| Title: | Methods to Analyse Ring Re-Encounter Data |
|---|---|
| Description: | R functions to read EURING data and analyse re-encounter data of birds marked by metal rings. For a tutorial, go to <doi:10.1080/03078698.2014.933053>. |
| Authors: | Fraenzi Korner-Nievergelt, Rob Robinson |
| Maintainer: | Fraenzi Korner-Nievergelt <[email protected]> |
| License: | GPL-2 |
| Version: | 1.6 |
| Built: | 2024-10-31 06:43:44 UTC |
| Source: | CRAN |
This package is a collection of functions or methods used to analyse ring reencounter data. Its purpose is to read EURING ring reencounter data into R, and to help mapping and analysing reencounter data. For a tutorial, go to http://www.tandfonline.com/doi/full/10.1080/03078698.2014.933053
| Package: | birdring |
| Type: | Package |
| Version: | 1.2 |
| Date: | 2014-09-24 |
| License: | GPL 2 |
| LazyLoad: | yes |
Fraenzi Korner-Nievergelt and Robert Robinson
Maintainer: Fraenzi Korner-Nievergelt <[email protected]>
Speek, G., Clark, J.A., Rhode, Z., Wassenaar, R.D. & van Noordwijk, A.J. (2001) The EURING exchange-code 2000. Dutch Ringing Scheme, Heteren.
Transforms the numeric code of the variable condition into a factor defining the state of the bird (dead, alive, sick).
birdstate(x)birdstate(x)
x |
variable condition with numeric code for the condition of the bird as given in the original EURING data |
a factor with the levels "dead", "alive", "sick" and "unknown"
F. Korner-Nievergelt
du Feu et al. (2012) EURING Exchange Code 2000+. www.euring.org
condition <- 0:9 birdstate(condition)condition <- 0:9 birdstate(condition)
EURING-code for finding circumstances as given in Speek et al. (2001)
data(circumstances)data(circumstances)
A data frame with 92 observations on the following 4 variables.
Codea numeric vector containing the code given in column 78 and 79 in EURING data of the format 2000
Namea factor with the names of the finding circumstances
BTOa factor with the shorter names of the finding circumstances as defined by the BTO (, http://www.bto.org/volunteer-surveys/ringing/publications/online-ringing-reports) )
Descriptiona factor with the description of the finding circumstances
Date.Updateda numeric vector
http://www.euring.org
Speek, G., Clark, J.A., Rhode, Z., Wassenaar, R.D. & van Noordwijk, A.J. (2001) The EURING exchange-code 2000. Dutch Ringing Scheme, Heteren.
data(circumstances) circumstancesdata(circumstances) circumstances
coordinates of the coastline of Europe used by the function draw.map
data(coastEU)data(coastEU)
A data frame with 7528 observations on the following 4 variables.
xa numeric vector, longitude
ya numeric vector, latitude
namename of the island
abstracta numeric vector
the data is used by the function draw.map
http://rimmer.ngdc.noaa.gov/mgg/coast/getcoast.html
http://rimmer.ngdc.noaa.gov/mgg/coast/getcoast.html
data(coastEU) head(coastEU)data(coastEU) head(coastEU)
coordinates of the palearctic coastline used by the function draw.map. The coordinates were downloaded from the sources indicated below and then cleaned by hand from too small details
data(coastpaleo)data(coastpaleo)
A data frame with 25042 observations on the following 5 variables.
xa numeric vector of longitude
ya numeric vector of latitude
namename of the island
entrydegree of detail to be entered in the map
kategoriea factor with levels i m s
http://rimmer.ngdc.noaa.gov/mgg/coast/getcoast.html
http://rimmer.ngdc.noaa.gov/mgg/coast/getcoast.html
data(coastpaleo) head(coastpaleo)data(coastpaleo) head(coastpaleo)
The function gives for the numeric codes for circumstances, condition and species the interpretable string name as given in the EURING code. The alphabetic scheme code is transformed into the town and country name of the scheme.
