)


par(mfrow=c(2,1))
plotproxy.error(x, y, gout, type = 2)

plotproxy.all2(gout,YAXstyle=1 )

## End(Not run)

Clam Proxy Data

Description

Proxy data from the Orknay Islands

Usage

data(CLAM1)

Format

The format is: List of 2 $ x: num [1:91] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... $ y: num [1:91] 2.14 2.11 2.4 2.21 2.32 2.44 2.85 2.78 2.27 2.05 ...

Details

Duplicate data has been removed.

Source

One-year data interval (4.68-9.31 mm) of \delta-18O record of an archaeological limpet Patella vulgata (specimen QG2-1064-1) from Orkney, Scotland (Surge and Barrett, 2012).

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

Examples

data(CLAM1)
## maybe str(CLAM1) ; plot(CLAM1) ...
plot(CLAM1$x, CLAM1$y, type="b", xlab="Distance", ylab="d18O" )

## Not run: 
###### this is an example from Wang et al.:
####  it takes too long to run on CRAN, but should work

shellx=CLAM1$x[38:70]
shelly=CLAM1$y[38:70]

window_shell=windowsize(shellx,shelly,1.8,9.4,0.2)

#the window size is 5mm, and make all the plots together
gout_shell = proxyJK(shellx, shelly, 5)

par(mfrow=c(3,2))
plot(shellx,shelly,type="b", xlab="Distance from Margin (mm)",
     ylab=expression(delta*"18O(ppm VPDB)"),  
     xlim=c(4,10), ylim = c(1.5,4))
plot((window_shell$win)/2,window_shell$error,xlab="Window Size (mm)", 
     ylab="Error",  xlim=c(1.6/2,9.4/2), ylim=c(0,0.5))
abline(v=4.63/2, lty="dotdash",col="black")
abline(v=5/2, col="black")
plotproxy1(shellx, shelly, gout_shell, xlim=c(4,10), ylim = c(1.5,4),
          xlab="Distance from Margin (mm)",
          ylab=expression(delta*"18O(ppm VPDB)"), main="")
plotproxy.all(gout_shell,YAXstyle=1, xlim=c(4,10), ylim1=c(0,4), 
             ylim2=c(-15,5))
plotproxy.error(shellx, shelly, gout_shell, type = 1, xlim=c(4,10), 
               ylim = c(1.5,4), xlab="Distance from Margin (mm)",
               ylab=expression(delta*"18O(ppm VPDB)"))
plotproxy.error(shellx, shelly, gout_shell, type = 2, xlim=c(4,10),
               ylim = c(1.5,4), xlab="Distance from Margin (mm)",
               ylab=expression(delta*"18O(ppm VPDB)"))




## End(Not run)

Next power of 2

Description

Find the next integer power of 2

Usage

NextPow2(x)

Arguments

Value

integer that is a power of 2 higher than given integer

Author(s)

Jonathan M. Lees<jonathan.lees@unc.edu>

Examples

NextPow2(600)
NextPow2(1023)
NextPow2(1025)

Rescale a vector to fit in a certain range

Description

Rescale a vector to fit in a certain range

Usage

RESCALE(x, nx1, nx2, minx, maxx)

Arguments

Details

Used for graphics.

Value

scale vector is returned

Author(s)

Jonathan M. Lees<jonathan.lees.edu>

Examples

x = rnorm(10)
RESCALE(x, 3, 9, min(x), max(x) )

Sine Model of climate time series

Description

Sine Model of climate time series

Usage

SinMod(x, myEx, dC2)

Arguments

Details

This is the function used in optimization of sinusoidal fits to climate data.

Value

squared sum of difference between obsereved and predicted

Note

Uses stats package for optimization

Author(s)

Jonathan M. Lees<jonathan.lees@unc.edu>

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

See Also

optim, proxyA, proxyJK

Examples

data(CLAM1)
x = CLAM1$x
y = CLAM1$y
 dx = 3.392

A1 = proxyA(x, y, dx)

RMSout = SinMod(A1$par, x, y)

Climate Record At Croig Cave

Description

Application to modern climate record at Croig Cave and make comparison between reconstructed temperatures and instrumentally measured temperatures.

Usage

data("climate")

Format

A data frame with 360 observations on the following 3 variables.

Month

a numeric vector

overall

a numeric vector

Temperature

a numeric vector

Source

Monthly sea surface temperature (SST) record for the years 1961-1990 derived from observations near Croig Cave, an archaeological site on the Isle of Mull in the Hebrides Islands west of mainland Scotland (Extended Reconstructed Sea Surface Temperature, Smith and Reynolds, 2004).

