Type: | Package |
Title: | Streamlined Analysis of Wild Pedigree Data |
Version: | 0.1.0 |
Description: | Analyzing pedigree data of wild populations. While primarily designed to process outputs from the 'COLONY' (Jones & Wang (2010) <doi:10.1111/j.1755-0998.2009.02787.x>) pedigree reconstruction software, it can also accommodate data from other sources. By linking reconstructed pedigrees with genetic sample metadata, 'wpeR' produces spatial and temporal visualizations as well as tabular summaries that support interpretation of family structures and dynamics. The main goal of the package is to provide a solution for the analysis of complex wild pedigree data and to help the user to gain insights into genetic relationships within wild animal populations. |
License: | GPL (≥ 3) |
URL: | https://gr3602.github.io/wpeR/ |
BugReports: | https://github.com/GR3602/wpeR/issues |
Depends: | R (≥ 4.1.0) |
Imports: | dplyr, ggplot2, sf, stats, utils |
Suggests: | basemaps, ggforce, ggrepel, gridExtra, kinship2, knitr, leaflet, leaflet.providers, rmarkdown, spelling, testthat (≥ 3.0.0) |
VignetteBuilder: | knitr |
Config/testthat/edition: | 3 |
Encoding: | UTF-8 |
Language: | en-US |
LazyData: | true |
RoxygenNote: | 7.3.2 |
NeedsCompilation: | no |
Packaged: | 2025-07-09 13:06:42 UTC; gregor |
Author: | Tomaz Skrbinsek [aut], Gregor Simcic [aut, cre] |
Maintainer: | Gregor Simcic <grega0simcic@gmail.com> |
Repository: | CRAN |
Date/Publication: | 2025-07-14 17:00:02 UTC |
Get dates of individuals first and last sample
Description
Takes data frame of all samples and returns the dates of individuals first and last sample. Besides that the functions determines if animal is dead based on predefined sample type eg. tissue.
Usage
anim_timespan(individual_id, sample_date, sample_type, dead = "Tissue")
Arguments
individual_id |
Column in the dataframe of all samples containing
individual animal identifier code.
Defined as |
sample_date |
Column in the dataframe of all samples containing
the date of sample collection.
Must be in |
sample_type |
Column in the dataframe of all samples containing the data
on the type (eg. scat, tissue, saliva) of particular sample.
Defined as |
dead |
Single value or vector of different lethal sample types. If no lethal
samples are included in the sampledata the dead parameter can be set to |
Value
A data frame with four columns and one row for each individual_id
.
Returned data frame columns correspond to individual identification key (ID
),
date of first (FirstSeen
) and last (LastSeen
) sample of individual and
logical (TRUE/FALSE
) value that identifies if the individual is dead (IsDead
).
Examples
anim_timespan(
individual_id = wolf_samples$AnimalRef,
sample_date = wolf_samples$Date,
sample_type = wolf_samples$SType,
dead = c("Tissue")
)
Check and prepare genetic sample metadata
Description
Verifies the consistency of columns in the genetic sample metadata and
prepares it for use with other functions in the wpeR
package. The function
ensures that the provided data is properly formatted and conforms to the standards
of functions that make up the wpeR
package.
Usage
check_sampledata(
Sample,
Date,
AnimalRef,
GeneticSex,
lat,
lng,
SType,
extraCols = NULL
)
Arguments
Sample |
A vector of sample unique identifier codes. |
Date |
A vector of sample collection dates in 'YYYY-MM-DD' format. |
AnimalRef |
A vector of identifier codes of the particular individual that the sample belongs to. |
GeneticSex |
A vector of genetic sex information ('F' for female, 'M' for male, NA for unknown). |
lat |
A vector of latitude coordinates in the WGS84 coordinate system (EPSG: 4326). |
lng |
A vector of longitude coordinates in the WGS84 coordinate system (EPSG: 4326). |
SType |
A vector of sample types eg.: scat, hair, tissue. |
extraCols |
A vector of extra column names that the user wants to include in sampledata data frame (see Details). |
Details
By specifying the extraCols
parameter additional information can be included
in the sampledata dataframe. Such additional information is not required for
the functioning of the wpeR
package functions, but can be useful to the user
when interpreting results. When including additional columns the function
inputs (Sample, Date, AnimalRef...) have to be defined as a vector extracted from
data frame column (eg. Sample = dataframe$column) and the extraCols
parameter is defined,
as a vector of column names form the same data frame (eg. extraCols = c(column1, column2,
column3)).