codes2names(x, variable = "circumstances", type="euring")codes2names(x, variable = "circumstances", type="euring")
x |
variable circumstances, condition, species or scheme from the output of |
variable |
character that declares the name of the variable x, should be one of c("circumstances" [default], "conditions", "schemes", "species"). |
type |
character that declares which names should be used, the one defined in the EURING manual, "euring" (default), or the ones used in the BTO ringing reports, "bto", (http://www.bto.org/volunteer-surveys/ringing/publications/online-ringing-reports). |
a factor with levels corresponding to the names of the EURING code
F. Korner-Nievergelt
http://www.euring.org/data_and_codes/euring_code_list/index.html
# circumstances examplecode <- c(20, 21, 35, 80) codes2names(examplecode) # conditions examplecodes <- c(0:9) codes2names(examplecodes, variable="conditions") # schemes codes2names("BGS", variable="schemes")# circumstances examplecode <- c(20, 21, 35, 80) codes2names(examplecode) # conditions examplecodes <- c(0:9) codes2names(examplecodes, variable="conditions") # schemes codes2names("BGS", variable="schemes")
EURING-code for finding conditions as given in Speek et al. (2001)
data(conditions)data(conditions)
A data frame with 10 observations on the following 2 variables.
Codea numeric vector containing the code given in column 77 in EURING data of the format 2000
Descriptiona factor with the finding conditions
http://www.euring.org
Speek, G., Clark, J.A., Rhode, Z., Wassenaar, R.D. & van Noordwijk, A.J. (2001) The EURING exchange-code 2000. Dutch Ringing Scheme, Heteren.
data(conditions) conditionsdata(conditions) conditions
Adds a variable ringing.event which is TRUE if exactly one ringing event exists and FALSE otherwise.
critical.check.ringing.event(dat, id = "birdID")critical.check.ringing.event(dat, id = "birdID")
dat |
a EURING data, read in using read.euring2000plus function |
id |
The name of the variable that contains the individual identifier, normally a combination of scheme and ring number |
A new variable called "ringing.event" is added to the data frame.
Kasper Thorup and Fraenzi Korner-Nievergelt
data(lancol) lancol$birdID <- paste(lancol$scheme, lancol$ring) critical.check.ringing.event(lancol)data(lancol) lancol$birdID <- paste(lancol$scheme, lancol$ring) critical.check.ringing.event(lancol)
Gives the day of the year, i.e. the number of days since the 31 December of the previous year.
dayofyear(m, d, y = 1960)dayofyear(m, d, y = 1960)
m |
month (integer between 1 and 12) |
d |
day (integer between 1 and 31) |
y |
year (integer such as 2013) |
numeric value, day of the year
Fraenzi Korner-Nievergelt
no references
dayofyear(3,1,2013) dayofyear(3,1,2012)dayofyear(3,1,2013) dayofyear(3,1,2012)
The function dc() calculates from the number of ringed birds per group and the number of reencountered birds per group in each destination area the estimated division coefficients per group and the estimated re-encounter probabilities per destination area as described in Kania and Busse (1987). The function bootci.dc() gives the bootstrap confidence intervals for the division coefficients and the re-encounter probabilities estimated by dc(). For details see Korner-Nievergelt et al. (2010).
dc(N, recmatrix, group.names = NA, area.names = NA, start = NA) bootci.dc(N, recmatrix, interval = 0.95, R = 1000, group.names = NA, area.names = NA)dc(N, recmatrix, group.names = NA, area.names = NA, start = NA) bootci.dc(N, recmatrix, interval = 0.95, R = 1000, group.names = NA, area.names = NA)
N |
a vector containing the number of ringed birds per group |
recmatrix |
a matrix containing the number of re-encountered birds per group and area. The rows of the matrix represent the bird groups; the columns represent the destination areas. |
interval |
proportion of the confidence interval (default = 0.95) |
R |
number of bootstrap replicates (default = 1000) |
group.names |
facultative vector of group names |
area.names |
facultative vector of area names |
start |
facultative vector of starting values for the least-square iteration for estimating the inverse of the recovery probability per destination area. The vector has the length of the number of areas and contains approximate inverse values of the recovery probabilities (default = N[1]/recmatrix[1,]/2). |
rec.probs |
estimated re-encounter probabilities per destination area |
division.coef |
estimated division coefficient per group and destination area |
div.coef.lower |
lower limits of the confidence intervals of the estimated division coefficients |
div.coef.upper |
upper limits of the confidence intervals of the estimated division coefficients |
Fraenzi Korner-Nievergelt
Kania W, Busse P (1987) An analysis of the recovery distribution based on finding probabilities. Acta Ornithologica 23: 121-128. Korner-Nievergelt F, Schaub M, Thorup K, Vock M, Kania W (2010) Estimation of bird distribution based on ring re-encounters: precision and bias of the division coefficient and its relation to multi-state models. Bird Study 57: 56-68.
