Generate Color Tag Sequences

Description

Implement a coherent and flexible protocol for animal color tagging. 'GenTag' provides a simple computational routine with low CPU usage to create color sequences for animal tag. First, a single-color tag sequence is created from an algorithm selected by the user, followed by verification of the combination uniqueness. Three methods to produce color tag sequences are provided. Users can modify the main function core to allow a wide range of applications.

Details

The DESCRIPTION file:

Index of help topics:

GenTag-package          Generate Color Tag Sequences
allequal                All equal tag sequence sample
erc                     Estimates remaining color
escode                  Empty synonym code
escombination           Empty synonym combination
esdataset               Empty synonym dataset
genseq                  Color tag combination generator
lifexp                  Life expectancy tag sequence sample
pre_used                Pre-used combinations combinations
scy                     Summary color year
vfrequency              Variable frequency tag sequence sample

Implement a coherent and flexible protocol for animal color tagging. 'GenTag' provides a simple computational routine with low CPU usage to create color sequences for animal tag. First, a single-color tag sequence is created from an algorithm selected by the user, followed by verification of the combination uniqueness. Three methods to produce color tag sequences are provided. Users can modify the main function core to allow a wide range of applications.

Author(s)

Carlos Biagolini-Jr.

Maintainer: Carlos Biagolini-Jr.<c.biagolini@gmail.com>

References

Alisauskas & Lindberg (2002). Effects of neckbands on survival and fidelity of White-fronted and Canada geese captured as non-breeding adults. doi: 10.1080/02664760120108575 Broughton (2015). Low incidence of leg and foot injuries in colour-ringed Marsh tits Poecile palustris. doi: 10.1080/03078698.2015.1059610 Burley (1986). Sex-ratio manipulation in color-banded populations of Zebra finches. doi: 10.1111/j.1558-5646.1986.tb05744.x Burley, Krantzberg & Radman (1982). Influence of colour-banding on the conspecific preferences of Zebra finches. doi: 10.1016/S0003-3472(82)80055-9 Calvo & Furness (1992). A review of the use and the effects of marks and devices on birds. doi: 10.1080/03078698.1992.9674036 Cresswell, Lind, Quinn, Minderman & Whitfield, (2007). Ringing or colour-banding does not increase predation mortality in Redshanks Tringa totanus. doi: 10.1111/j.2007.0908-8857.3925.x Cuthill, Hunt, Cleary, & Clark (1997). Colour bands, dominance, and body mass regulation in male Zebra finches (Taeniopygia guttata). doi: 10.1098/rspb.1997.0151 Fiske & Amundsen (1997). Female bluethroats prefer males with symmetric colour bands. doi: 10.1006/anbe.1996.0436 Gil, Graves, Hazon, & Wells, (1999). Male attractiveness and differential testosterone investment in Zebra finch eggs. doi: 10.1126/science.286.5437.126 Griesser, Schneider, Collis, Overs, Guppy, Guppy, Takeuchi, Collins, Peters & Hall (2012). Causes of ring-related leg injuries in birds - evidence and recommendations from four field studies. doi: 10.1371/journal.pone.0051891 Jennions (1998). The effect of leg band symmetry on female-male association in Zebra finches. doi: 10.1006/anbe.1997.0579 Johnsen, Fiske, Amundsen, Lifjeld, & Rohde (2000). Colour bands, mate choice and paternity in the Bluethroat. doi: 10.1006/anbe.1999.1274 Johnsen, Lifjeld, & Rohde (1997). Coloured leg bands affect male mate-guarding behaviour in the Bluethroat. doi: 10.1006/anbe.1996.0437 Johnson, Dalton & Burley (1993). Preferences of female American goldfinches (Carduelis tristis) for natural and artificial male traits. doi: 10.1093/beheco/4.2.138 Kosinski (2004). The removal of colour rings by Greenfinches Carduelis chloris. doi: 10.1080/03078698.2004.9674304 McCrea & Morgan (2014). Analysis of capture-recapture data. Boca Raton, Chapman and Hall/CRC. Nietmann & Ha (2018). Site-specific incidence of ring-related injuries in Rufous fantails Rhipidura rufifrons. doi: 10.1080/03078698.2018.1505109 Pierce, Stevens, Mulder & Salewski (2007). Plastic colour rings and the incidence of leg injury in Flycatchers (Muscicapidae, Monarchidae). doi: 10.1080/03078698.2007.9674365 Schlich & Kempenaers (2018). The immediate impact of ringing, blood sampling and PIT-tag implanting on the behaviour of Blue tits Cyanistes caeruleus. doi: 10.5253/arde.v106i1.a8 Sedgwick & Klus (1997). Injury due to leg bands in Willow flycatchers. Song, Liu, Booksmythe & Ding (2017). Effects of individual-based preferences for colour-banded mates on sex allocation in Zebra finches. doi: 10.1093/beheco/arx069 Sutherland (2006). Ecological census techniques: a handbook (2nd ed.). New York, Cambridge University Press. Weiser et al (2018). Effects of leg flags on nest survival of four species of Arctic-breeding shorebirds. doi: 10.1111/jofo.12264 Zann (1994). Effects of band color on survivorship, body condition and reproductive effort of free-living Australian Zebra finches. doi: 10.2307/4088512