Value
A data frame with at least 7 columns and a number of rows equal to the length
of the input vector. Each column corresponds to one of the input parameters.
If the function executes without warnings or errors, the result from
check_sampledata()
can be used as an input parameter for other functions
within this package: get_colony()
, get_ped()
, org_fams()
and plot_table()
.
Examples
sampledata <- check_sampledata(
Sample = wolf_samples$Sample,
Date = wolf_samples$Date,
AnimalRef = wolf_samples$AnimalRef,
GeneticSex = wolf_samples$GeneticSex,
lat = wolf_samples$lat,
lng = wolf_samples$lng,
SType = wolf_samples$SType
)
Get matrix of apparent survival
Description
Creates a matrix that shows number of captured animals between multiple seasons.
Usage
dyn_matrix(animal_id, capture_date, start_dates, end_dates)
Arguments
animal_id |
A column in the dataframe of all samples that stores individual animal identifier code. |
capture_date |
A column in the dataframe of all samples that stores
the date of sample collection. Must be in |
start_dates |
Vector of dates in |
end_dates |
Vector of dates in |
Value
A matrix with 1 + no. seasons rows and columns.
diagonal: number of new captures in each session,
above diagonal: number of recaptures from season x to season y,
below diagonal: number of animals from season y that skipped season x.
Season x is defined in first row, season y in first column.
Column Tot. Capts
gives all detected individuals in season y.
Row Tot. Skipped
gives all individuals skipped in season x but detected
later.
Examples
# Define start and end dates for sampling seasons.
seasons <- data.frame(
start = c(
as.Date("2017-01-01"),
as.Date("2018-01-01"),
as.Date("2019-01-01")
),
end = c(
as.Date("2017-12-31"),
as.Date("2018-12-31"),
as.Date("2019-12-31")
)
)
# Create a dynamics matrix for animal captures.
dyn_matrix(
animal_id = wolf_samples$AnimalRef,
capture_date = wolf_samples$Date,
start_dates = seasons$start,
end_dates = seasons$end
)
Organizes COLONY output
Description
Extends BestConfig_Ordered
output from COLONY
pedigree reconstruction software with additional data about individuals included
in pedigree. The function adds missing parents to OffspringID
, assigns
sex to each individual included in OffspringID
and adds the computed
probabilities of paternity and maternity assignments (probability of assignments is visible
only if the out
parameter is set to "table"
).
The function also prepares data so that the output of the function can be directly analyzed with
kinship2
,
pedtools
or
FamAgg
packages.
Usage
get_colony(
colony_project_path,
sampledata,
rm_obsolete_parents = TRUE,
out = "FamAgg"
)
Arguments
colony_project_path |
Character string. Path to the folder where COLONY output files are saved. Has to include file path and project name (see Details). |
sampledata |
Data frame. Metadata for all genetic samples that belong
to the individuals included in pedigree reconstruction analysis.
This data frame should adhere to the formatting and naming conventions
outlined in the |
rm_obsolete_parents |
Logical. Should unknown parents be removed from output.
Applies just to offspring for which both parents are unknown. Defaults to |
out |
Character string. For use with which package should the output be formatted?
|
Details
COLONY output tables needed for this function (.BestConfig_Ordered
,
.Maternity
and .Paternity
) are read directly
from the colony output folder and do not need to be imported into R session.
The path to the outputs is defined with colony_project_path
parameter.
When defining colony_project_path
the user needs to define a complete path to
the directory where colony outputs are stored and also the file name
(file name of COLONY outputs equals the project name
eg. /path/to/the/COLONY/output/folder/COLONY_project_name).