Example data are from: Bauthian I, Gossmann F, Ferrand Y, Julliard R. (2007) Quantifying the origin of Woodcock wintering in France. Journal of Wildlife Management 71: 701-705.
N<-c(7125, 9661, 5266, 3240, 3643, 3192, 3227) recmatrix<-matrix(c(22,25, 6, 2, 4, 1, 0, 47, 78, 49, 28, 38,27, 34), ncol=2) colnames(recmatrix) <- c("Scandinavian", "Eastern") rownames(recmatrix) <- c("North", "West", "Southwest", "Central North", "Central South", "Northeast","Southeast") dc(N, recmatrix, group.names= c("North", "West", "Southwest", "Central North", "Central South", "Northeast","Southeast"), area.names= c("Scandinavian", "Eastern"))N<-c(7125, 9661, 5266, 3240, 3643, 3192, 3227) recmatrix<-matrix(c(22,25, 6, 2, 4, 1, 0, 47, 78, 49, 28, 38,27, 34), ncol=2) colnames(recmatrix) <- c("Scandinavian", "Eastern") rownames(recmatrix) <- c("North", "West", "Southwest", "Central North", "Central South", "Northeast","Southeast") dc(N, recmatrix, group.names= c("North", "West", "Southwest", "Central North", "Central South", "Northeast","Southeast"), area.names= c("Scandinavian", "Eastern"))
transforms degrees and minutes into decimal coordinates
decimal.coord(x)decimal.coord(x)
x |
scalar or vector containing degrees and minutes, e.g. for 45 degrees and 30 minutes = 45.3 |
a scalar or a vector containing the decimal coordinates
Fraenzi Korner-Nievergelt
This function just multiplies the decimals by 5/3... (no reference)
decimal.coord(45.3)decimal.coord(45.3)
These functions provide the density function and a random number generator for the multivariate normal distribution with mean equal to mean and covariance matrix sigma.
dmvnorm(x, mean, sigma, log = FALSE)dmvnorm(x, mean, sigma, log = FALSE)
x |
Vector or matrix of quantiles. If x is a matrix, each row is taken to be a quantile. |
mean |
Mean vector, default is rep(0, length = ncol(x)). |
sigma |
Covariance matrix, default is diag(ncol(x)). |
log |
Logical; if TRUE, densities d are given as log(d). |
This function is copied to birdring from mvtnorm. If you use this function, please use and cite the original function from the package mvtnorm!
Friedrich Leisch and Fabian Scheipl
Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich Leisch, Fabian Scheipl, Torsten Hothorn (2013). mvtnorm: Multivariate Normal and t Distributions. R package version 0.9-9995. URL http://CRAN.R-project.org/package=mvtnorm
Alan Genz, Frank Bretz (2009), Computation of Multivariate Normal and t Probabilities. Lecture Notes in Statistics, Vol. 195., Springer-Verlage, Heidelberg. ISBN 978-3-642-01688-2
see functions and documentations in the package mvtnorm
dmvnorm(x=c(0,0))dmvnorm(x=c(0,0))
Draws a map of the palearctic region that can be used as basis for showing ring reencounter data.
