This function writes measured or derived (standardized, averaged) series of values to a TRiDaS format file. Some metadata are also supported.
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],
...)fname
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 is produced by
read.tucson, read.compact and
read.tridas. Defaults to NULL: no measurement
series are written.
character vector giving the file name of the rwl
file
data.frame or a list of data.frames
containing tree-ring chronologies. Accepts data.frames of
the type produced by chron. Additionally, allows
several chronologies per data.frame. Any column of the
data.frame(s) with a name starting with "samp.depth"
is interpreted as a sample depth. The rest of the columns are
interpreted as chronologies whose titles are determined from the
column names (optionally from parameter crn.titles).
Chronology columns and sample depth columns are paired in order so
that the first chronology gets the first sample depth column, second
chronology gets the second set of sample depths, etc. If there are
less sample depth columns than chronologies, the sample depths are
recycled. Defaults to NULL: no chronologies are written.
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 (non-integer) millimetres.
Possible numeric values are 0.001, 0.01, 0.05, 0.1, 1, 10,
100 and 1000, which cause the data to be transformed to micrometres,
1/100th millimetres, 1/20th millimetres, 1/10 millimetres,
(millimetres), centimetres, decimetres or metres, respectively, and
then rounded to integral values. Data rounded to decimetres are
written in centimetres (values always ending in zero). Otherwise,
the matching unit is used in the file.
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 core, optional column three named
"radius" giving the numeric ID of the
radius, and optional column four named "measurement" giving
the numeric ID of the measurement. If column
"measurement" exists, column "radius" must also exist.
Defaults to one core, radius and measurement per tree:
data.frame(tree=1:n.col, core=rep(1,n.col),
radius=rep(1,n.col), measurement=rep(1,n.col))where n.col is the number of columns in
rwl.df.
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, and column four
named "measurement" giving the title of the measurement. By
default, titles is NULL, and the title hierarchy
is automatically created out of the column names of
rwl.df, taking ids into account.
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, recycled if not long enough.
A list of vectors is interpreted as one list element per
data.frame. In this case, the list is recycled to the
correct length. After that, the vectors inside the list are
recycled to match the number of derived series in each
data.frame of crn. The default is to write
empty <type> elements.
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, except that the default is to derive the
titles from the column names of crn. Also NA
means that the column name is used.
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, except that the default is to mark the
series as <unitless>. Also NA means
<unitless>.
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
tridas.vocabulary. If the vector is shorter than the
number of columns in rwl.df, it is recycled to the
correct length. The default is to use the information in
other.measuring.method instead. Also, NA in any
position of the vector means that the measuring method information
for that series is looked up in 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 shorter than the
number of columns in rwl.df, it is recycled to the
correct length. The default value is "unknown".
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, or it is recycled to the correct length. If
there are several measurements per sample, some elements of
sample.type are redundant. The default is to use
"core" for all series.
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 expected to be a
subset of the following (descriptions almost directly quoted from
TRiDaS specification):
Field for recording whether there are any rings at the inner (i.e. towards pith) edge of the sample that have not been measured. Typically used to note when rings are too damaged to measure. Non-negative integral value.
Field for recording whether there are any rings at the outer (i.e. towards bark) edge of the sample that have not been measured. Typically used to note when rings are too damaged to measure. Non-negative integral value.
Whether the pith is present or absent.
Each element must be a partial match with the contents of
category "complex presence / absence" in
tridas.vocabulary.
Whether the outer (youngest) heartwood is present and if so whether it is complete.
Category "complex presence / absence" in
tridas.vocabulary.
Estimated number of missing heartwood rings to the pith. Non-negative integral value.
Description of the way the estimation of how many heartwood rings are missing was made and what the certainty is. Free-form string.
Whether the sapwood is present or not.
Category "complex presence / absence".
Number of sapwood rings measured. Non-negative integral value.
Last ring under the bark is present or absent.
Category "presence / absence".
If the last ring under the bark is present, include information about the completeness of this ring and/or season of felling. Free-form string.
Estimated number of missing sapwood rings to the bark. Non-negative integral value.
Description of the way the estimation of how many sapwood rings are missing was made and what the certainty is. Free-form string.
Bark is present or absent.
Category "presence / absence" in
tridas.vocabulary.
character string. The most detailed taxonomic
name known for this element (species, genus, family etc).
Preferably from the Catalogue
of Life controlled vocabulary. The same string is used for all of
rwl.df. The default value is an empty string, but a
proper value should really be given.
character string. Measured variable
(ring width, earlywood, latewood etc) taken from the TRiDaS
controlled vocabulary (tridas.vocabulary, category
"variable"). The same string is used for all of
rwl.df. Defaults to "ring width".
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.
list containing information about the
project. Elements are the following (includes quotes from the
TRiDaS specification):
character vector. The type(s) of the project.
Defaults to "unknown".
character string. A description of the
project. Defaults to NULL: no description.
character string. The title of the project.
Defaults to an empty string.
character string. Category of research
this project falls into. Defaults to an empty string.
character string. Principal
investigator of this project. Defaults to an empty string.
character string. When the
dendrochronological project took place. Could consist of a
start- and end-date. If unknown it should be estimated.
Defaults to an empty string.
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 a
subset of the following:
Name of the laboratory
Optional acronym of the laboratory
Optional identifier of the laboratory
The domain which the identifier of the laboratory is applicable to. Could be the URL of the organization’s server or the name of the organization as long as it is not ambiguous.
First address line
Second address line
City or town
State, province or region
Postal code. Beware of ignored leading zeros
if these are given in numeric or integer type
values. It is always safe to use character values.
Country
optional data.frame with information
about the systems in which the research project is
registered. Columns are the following:
Identifier
Domain which the identifier is applicable to
General description
list containing information about the site
(<object>). Elements are the following, and all are
character strings:
Type of the site. Defaults to "unknown".
Description. Defaults to no description.
Title of the site. Defaults to an empty string.
logical flag. If TRUE,
unique random identifiers are created with uuid.gen
and attached to each <project> (one in the file),
object (site, one in the file), <element> (tree),
<sample> (core), <radius>, <measurementSeries>
(measurement) and <derivedSeries> element in the resulting
TRiDaS file.
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
of the first laboratory in lab.info.
Unknown arguments are accepted but not used.
Mikko Korpela
The Tree Ring Data Standard (TRiDaS) is described in Jansma et. al (2010).
Jansma, E., Brewer, P. W., and Zandhuis, I. (2010) TRiDaS 1.1: The tree-ring data standard. Dendrochronologia, 28(2), 99--130.
write.rwl, write.tucson,
write.compact, write.crn,
read.tridas
library(utils)
if (FALSE) {
## Write raw ring widths
data(co021)
fname1 <- write.tridas(rwl.df = co021,
fname = tempfile(fileext=".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"))
print(fname1) # tempfile used for output
## Write mean value chronology of detrended ring widths
data(ca533)
ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp")
ca533.crn <- chron(ca533.rwi, prewhiten = TRUE)
fname2 <- write.tridas(crn = ca533.crn,
fname = tempfile(fileext=".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"))
print(fname2) # tempfile used for output
unlink(c(fname1, fname2)) # remove the files
}
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