Value
A data frame describing a common pedigree structure. Each individual included in
pedigree represents one row. Columns describe individual identifier code, identifier code for
mother and father, sex and family of individual. Column names and arrangement depends on selected
output (out
parameter).
Examples
# Define the path to COLONY output
path <- paste0(system.file("extdata", package = "wpeR"), "/wpeR_samplePed")
# Get pedigree data in FamAgg format
get_colony(
colony_project_path = path,
sampledata = wolf_samples
)
Organizes pedigree data
Description
Offers an alternative to get_colony()
function in cases where the pedigree
was not reconstructed with COLONY
software. It takes a pedigree dataframe and assigns sex to each individual.
The function also prepares data so that the output of the function can be directly analyzed with
kinship2
,
pedtools
or
FamAgg
packages.
Usage
get_ped(ped, sampledata, out = "FamAgg")
Arguments
ped |
Data frame. Pedigree data frame with the most basic structure.
Three columns corresponding to offspring, father and mother (see
Details). Unknown parents should be represented by |
sampledata |
Data frame. Metadata for all genetic samples that belong
to the individuals included in pedigree reconstruction analysis.
This data frame should adhere to the formatting and naming conventions
outlined in the |
out |
Character string. For use with which package should the output be formatted?
|
Details
The custom pedigree specified through the ped
parameter should mirror the
structure of a COLONY pedigree and share the same column names.
It should consist of three columns for each offspring:
OffspringID
, FatherID
, MotherID
. When considering
unknown parents they should be represented by NA
values.
Value
A data frame describing a common pedigree structure. Each individual included in
pedigree represents one row. Columns describe individual identifier code, identifier code for
mother and father and sex of individual. Column names and arrangement depends on selected
output (out
parameter).
Examples
#example pedigree dataframe
ped <- data.frame(
OffspringID = c(
"M273P", "M20AM", "M2757", "M2ALK", "M2ETE", "M2EUJ", "MSV00E",
"MSV018", "MSV05L", "MSV0M6", "MSV0T4", "MSV0T7", "MSV0TJ", "MSV0UL"
),
FatherID = c(
NA, NA, "M20AM", "M20AM", "M20AM", "M20AM", "M20AM",
"M20AM", "M20AM", "M20AM", "M20AM", "M20AM", "M20AM", "M20AM"
),
MotherID = c(
NA, NA, "M273P", "M273P", "M273P", "M273P", "M273P",
"M273P", "M273P", "M273P", "M273P", "M273P", "M273P", "M273P"
)
)
#Get pedigree data in FamAgg format
get_ped(
ped = ped,
sampledata = wolf_samples
)
Number of detected animals between two sampling seasons
Description
Gives an numeric overview of individuals captured within the second sampling season compared tho the first one.
Usage
nbtw_seasons(
animal_id,
capture_date,
season1_start,
season1_end,
season2_start,
season2_end
)
Arguments
animal_id |
A column in the dataframe of all samples that stores individual animal identifier code. |
capture_date |
A column in the dataframe of all samples that stores
the date of sample collection. Must be in |
season1_start |
String in |
season1_end |
String in |
season2_start |
String in |
season2_end |
String in |
Value
A data frame with one row and six columns corresponding to season 1 and 2
start and end dates, number of detected animals in season 2 (total_cap
),
number of new detentions in season 2 (new_captures
), umber of animals from
season 1 detected within season 2 (recaptured
) and number of individuals
skipped in season 2 but detected after the end of that season (skipped
).
Examples
# Calculate the number of animals detected between two sampling seasons.
nbtw_seasons(
animal_id = wolf_samples$AnimalRef,
capture_date = wolf_samples$Date,
season1_start = as.Date("2017-01-01"),
season1_end = as.Date("2017-12-31"),
season2_start = as.Date("2018-01-01"),
season2_end = as.Date("2018-12-31")
)
Organize animals into families and expand pedigree data
Description
Takes pedigree data from get_colony()
or get_ped()
function and groups animals into families.
It also expands the pedigree data by adding information about the family that each individual was born in and the
family in which the individual is the reproductive animal.