draw.map(a=-10, b=30, c=23, d=65, bbox=NULL, fill = TRUE, col.land = grey(0.5), col.water = "white", border = NA, detail = FALSE, box = TRUE, axes = FALSE, las = 1, cex.axis = 0.8, dist.axislab = 0.2, whichaxis = c(1:4), tck = -0.005, mercator = FALSE, mar = rep(0.5, 4), asp=NA)draw.map(a=-10, b=30, c=23, d=65, bbox=NULL, fill = TRUE, col.land = grey(0.5), col.water = "white", border = NA, detail = FALSE, box = TRUE, axes = FALSE, las = 1, cex.axis = 0.8, dist.axislab = 0.2, whichaxis = c(1:4), tck = -0.005, mercator = FALSE, mar = rep(0.5, 4), asp=NA)
a |
left edge of the map (longitude), can be used alternatively to the argument bbox |
b |
right edge of the map (longitude), can be used alternatively to the argument bbox |
c |
lower edge of the map (latitude), can be used alternatively to the argument bbox |
d |
upper edge of the map (latitude), can be used alternatively to the argument bbox |
bbox |
a numeric vector giving the map boundary in decimal degrees as c(long_min, long_max, lat_min, lat_max), can be used alternatively to the arguments a, b, c, and d. |
fill |
logical value, TRUE = land and water masses are filled with a color |
col.land |
color of the land |
col.water |
color of the water |
border |
color of the coastline, NA = no coastline is drawn |
detail |
if TRUE: an alternative way to draw coastlines |
box |
logical, TRUE = a box is drawn around the map |
axes |
logical, indicates whether axis should be drawn |
las |
see par |
cex.axis |
see par |
dist.axislab |
distance from the axis to the axis labels |
whichaxis |
vector of length 1 to 4 containing the axis that should be drawn, default is c(1,2,3,4), i.e. all axes |
tck |
see par |
mercator |
logical, if TRUE a mercator projection is plotted. see details below |
mar |
see par |
asp |
if set to 1 x and y axes are scaled equally (not recommended if mercator=TRUE), see par |
If a mercator projection is used, the values for a, b, c and d will be adjusted.
this is a plotting function only
some times it does not do what we expect....
Fraenzi Korner-Nievergelt
Rummler, H. 2002. Mercatorkarte und hyperbolische Geometrie. Elem. Math., 57, 168-173.
draw.map(-18, 50, -5, 56, col.land="white", col.water=grey(0.5), detail=FALSE, axes=TRUE) draw.map(a=0, b=30, c=35, d=60, col.land="white", col.water=grey(0.5), detail=FALSE, axes=TRUE, mercator=TRUE)draw.map(-18, 50, -5, 56, col.land="white", col.water=grey(0.5), detail=FALSE, axes=TRUE) draw.map(a=0, b=30, c=35, d=60, col.land="white", col.water=grey(0.5), detail=FALSE, axes=TRUE, mercator=TRUE)
Ringing and recovery data of the Red-backed Shrike in the EURING2000 format
data(lancol)data(lancol)
A data frame with 2483 observations of the 40 variables of the EURING2000.
http://www.euring.org
Speek, G., Clark, J.A., Rhode, Z., Wassenaar, R.D. & van Noordwijk, A.J. (2001) The EURING exchange-code 2000. Dutch Ringing Scheme, Heteren.
data(lancol)data(lancol)
calculates the loxodromic distance and direction between two points on the earth
loxodrom.dir(x1, y1, x2, y2, epsilon = 1e-06) loxodrom.dist(x1, y1, x2, y2, epsilon = 1e-04, package="geosphere")loxodrom.dir(x1, y1, x2, y2, epsilon = 1e-06) loxodrom.dist(x1, y1, x2, y2, epsilon = 1e-04, package="geosphere")
x1 |
x-coordinate/longitude of the first point (in decimal coordinates), can be a scalar or a vector |
y1 |
y-coordinate/latitude of the first point (in decimal coordinates), can be a scalar or a vector |
x2 |
x-coordinate/longitude of the second point (in decimal coordinates), can be a scalar or a vector |
y2 |
y-coordinate/latitude of the second point (in decimal coordinates), can be a scalar or a vector |
epsilon |
a threshold value for considering a number as zero. See details. |
package |
if "geosphere" (default) the function is based on the geosphere package, if "birdring" the function written by F. Korner is used. The latter is less reliable. |
If you use the birdring package, please, check the results carefully, especially when vectors instead of scalars are given as arguments. If some distances or directions are obviously wrong (such cases occurred predominantly when the bird moved exactly into one of the four directions 0, 90, 180 or 270 degrees) then it might help to increase the value of epsilon.
