Nothing
## ----fig.width=7,fig.height=4-------------------------------------------------
library(ggplot2)
library(oxcAAR)
quickSetupOxcal()
#setOxcalExecutablePath("~/OxCal/bin/OxCalLinux")
my_date <- oxcalCalibrate(5000,25,"KIA-12345")
my_date
plot(my_date)
## ----fig.width=7,fig.height=4-------------------------------------------------
my_uncal_dates <- data.frame(bp=c(5000,4500,4000),
std=c(45,35,25),
names=c("Date 1", "Date 2", "Date 3")
)
my_cal_dates <- oxcalCalibrate(my_uncal_dates$bp, my_uncal_dates$std, my_uncal_dates$names)
my_cal_dates
plot(my_cal_dates)
## ----fig.width=7,fig.height=4-------------------------------------------------
calcurve_plot(my_cal_dates)
## -----------------------------------------------------------------------------
str(my_cal_dates, max.level = 1)
my_cal_dates[[1]] # equivalent to my_cal_dates[["Date 1"]] or my_cal_dates$`Date 1`
str(my_cal_dates$`Date 1`)
plot(
my_cal_dates$`Date 1`$raw_probabilities$dates,
my_cal_dates$`Date 1`$raw_probabilities$probabilities,
type = "l",
xlab = "years",
ylab = "probs"
)
## ----fig.width=7,fig.height=4-------------------------------------------------
my_cal_date <- data.frame(bp=c(-3400),
std=c(25),
names=c("SimDate_1")
)
my_simulated_dates <- oxcalSimulate(my_cal_date$bp,
my_cal_date$std,
my_cal_date$names
)
# equivalent to
my_simulated_dates <- oxcalSimulate(-3400, 25, "SimDate_1")
my_simulated_dates
plot(my_simulated_dates)
## ----fig.width=7,fig.height=4-------------------------------------------------
my_sum_sim<-oxcalSumSim(
timeframe_begin = -4000,
timeframe_end = -3000,
n = 50,
stds = 35,
date_distribution = "uniform"
)
str(my_sum_sim)
plot(my_sum_sim)
## ---- echo=F------------------------------------------------------------------
library(knitr)
hook_output <- knit_hooks$get("output")
knit_hooks$set(output = function(x, options) {
lines <- options$output.lines
if (is.null(lines)) {
return(hook_output(x, options)) # pass to default hook
}
x <- unlist(strsplit(x, "\n"))
more <- "..."
if (length(lines)==1) { # first n lines
if (length(x) > lines) {
# truncate the output, but add ....
x <- c(head(x, lines), more)
}
} else {
x <- c(more, x[lines], more)
}
# paste these lines together
x <- paste(c(x, ""), collapse = "\n")
hook_output(x, options)
})
## -----------------------------------------------------------------------------
R_Simulate(-4000, 25, "MySimDate")
my_dates <- R_Date(c("Lab-12345","Lab-54321"), c(5000,4500), 25)
cat(my_dates)
my_sum <- oxcal_Sum(my_dates)
cat(my_sum)
## ---- output.lines=8----------------------------------------------------------
knitr::opts_chunk$set(cache=TRUE)
my_oxcal_code <- ' Plot()
{
Sequence("Sequence1")
{
Boundary("Beginn");
Phase("Phase1")
{
R_Date("Lab-1",5000,25);
R_Date("Lab-2",4900,37);
};
Boundary("Between");
Phase("Phase2")
{
R_Date("Lab-3",4800,43);
};
Boundary("End");
};
};'
my_result_file <- executeOxcalScript(my_oxcal_code)
my_result_text <- readOxcalOutput(my_result_file)
## ---- output.lines=8----------------------------------------------------------
my_result_data <- parseOxcalOutput(my_result_text)
str(my_result_data)
print(my_result_data)
## ---- output.lines=8----------------------------------------------------------
my_result_data <- parseFullOxcalOutput(my_result_text)
str(my_result_data)
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