Usage
org_fams(ped, sampledata, output = "both")
Arguments
ped |
Data frame. |
sampledata |
Data frame. Metadata for all genetic samples that belong
to the individuals included in pedigree reconstruction analysis.
This data frame should adhere to the formatting and naming conventions
outlined in the |
output |
Character string. Determines the format of the output. Options are: "ped": returns an extended pedigree data frame. "fams": returns a table of all families present in the pedigree. "both": returns a list with two data frames: "ped" and "fams". (Default) |
Details
The result of org_fams()
function introduces us to two important concepts
within the context of this package: family and half-sib group. A family in the
output of this function is defined as a group of animals where at least one
parent and at least one offspring is known. A half-sib group refers to a
group of half-siblings, either maternally or paternally related. In the
function output the DadHSgroup
groups paternal half-siblings and MomHSgroup
maternal half-siblings.
The fams
output dataframe contains famStart
and famEnd
columns, which estimate
a time window for the family based solely on sample collection dates provided in sampledata
.
famStart
marks the date of the earliest sample collected from any offspring
belonging to that family. famEnd
indicates the date of the latest sample collected
from either the mother or the father of that family. It is important to recognize that this
method relies on observation (sampling) times. Consequently, famEnd
(last parental sample date)
can precede famStart
(first offspring sample date), creating a biologically impossible sequence
and a negative calculated family timespan. Users should interpret the interval
between famStart
and famEnd
with this understanding.
Value
Depending on the output
parameter, the function returns either a data frame
(ped
or fams
) or a list containing both data frames (ped
and fams
).
-
ped
data frame. An extended version of the pedigree data fromget_colony()
/get_ped()
. In addition to common pedigree information (individual, mother, father, sex, family),ped
includes columns for:-
parents
: Identifier codes of both parents separated with_
. -
FamID
: Numeric identifier for the family to which the individual belongs (seefams
below). -
FirstSeen
: Date of first sample of individual. -
LastSeen
: Date of last sample of individual. -
IsDead
: Logical value (TRUE/FALSE
) that identifies if the individual is dead. -
DadHSgroup
: Identifier of paternal half-sib group (see Details). -
MomHSgroup
: Identifier of maternal half-sib group (see Details). -
hsGroup
: Numeric value indicating if the individual is part of a half-sib group (see Details).
-
-
fams
data frame includes information on families that individuals in the pedigree belong to. The families are described by:-
parents
: Identifier codes of both parents separated with_
. -
father
: Identifier code of the father. -
mother
: Identifier code of the mother. -
FamID
: Numeric identifier for the family. -
famStart
: Date when the first sample of one of the offspring from this family was collected (see Details). -
famEnd
: Date when the last sample of mother or father of this family was collected (see Details). -
FamDead
: Logical value (TRUE/FALSE
) indicating if the family no longer exists. -
DadHSgroup
: Identifier connecting families that share the same father. -
MomHSgroup
: Identifier connecting families that share the same mother. -
hsGroup
: Numeric value connecting families that share one of the parents.
-
Examples
# Prepare the data for usage with org_fams() function.
# Get animal timespan data using the anim_timespan() function.
animal_ts <- anim_timespan(
wolf_samples$AnimalRef,
wolf_samples$Date,
wolf_samples$SType,
dead = c("Tissue")
)
# Add animal timespan to the sampledata
sampledata <- merge(wolf_samples, animal_ts, by.x = "AnimalRef", by.y = "ID", all.x = TRUE)
# Define the path to the pedigree data file.
path <- paste0(system.file("extdata", package = "wpeR"), "/wpeR_samplePed")
# Retrieve the pedigree data from the get_colony function.
ped_colony <- get_colony(path, sampledata, rm_obsolete_parents = TRUE, out = "FamAgg")
# Run the function
# Organize families and expand pedigree data using the org_fams function.
org_fams(
ped = ped_colony,
sampledata = sampledata
)
Temporal plot of pedigree
Description
Creates "capture" history plot of individuals
arranged by families included in data frame created by plot_table()
function.