The function loxodrom.dist() gives back a number or a vector with the distances in km between the two points on earth. The function loxodrom.dir() gives back a number or a vector with the directions in degees from North (clockwise) between the two points on earth.
see details
Fraenzi Korner-Nievergelt
Imboden, C., Imboden D. (1972) Orthodromic and loxodromic formula for the calculation of distance and direction between ringing and finding place. Vogelwarte 26: 336-346.
ringingx<-7.30 ringingy<-47.41 findingx<-5.1 findingy<-32.01 rxdec<-decimal.coord(ringingx) rydec<-decimal.coord(ringingy) fxdec<-decimal.coord(findingx) fydec<-decimal.coord(findingy) loxodrom.dist(rxdec, rydec, fxdec, fydec) loxodrom.dir(rxdec, rydec, fxdec, fydec)ringingx<-7.30 ringingy<-47.41 findingx<-5.1 findingy<-32.01 rxdec<-decimal.coord(ringingx) rydec<-decimal.coord(ringingy) fxdec<-decimal.coord(findingx) fydec<-decimal.coord(findingy) loxodrom.dist(rxdec, rydec, fxdec, fydec) loxodrom.dir(rxdec, rydec, fxdec, fydec)
Given a month, day, and year, returns the number of days since January 1, 1960.
mdy.date(month, day, year, nineteen = TRUE, fillday = FALSE, fillmonth = FALSE)mdy.date(month, day, year, nineteen = TRUE, fillday = FALSE, fillmonth = FALSE)
month |
vector of months. |
day |
vector of days. |
year |
vector of years. |
nineteen |
if TRUE, year values between 0 and 99 are assumed to be in the 20th century A.D.; otherwise, if FALSE, they are assumed to be in the 1st century A.D. |
fillday |
if TRUE, then missing days are replaced with 15. |
fillmonth |
if TRUE, then a missing month causes the month and day to be set to 7/1. |
The date functions are particularly useful in computing time spans, such as number of days on test, and similar functions can be found in other statistical packages. The baseline date of Jan 1, 1960 is, of course, completely arbitrary (it is the same one used by SAS).
The fillday and fillmonth options are perhaps useful only to the author and a very few others: we sometimes deal with patients whose birth date was in the 1800's, and only the month or even only the year is known. When the interval is greater than 80 years, a filler seems defensible.
a vector of Julian dates.
Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (1992). Numerical Recipes: The Art of Scientific Computing (Second Edition). Cambridge University Press.
Terry Therneau and Thomas Lumley and Kjetil Halvorsen and Kurt Hornik (2012). date: Functions for handling dates. R package version 1.2-33.
see documentation and other functions in the package date
mdy.date(3, 10, 53)mdy.date(3, 10, 53)
this function is only used internally by the function draw.map
mercatorlat(x)mercatorlat(x)
x |
latitude in decimal coordinates |
numeric: latitude to draw a mercator map
Fraenzi Korner-Nievergelt
Rummler, H. (2002) Mercatorkarte und hyperbolische Geometrie. Elem. Math., 57, 168-173.
mercatorlat(41.6)mercatorlat(41.6)
calculates the orthodromic (great circle, shortest distance) distance between two points on the earth
orthodrom.dist(x1, y1, x2, y2)orthodrom.dist(x1, y1, x2, y2)
x1 |
x-coordinate/longitude of the first point (in decimal coordinates), can be a scalar or a vector |
y1 |
y-coordinate/latitude of the first point (in decimal coordinates), can be a scalar or a vector |
x2 |
x-coordinate/longitude of the second point (in decimal coordinates), can be a scalar or a vector |
y2 |
y-coordinate/latitude of the second point (in decimal coordinates), can be a scalar or a vector |
The function is a wrapper of the distMeeus function of the geosphere package.
gives back a number or a vector with the distances in km between the two points on earth.
see details
Fraenzi Korner-Nievergelt
Imboden, C., Imboden D. (1972) Orthodromic and loxodromic formula for the calculation of distance and direction between ringing and finding place. Vogelwarte 26: 336-346.