Examples

genseq(30, 4,c("Black","Blue","Brown","Gray","Green"))

All equal tag sequence sample

Description

Create combinations with equal sample probability to all colors.

Usage

allequal(ntag, colorsname, nspecial = 0, name1 = "Metal", name2 = "EMPTY", location1 = 1,
location2 = 2, nspecial1 = 1, nspecial2 = 1)

Arguments

Value

A sequencie of tags

Author(s)

Biagolini-Jr.

See Also

genseq vfrequency lifexp

Examples

# Create an object contain the name/code of tag colors 
tcol<-c("Black","Blue","Brown","Gray","Green","Pink","Purple","Red","White","Yellow")
# Generate color tag combination without especial tags
genseq(30, 4, colorsname= tcol) 
#Generate color tag combination with especial color (ex metallic tag for numeric identification)
genseq(30, 4, tcol, nspecial=1, name1="Metal",location1=c(2,4)) 
# For ongoing works, use the argument usedcombinations to informe the previus used combinations
data(pre_used) # Data example
genseq(100, 4, tcol, usedcombinations=pre_used[,1:4]) 

Estimates remaining color

Description

Estimates number of remaining color tags in the field

Usage

erc(usedcombinations, yearusedcombinations, currentyear = NA,
  yearsurvival = NA, lifespan = NA, hide_color = NA)

Arguments

Value

A estimation of the number of remaining color tags in the field.

Author(s)

Biagolini-Jr.

See Also

scy

Examples

## The function is currently defined as
data(pre_used) # Data example
erc(pre_used[,1:4],pre_used[,5],2019,0.85, hide_color="EMPTY")

Empty synonym code

Description

Find synonyms in a group of colors with code for empty tag.

Usage

escode(row_under_review, emptyname = NA, columns_set = NA)

Arguments

Value

Matrix with all synonym

Examples

# Example of a full sequence
combination<- c("EMPTY","Red","Yellow","Red","Blue","Green")
# See synonym for the code group 1 to 3
escode(combination,"EMPTY",columns_set=1:3) 

Empty synonym combination

Description

Find synonyms of a sequence with code for empty tag.

Usage

escombination(row_under_review, emptyname,
g1 = NA, g2 = NA, g3 = NA, g4 = NA, g5 = NA, g6 = NA)

Arguments

Value

Matrix with all synonyms

Author(s)

Biagolini-Jr

See Also

escode esdataset

Examples

# Example of a full sequence
combination<- c("EMPTY","Red","Yellow","Red","Blue","Green")  # See synonym for the full sequence
escombination(combination,"EMPTY",g1=1:3,g2=4:6)

Empty synonym dataset

Description

Find synonyms in a dataset contain combination with code for empty tag.

Usage

esdataset(tag_sheet, emptyname, g1 = NA, g2 = NA, g3 = NA, g4 = NA, g5 = NA, g6 = NA)

Arguments

Value

Matrix with all synonyms for from entire dataset

Author(s)

Biagolini-Jr.

See Also

escode escombination

Examples

(combination<- matrix(c("EMPTY","Red","Blue","Green"),4,6,TRUE)) # Example of a dataset
esdataset(combination,"EMPTY",g1=1:3,g2=4:6)

Color tag combination generator

Description

Create sequences of color tags for animal identification.

