dplR (version 1.5.3)

write.tridas: Write Tree Ring Data Standard (TRiDaS) file

Description

This function writes measured or derived (standardized, averaged) series of values to a TRiDaS format file. Some metadata are also supported.

Usage

write.tridas(rwl.df = NULL, fname, crn = NULL, prec = NULL, ids = NULL,
    titles = NULL, crn.types = NULL, crn.titles = NULL,
    crn.units = NULL, tridas.measuring.method = NA,
    other.measuring.method = "unknown", sample.type = "core",
    wood.completeness = NULL, taxon = "",
    tridas.variable = "ring width", other.variable = NA,
    project.info = list(type = c("unknown"), description = NULL,
                        title = "", category = "", investigator = "",
                        period = ""),
    lab.info = data.frame(name = "", acronym = NA, identifier = NA,
                          domain = "", addressLine1 = NA,
                          addressLine2 = NA, cityOrTown = NA,
                          stateProvinceRegion = NA, postalCode = NA,
                          country = NA),
    research.info = data.frame(identifier = NULL, domain = NULL,
                               description = NULL),
    site.info = list(type = "unknown", description = NULL, title = ""),
    random.identifiers = FALSE, identifier.domain = lab.info$name[1],
    ...)

Arguments

rwl.df

data.frame containing tree-ring ring widths in millimetres with the series in columns and the years as rows. The series IDs are the column names and the years are the row names. This type of data.frame

fname

character vector giving the file name of the rwl file

crn

data.frame or a list of data.frames containing tree-ring chronologies. Accepts data.frames of the type produced by chron. Additionally, allows several chro

prec

optional numeric indicating the rounding precision of the output file when writing the data contained in rwl.df. Defaults to NULL -- no rounding is done and the measurements are written in (no

ids

optional data.frame with column one named "tree" giving the numeric ID of the tree, column two named "core" giving the numeric ID of the cor

titles

optional data.frame with column one named "tree" giving the title of the tree, column two named "core" giving the title of the core, column three named "radius" giving the title of the radius

crn.types

character vector or a list of character vectors giving the types of the derived series in crn. A single vector is interpreted as one type per data.frame in

crn.titles

optional character vector or a list of character vectors giving the titles of the derived series in crn. The interpretation is the same as with crn.types,

crn.units

optional character vector or a list of character vectors giving the units of the derived series in crn. The interpretation is the same as with crn.types, e

tridas.measuring.method

character vector giving the measuring method used to acquire each series of rwl.df. Partial matching is used to replace these with the complete terms in trida

other.measuring.method

character vector giving the measuring method used to acquire each series of rwl.df. In contrast to tridas.measuring.method, these are free-form strings in English. If the vector is

sample.type

optional character vector giving the type of the samples, corresponding to "core" in ids. The length of the vector, however, must match the number of columns in rwl.df,

wood.completeness

optional data.frame giving wood completeness information for the measurement series in rwl.df. The number of rows must match the number of columns in rwl.df. The columns are expect

taxon

character string. The most detailed taxonomic name known for this element (species, genus, family etc). Preferably from the http://www.catalogueoflife.org/{Catalogue of Life} controlled vocabulary. The same string

tridas.variable

character string. Measured variable (ring width, earlywood, latewood etc) taken from the TRiDaS controlled vocabulary (tridas.vocabulary, category "variable"

other.variable

character string. Measured variable as a free-form string. The same string is used for all of rwl.df. This is only used if tridas.variable is NA.

project.info

list containing information about the project. Elements are the following (includes quotes from the TRiDaS specification):

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

lab.info

data.frame. Information about the dendrochronological research laboratories where this work was done. One row per laboratory. Defaults to one laboratory with an empty name and no other information. The columns are expected to be

research.info

optional data.frame with information about the systems in which the research project is registered. Columns are the following:

[object Object],[object Object],[object Object]

site.info

list containing information about the site (). Elements are the following, and all are character strings:

[object Object],[object Object],[object Object]

random.identifiers

logical flag. If TRUE, unique random identifiers are created with uuid.gen and attached to each (one in the file), object (site, o

identifier.domain

character string. The domain which the random identifiers are applicable to. Could be the URL of the organization's server or the name of the organization as long as it is not ambiguous. Defaults to the name

...

Unknown arguments are accepted but not used.

Value

• None. Invoked for side effect (file is written).

References

TRiDaS - The Tree Ring Data Standard, http://www.tridas.org/

See Also

write.rwl, write.tucson, write.compact, write.crn, read.tridas

Examples

## Write raw ring widths
data(co021)
write.tridas(rwl.df = co021, fname = "tmp1.xml", prec = 0.01,
    site.info = list(title = "Schulman old tree no. 1, Mesa Verde",
                     type = "unknown"),
    taxon = "Pseudotsuga menziesii var. menziesii (Mirb.) Franco",
    project.info = list(investigator = "E. Schulman",
                        title = "", category = "",
                        period = "", type = "unknown"))

## Write mean value chronology of detrended ring widths
data(ca533)
ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp")
ca533.crn <- chron(ca533.rwi, prefix = "CAM", prewhiten = TRUE)
write.tridas(crn = ca533.crn, fname = "tmp2.xml",
    taxon = "Pinus longaeva D.K. Bailey",
    project.info =
        list(investigator = "Donald A. Graybill, V.C. LaMarche, Jr.",
             title = "Campito Mountain", category = "",
             period = "", type = "unknown"))