ringingx<-7.30 ringingy<-47.41 findingx<-5.1 findingy<-32.01 rxdec<-decimal.coord(ringingx) rydec<-decimal.coord(ringingy) fxdec<-decimal.coord(findingx) fydec<-decimal.coord(findingy) orthodrom.dist(rxdec, rydec, fxdec, fydec)ringingx<-7.30 ringingy<-47.41 findingx<-5.1 findingy<-32.01 rxdec<-decimal.coord(ringingx) rydec<-decimal.coord(ringingy) fxdec<-decimal.coord(findingx) fydec<-decimal.coord(findingy) orthodrom.dist(rxdec, rydec, fxdec, fydec)
Gives the overlap of two distributions (such as a prior and a posterior distribution) based on one sample of simulated values from each distribution
overlap(posterior, prior, from = 0, to = 1, nsim = 1e+05, edge.of.parameter.space=FALSE)overlap(posterior, prior, from = 0, to = 1, nsim = 1e+05, edge.of.parameter.space=FALSE)
posterior |
A numeric vector, a sample of simulated random values from the posterior distribution |
prior |
A numeric vector, a sample of simulated random values from the prior distribution |
from |
Lower limit of the parameter space over which the posterior and prior distributions are compared. |
to |
Upper limit of the parameter space over which the posterior and prior distributions are compared. |
nsim |
Number of simulated values used for the Monte Carlo simulation to measure the overlap. |
edge.of.parameter.space |
logical value; Two different methods are implemented to calculate the overlap. First (edge.of.parameter.space=FALSE), smoothers are fitted to the histograms of the simulated values from the posterior and prior distributions, and the overlap is calculated based on this smoothed density functions. This has the advantage to be more exact when the number of simulated values from the posterior distribution is small. However, it can be unreliable when the mean of the posterior distribution is close to the edge of the parameter space. In such cases (edge.of.parameter.space=TRUE), it is more reliable to calculate the overlap directly from histograms of the simulated values from the posterior and prior distributions. See also details. |
If edge.of.parameter.space=FALSE, the function first uses the function density to obtain density functions of the prior and posterior distributions and then the overlap is measured by a Monte Carlo simulation. If edge.of.parameter.space=TRUE, two histrograms of the simulated values from the posterior and prior distributions are drawn with 999 classes and breaks 1000 equally spaced values between from and to. The overlap is then calculated directly from these histograms.
a numeric value which is an approximation of the proportion of the overlap of the posterior with the prior distribution.
Fraenzi Korner-Nievergelt
Gimenez, O., S. P. Brooks, et al. (2009). Weak identiability in models for mark-recapture-recovery data. Modelling Demographic Processes in Marked Populations. Series: Environmental and Ecological Statistics. D. L. Thomson, E. G. Cooch and M. J. Conroy.
prior <- rbeta(2000, 1,1) posterior <- rbeta(2000, 14, 35) overlap(posterior, prior)prior <- rbeta(2000, 1,1) posterior <- rbeta(2000, 14, 35) overlap(posterior, prior)
Converts Euring country and region codes into their text names.
place2name(x)place2name(x)
x |
a variable containing four character Euring place code. |
A warning is given if any place codes are not matched, these will be returned as NA.
a dataframe with three columns: 'country.name', 'region.name', 'current', the last of which indicates whether the code is currently use or deprecated.
Rob Robinson
examplecodes <- c('BL20', 'GBTR') place2name(examplecodes)examplecodes <- c('BL20', 'GBTR') place2name(examplecodes)
EURING-code for places as given in Speek et al. (2001)
data(places)data(places)
A data frame with 1852 rows of the following 5 variables.
countryname of country. non-ASCII characters have been exchanged, please change back for Cote d Ivoire and Suqutra
regionname of region. non-ASCII characters have been exchanged, please check an change back!
codethe code used by EDB
currentdate.updateddate of update
http://www.euring.org
Speek, G., Clark, J.A., Rhode, Z., Wassenaar, R.D. & van Noordwijk, A.J. (2001) The EURING exchange-code 2000. Dutch Ringing Scheme, Heteren.