Usage

genseq(ncombinations = 100, ntag = 4, colorsname, gen_method = "allequal", 
usedcombinations = NA, colorsf = NA, nspecial = 0, name1 = "Metal", name2 = "EMPTY", 
location1 = 1, location2 = 2, nspecial1 = 1, nspecial2 = 1, emptyused = FALSE, 
emptyname = "EMPTY", currentyear = NA, yearsurvival = 1, lifespan = NA, iotf = FALSE, 
yearusedcombinations = NA, speed = 1, ignorecolor = NA, 
g1 = NA, g2 = NA, g3 = NA, g4 = NA, g5 = NA, g6 = NA, parameterslist = NA)

Arguments

Value

A list of combinations

Author(s)

Biagolini-Jr.

See Also

allequal vfrequency lifexp

Examples

# Create an object contain the name/code of tag colors 
tcol<-c("Black","Blue","Brown","Gray","Green","Pink","Purple","Red","White","Yellow")
# Generate color tag combination without especial tags
genseq(30, 4, colorsname= tcol) 
#Generate color tag combination with especial color (ex metallic tag for numeric identification)
genseq(30, 4, tcol, nspecial=1, name1="Metal", location1=c(2,4)) 
# For ongoing works, use the argument usedcombinations to informe the previus used combinations
data(pre_used) # Data example
genseq(30, 4, colorsname= tcol, usedcombinations=pre_used[,1:4]) 
combinations<-genseq(100, 4, tcol) # save combinations into an object

Life expectancy tag sequence sample

Description

Create combinations with variable sample probability.

Usage

lifexp(ntag, colorsname, nspecial = 0, name1 = "Metal", name2 = "EMPTY", 
location1 = 1, location2 = 2, nspecial1 = 1, nspecial2 = 1, currentyear = NA,
 yearsurvival = 1, lifespan = NA, yearusedcombinations, 
usedcombinations, speed = 1, ignorecolor = NA)

Arguments

Value

A sequencie of tags

Author(s)

Biagolini-Jr.

See Also

allequal genseq vfrequency

Examples

data(pre_used) # Data example
# Create an object contain the name/code of tag colors 
tcol<-c("Black","Blue","Brown","Gray","Green","Pink","Purple","Red","White","Yellow")
genseq(30, 4,tcol, "lifexp", pre_used[,1:4], 
yearusedcombinations=pre_used[,5], yearsurvival= 0.8, lifespan=5, currentyear=2019)

Pre-used combinations combinations

Description

Simulated data of pre-used combinations

Usage

data("pre_used")

Format

A data frame with 1200 observations on the following 5 variables.

Tag_1

a factor with levels Black Brown Dark_Blue EMPTY Gray Green Light_Blue Orange Pink Red White Yellow

Tag_2

a factor with levels Black Brown Dark_Blue Gray Green Light_Blue Metal Orange Pink Red White Yellow

Tag_3

a factor with levels Black Brown Dark_Blue EMPTY Gray Green Light_Blue Orange Pink Red White Yellow

Tag_4

a factor with levels Black Brown Dark_Blue Gray Green Light_Blue Metal Orange Pink Red White Yellow

Year

a numeric vector

Details

Simulated database to example of registers of color tag sequences usage. Columns 1, 2 ,3 and 4 represent the tag code, and column 5 is the date of tagging.

Source

Simulated database

Examples

data(pre_used)

Summary color year

Description

Summary the number of each color tag used per year.

Usage

scy(usedcombinations, yearusedcombinations, hide_color = NA)

Arguments

Value

A summary of the numeber of tag colors used by year

Author(s)

Biagolini-Jr.

See Also

erc

Examples

data(pre_used) # Data example
scy(pre_used[,1:4],pre_used[,5], hide_color="EMPTY")

Variable frequency tag sequence sample

Description

Create combinations with defined sample probability to each colors.

Usage

vfrequency(ntag, colorsname, colorsf, nspecial = 0, name1 = "Metal", 
name2 = "EMPTY", location1 = 1, location2 = 2, nspecial1 = 1, nspecial2 = 1)

Arguments

Value

A sequencie of tags

Author(s)

Biagolini-Jr

See Also

allequal genseq lifexp

Examples

tcol<-c("Black","Blue","Brown","Gray","Green","Pink","Purple","Red","White","Yellow")
p<-c(1,2,5,1,2,2,4,5,8,5)
genseq(30, 4, tcol, gen_method="vfrequency", colorsf=p)