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

Examples

data(climate)
climate_month <- climate$overall
climate_temp <- climate$Temperature

plot(climate_month,climate_temp,type="l",
    xlab="month",ylab=expression(paste("Temperature ("^"o","C)")))

Elliot Data Summer

Description

Two years of data from Elliot

Usage

data("elliot_yr1")

Format

The format is: List of 4 $ date1 : num [1:28] 1995 1995 1995 1995 1995 ... $ d18o1 : num [1:28] -0.036 0.244 0.525 0.332 0.148 -0.43 -0.583 -0.366 -0.641 -0.86 ... $ date_temp1: num [1:31] 1995 1995 1995 1995 1995 ... $ d18o_pred1: num [1:31] -0.58 0 0.54 0.88 0.66 0.35 0.09 -0.09 -0.53 -1.1 ...

Details

Data consists of date, \delta 18O, temperature and predicted anomaly for two years of data.

Source

Data sets are selected from the \delta 18O record of a modern Mercenaria mercenaria shell collected live from Cedar Key in northern Florida and analyzed by Elliot et al. (2003). Series elliot_yr1 records one summer (including the most negative \delta 18O). Series elliot_yr2 records one winter (including the most positive \delta 18O).

Because the modern Mercenaria mercenaria shell by Elliot et al. (2003) is well dated and its in situ records of SST and salinity are available, the predicted \delta 18O are also derived from the local instrumental data. Temp is the predicted \delta 18O for the summer interval of Year1 and Temp2 is the predicted \delta 18O for the winter interval of Year2.

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

Examples

data(elliot_yr1)
plot(elliot_yr1$date1,elliot_yr1$d18o1,xlab="Age(years)",
     ylab=expression(delta*'18O(ppm VPDB)'), xlim=c(1994.9,1996.2), ylim=c(-2.5,2))

Elliot Data Winter

Description

Winter season of data from Elliot data.

Usage

data("elliot_yr2")

Format

The format is: List of 4 $ date1 : num [1:28] 1995 1995 1995 1995 1995 ... $ d18o1 : num [1:28] -0.036 0.244 0.525 0.332 0.148 -0.43 -0.583 -0.366 -0.641 -0.86 ... $ date_temp1: num [1:31] 1995 1995 1995 1995 1995 ... $ d18o_pred1: num [1:31] -0.58 0 0.54 0.88 0.66 0.35 0.09 -0.09 -0.53 -1.1 ...

Details

Data consists of date, \delta O18, temperature and predicted data for winter season of data.

Source

See explanation in elliot_yr1.

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

Examples

data(elliot_yr2)
plot(elliot_yr2$date2,elliot_yr2$d18o2,xlab="date(year)",
ylab=expression(delta*'18O(ppm VPDB)'), xlim=c(1995.2,1996.85), ylim=c(-2.5,1.8))

Error bar plot

Description

Make an X-Y plot with error bars.

Usage

error.bar(x, y, lo, hi, pch = 1, col =1, barw = 0.1, add = FALSE, ...)

Arguments

Value

graphical side effects

Author(s)

Jonathan M. Lees<jonathan.lees@unc.edu>

Examples

x = 1:10
y = 2*x+5
zup = rnorm(10)
zup = zup-min(zup)+.5
zdown = rnorm(10)
zdown = zdown-min(zdown)+.2
####  example with same error on either side:
error.bar(x, y, y-zup, y+zup, pch = 1, col = 'brown' , barw = 0.1, add =
FALSE)
####  example with different  error on either side:
error.bar(x, y, y-zdown, y+zup, pch = 1, col = 'brown' , barw = 0.1, add
= FALSE)

otolith Proxy Data

Description

Early Oligocene otolith from the US Gulf Coast.

Usage

data(otolith)

Format

A data frame with 63 observations on the following 2 variables.

distance

a numeric vector

d18O

a numeric vector

Details

Duplicate data have been removed.

Source

\delta 18O record of an aragonite otolith from the early Oligocene Rosefield Clay in the US Gulf Coast (Ivany, 2000).

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.\

Examples

data(otolith)

plot(otolith$distance, otolith$d180)

Plot Output Jack-Knife

Description

Plot output of proxyJK, the jackknife estimate of the time series analysis fitting curves.

Usage

plotproxy.error(x,y,gout, type=1, xlim=NULL, ylim=NULL, ylab="", xlab="", main="" )

plotproxy.all(gout, ylab1="", ylab2="",xlab="", main="",
xlim=NULL, ylim1=NULL, ylim2=NULL, legposition="topleft",
YAXstyle=0, pbox=TRUE,
legnames  = c('Phs', 'Pos', 'Amp', 'Prd')  )

plotproxy1(x, y, gout, xlim = NULL, ylim = NULL, ylab = "", xlab = "",
main = "")

plotproxy.error11(x, y, gout, type = 1, xlim = NULL,
ylim = NULL, ylab = "", xlab = "", main = "")

plotproxy.all2(gout, ylab1 = "", ylab2 = "", xlab = "", main = "",
xlim = NULL, ylim1 = NULL, ylim2 = NULL,
 legposition = "topleft", YAXstyle = 0,
pbox = TRUE, legnames = c("Phs", "Pos", "Amp",
 "Prd"))