data(places)data(places)
Reads EURING data (format EURING exchange code 2000) into R and creates a data.frame
read.euring2000(filename, quote="", ...)read.euring2000(filename, quote="", ...)
filename |
character string of the data file obtained from EURING (format: exchange code 2000) |
quote |
default is to ignore quotemarks as much as possible, see notes. |
... |
extra arguments to pass to read.table |
A data.frame containing the following variables from the EURING 2000 code:
| scheme | Factor | ringing scheme (code) |
| id.method | Factor | identification method |
| ring | Factor | ring number |
| ring.verif | character | verification of the metal ring |
| metal.ring.info | character | metal ring information |
| marks.info | character | other marks information |
| spec.byringer | character | species + subsp., mentioned by person |
| spec.byscheme | character | species + subsp., concluded by scheme |
| manipulated | character | manipulated |
| moved | character | moved before the (re)capture/recovery |
| catching.method | character | catching method |
| catching.lures | character | catching lures |
| sex.byringer | character | sex, by the person who handled the bird |
| sex.byscheme | character | sex, as concluded by scheme |
| age.byringer | character | age, by the person who handled the bird |
| age.byscheme | character | age, as concluded by scheme |
| status | character | status |
| broodsize | character | broodsize |
| pullus.age | character | pullus age |
| pullus.age.acc | character | accuracy of pullus age |
| day | numeric | day of record, derived from date |
| month | numeric | month of record, derived from date |
| year | numeric | year of record, derived from date |
| date.acc | character | accuracy of date |
| time | character | time |
| place.code | character | place code |
| country | character | country derived from place code |
| region | character | region (county) derived from place code |
| lat | numeric | latitude in decimal coordinates |
| lon | numeric | longitude in decimal coordinates |
| coord.acc | character | accuracy of coordinates |
| condition | character | condition |
| circumstances | character | finding circumstances |
| circumstances.presumed | character | finding circumstances presumed |
| euring.codeid | character | EURING-code identifier |
| distance | numeric | distance to place of ringing (km) |
| direction | numeric | direction to place of ringing (km) |
| time.elapsed | numeric | time since ringing (days) |
Quotemarks, apostrophes and backticks can cause havoc when reading in files; if things do not work as you expect, check for their presence of these and consider removing!
Fraenzi Korner-Nievergelt
Speek et al. 2007: The EURING exchange-code 2000. www.euring.org
filename <- system.file("extdata", "RBShrike2000.TXT", package = "birdring") dat <- read.euring2000(filename) str(dat)filename <- system.file("extdata", "RBShrike2000.TXT", package = "birdring") dat <- read.euring2000(filename) str(dat)
Reads EURING data (format EURING exchange code 2000\+) into R and creates a data.frame
read.euring2000plus(filename, quote="", ...)read.euring2000plus(filename, quote="", ...)
filename |
character string of the psv-file obtained from EURING (format: exchange code 2000\+) |
quote |
default is to ignore quotemarks as much as possible, see notes. |
... |
extra arguments to pass to read.table |
A data.frame containing the following variables from the EURING 2000\+ code:
| scheme | Factor | ringing scheme (code) |
| id.method | Factor | identification method |
| ring | Factor | ring number |
| ring.verif | character | verification of the metal ring |
| metal.ring.info | character | metal ring information |
| marks.info | character | other marks information |
| spec.byringer | character | species + subsp., mentioned by person |
| spec.byscheme | character | species + subsp., concluded by scheme |
| manipulated | character | manipulated |
| moved | character | moved before the (re)capture/recovery |
| catching.method | character | catching method |
| catching.lures | character | catching lures |
| sex.byringer | character | sex, by the person who handled the bird |
| sex.byscheme | character | sex, as concluded by scheme |
| age.byringer | character | age, by the person who handled the bird |
| age.byscheme | character | age, as concluded by scheme |
| status | character | status |
| broodsize | character | broodsize |
| pullus.age | character | pullus age |
| pullus.age.acc | character | accuracy of pullus age |
| day | numeric | day of record, derived from date |
| month | numeric | month of record, derived from date |
| year | numeric | year of record, derived from date |
| date.acc | character | accuracy of date |
| time | character | time |
| place.code | character | place code |
| country | character | country extracted from place code |
| region | character | region (county) extracted from place code |
| lat | numeric | latitude in decimal coordinates |
| lon | numeric | longitude in decimal coordinates |
| coord.acc | character | accuracy of coordinates |
| condition | character | condition |
| circumstances | character | finding circumstances |
| circumstances.presumed | character | finding circumstances presumed |
| euring.codeid | character | EURING-code identifier |
| distance | numeric | distance to place of ringing (km) |
| direction | numeric | direction to place of ringing (km) |
| time.elapsed | numeric | time since ringing (days) |
| wing.length | numeric | maximum chord measurement in mm, Svensson (1992) |
| third.primary | numeric | Length of the third primary feather, in mm |
| state.of.wing.point | character | condition of the longest primary feather |
| mass | numeric | body, in grams, measured to a maximum precision of 0.1 g. |
| moult | character | code for main, clearly identifiable moult states |
| plumage.code | character | extra information to enhance age code |
| hind.claw | numeric | in mm, for details of method see Svensson (1992) |
| bill.length | numeric | in mm, see du Feu (2012). |
| bill.method | character | a single letter code, for details see Svensson (1992). |
| total.head.length | numeric | in mm, see du Feu (2012) |
| tarsus | numeric | in mm, see du Feu (2012) |
| tarsus.method | character | tarsus method used, see du Feu (2012) |
| tail.length | numeric | in mm, details of the method see Svensson (1992). |
| tail.difference | numeric | according to Svensson (1992) |
| fat.score | numeric | fat score, see du Feu (2012) for details. |
| fat.score.method | character | fat score method used, see du Feu (2012) |
| pectoral.muscle | numeric | state of pectoral muscle |
| brood.patch | character | state of the brood patch in the breeding season |
| primary.score | numeric | the sum of the primary moult scores |
| primary.moult | character | state of the 10 primary feathers |
| old.greater.coverts | numeric | the number of unmoulted greater coverts |
| alula | character | state of the three alula feathers |
| carpal.covert | numeric | state of moult of the carpal covert: 0=old, 1=new. |
| sexing.method | character | for code description see du Feu (2012). |
For three additional optional variables, see du Feu (2012).
Quotemarks, apostrophes and backticks can cause havoc when reading in files; if things do not work as you expect, check for their presence of these and consider removing!
Fraenzi Korner-Nievergelt
du Feu et al. 2012: EURING exchange-code 2000\+. www.euring.org
filename <- system.file("extdata", "REEWAExport_50.psv", package = "birdring") dat <- read.euring2000plus(filename) str(dat)filename <- system.file("extdata", "REEWAExport_50.psv", package = "birdring") dat <- read.euring2000plus(filename) str(dat)
Transforms the scheme codes into country name.
scheme2country(x)scheme2country(x)
x |
variable scheme from the data frame produced by read.EURING2000 or |
a factor with levels coresponding to the country names
F. Korner-Nievergelt
www.euring.org
schemecode <- "HES" scheme2country(schemecode)schemecode <- "HES" scheme2country(schemecode)
EURING-code for ringing scheme as given in Speek et al. (2001)
data(schemes)data(schemes)
A data frame with 39 observations on the following 7 variables.
Codea factor with the EURING code
Countrya factor with the country of the scheme
Centrea factor with the city of the place of the scheme
EURINGa factor with levels Y
Currenta factor with levels Y
Date.Updateda factor
Notesa factor with additional remarks
http://www.euring.org
Speek, G., Clark, J.A., Rhode, Z., Wassenaar, R.D. & van Noordwijk, A.J. (2001) The EURING exchange-code 2000. Dutch Ringing Scheme, Heteren.
data(schemes)data(schemes)
EURING-code for species as given in Speek et al. (2001)
data(species)data(species)
A data frame with 3311 observations on the following 3 variables.
Codea numeric vector with the EURING species code
Namea factor with the species names
Date.Updateda factor
http://www.euring.org
Speek, G., Clark, J.A., Rhode, Z., Wassenaar, R.D. & van Noordwijk, A.J. (2001) The EURING exchange-code 2000. Dutch Ringing Scheme, Heteren.
data(species)data(species)