Arguments

Details

Takes output directly from program

Value

graphical side effects

Author(s)

Jonathan M. Lees<jonathan.lees@unc.edu>

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

See Also

proxyJK

Examples

## Not run: 
##  example to read in your data from csv file (for non ClamR data

## fn = "donna_viking_1.csv"
## C1 = scan(file=fn, what=list(mm="", o18=""), sep=",")
## x = as.numeric(C1$mm)
## y = as.numeric(C1$o18)
## x = x[!is.na(y)]
## y = y[!is.na(y)]


data(CLAM1)

x = CLAM1$x
y = CLAM1$y

dx = 3.392

gout = proxyJK(x, y, dx)

plotproxy1(x,y,gout)


## End(Not run)

Optimum Wilkinson Curve Fitting

Description

Runs one cycle of optimum Wilkinson curve fitting for a single sinusoid fitting.

Usage

proxyA(ax, ay, xin)

Arguments

Details

This program implements the Wilkinson and ivany approach to climate time series modeling. This is used in the more sophisticated proxyJK code.

Value

Optimum model, vector of 4 values

Note

Uses stats package routine optim for optimization

Author(s)

Jonathan M. Lees<jonathan.lees@unc.edu>

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.\

Wilkinson, B. H. and Ivany, L. C., Paleoclimatic inference from stable isotope profiles of accretionary biogenic hardparts; a quantitative approach to the evaluation of incomplete data, Palaeogeography, Palaeoclimatology, Palaeoecology, vol. 185, no. 1-2, pp.95-114, 01 Sep 2002

See Also

proxyJK

Examples

data(CLAM1)
x = CLAM1$x
y = CLAM1$y

dx = 3.392

Aout = proxyA(x, y, dx)

Jackknife Wilkinson Curve Fitting

Description

Perform a jackknife estimate of proxy curve fitting for time series analysis.

Usage

proxyJK(x, y, dx)

Arguments

Details

Routine that improves on the Wilkinson and Ivany(2002) approach to climate time series modeling. The jackknife is used to estimate the 95 percent confidence bounds for the modeled estimates. dx should be chosen to be approximately half a cycle or more.

Value

List:

Note

See proxyA for a duplication of the Wilkinson codes.

Author(s)

Jonathan M. Lees<jonathan.lees@unc.edu>

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

See Also

proxyA

Examples

## Not run: 

##########   this is for reading in data
########  fn = "/home/lees/DONNA/donna_viking_1.csv"

## fn = "donna_viking_1.csv"
######## C1 = scan(file=fn, what=list(mm="", o18=""), sep=",")
######## x = as.numeric(C1$mm)
######## y = as.numeric(C1$o18)
########x = x[!is.na(y)]
########y = y[!is.na(y)]


data(CLAM1)
x = CLAM1$x
y = CLAM1$y

dx = 3.392

gout = proxyJK(x, y, dx)

plotproxy1(x, y, gout)

par(mfrow=c(2,1))

plotproxy.error(x, y, gout, type = 1)
plotproxy.error(x, y, gout, type = 2)


par(mfrow=c(2,1))
plotproxy.error(x, y, gout, type = 2)

plotproxy.all2(gout, YAXstyle=1 )


## End(Not run)

Reconstructed Temperature Record

Description

Application to estimated temperatures from archaeological RWP shell 103a-39-1 with 3 years of temperature data.

Usage

data("rwp_limpet")

Format

A data frame with 74 observations on the following 8 variables.

distance_all

a numeric vector

temp_all

a numeric vector

distance1

a numeric vector

temp1

a numeric vector

distance2

a numeric vector

temp2

a numeric vector

distance3

a numeric vector

temp3

a numeric vector

Source

RWP shell 103a-39-1

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

Examples

data(rwp_limpet)
plot(rwp_limpet$distance_all, rwp_limpet$temp_all, type='b')

Find Window Size

Description

Estimate optimal window size for seasonal time series analysis.

Usage

windowsize(x, y, winmin, winmax, winstep)

Arguments

Value

Author(s)

Jonathan M. Lees<jonathan.lees@unc.edu>

References

Wang, T., Surge, D., and Lees, J. M., (2015) ClamR: A Statistical Evaluation of Isotopic and Temperature Records in Sclerochronologic Studies. Palaeogeography, Palaeoclimatology, Palaeoecology, doi:10.1016/j.palaeo.2015.07.008.

Examples

## Not run: 
data(CLAM1)
shellx=CLAM1$x[38:70]
shelly=CLAM1$y[38:70]

window_shell=windowsize(shellx,shelly,1.8,9.4,0.2)


## End(Not run)