Usage
ped_satplot(
plottable,
famSpacing = 2,
hsGroupSpacing = 2,
xWhiteSpace = 100,
xlabel = "Date",
ylabel = "Animal",
title = "",
subtitle = "",
LegendLabel = "Sex",
xlegend = 0.2,
ylegend = 0.94,
text_size = 2.5,
fam_label_size = 2
)
Arguments
plottable |
Data frame. Output of |
famSpacing |
Y-axis spacing between families. Should be even number! |
hsGroupSpacing |
Y-axis spacing between half-sib groups. Should be even number! |
xWhiteSpace |
Spacing on the X-axis at the beginning and end of the plot. |
xlabel |
X-axis label. |
ylabel |
Y-axis label. |
title |
Plot title. |
subtitle |
Plot subtitle. |
LegendLabel |
Title of the legend. |
xlegend |
Horizontal position of the legend. |
ylegend |
Vertical position of the legend. |
text_size |
Plot text size. |
fam_label_size |
Family label text size. |
Value
A graphical representation of detected family members trough time.
Examples
# Prepare the data for usage with plot_table() function.
# Get animal timespan data using the anim_timespan() function.
animal_ts <- anim_timespan(wolf_samples$AnimalRef,
wolf_samples$Date,
wolf_samples$SType,
dead = c("Tissue")
)
# Add animal timespan to the sampledata
sampledata <- merge(wolf_samples, animal_ts, by.x = "AnimalRef", by.y = "ID", all.x = TRUE)
# Define the path to the pedigree data file.
path <- paste0(system.file("extdata", package = "wpeR"), "/wpeR_samplePed")
# Retrieve the pedigree data from the get_colony function.
ped_colony <- get_colony(path, sampledata, rm_obsolete_parents = TRUE, out = "FamAgg")
# Organize families and expand pedigree data using the org_fams function.
org_tables <- org_fams(ped_colony, sampledata, output = "both")
# Prepare data for plotting.
pt <- plot_table(plot_fams = 1,
org_tables$fams,
org_tables$ped,
sampledata,
deadSample = c("Tissue")
)
# Run the function.
# Get a temporal pedigree plot.
ped_satplot(plottable = pt)
Get files for spatial representation of pedigree
Description
Creates georeferenced data for spatial
pedigree representation form the output of plot_table()
function.
Usage
ped_spatial(
plottable,
na.rm = TRUE,
output = "list",
fullsibdata = NULL,
sibthreshold = 0,
path = "",
filename = "",
out.format = "geopackage",
time.limits = c(as.Date("1900-01-01"), as.Date("2100-01-01")),
time.limit.rep = FALSE,
time.limit.offspring = FALSE,
time.limit.moves = FALSE
)
Arguments
plottable |
Data frame. Output of |
na.rm |
Logical ( |
output |
Character vector specifying the desired output type ('list' - default or 'gis'). Available outputs: list: all spatial data returned as list, gis: all spatial data returned as georeferenced files. |
fullsibdata |
Data frame with COLONY full-sibling data. |
sibthreshold |
Numeric. P-value threshold for sibship assignment. |
path |
System path for storing georeferenced files. |
filename |
Common name for all georeferenced files. |
out.format |
Character string. Type of georeferenced files to be generated.
Can be ether |
time.limits |
Vector of two |
time.limit.rep |
Logical ( |
time.limit.offspring |
Logical ( |
time.limit.moves |
Logical ( |
Details
The parameters path
, filename
and out.format
, are used only when output
parameter is set to "gis", since they control which georeferenced files should
be created, where they will be saved and which common file name will they have.
Value
Depending on the output
parameter the function can return a list of sf
objects,
a georeferenced vector data files or both.
Most of the objects are created separately for mothers, fathers and offspring, this include:
Reference Points (
motherRpoints
,fatherRpoints
, andoffspringRpoints
).Each point corresponds to an animal included in the 'plot_table()' function output.
For reproductive animals (mothers and fathers), a reference point is the location of their last sample within the specified time window.
For offspring, the reference point is the location of their first sample within the time window.
Movement Points (
motherMovePoints
,fatherMovePoints
, andoffspringMovePoints
).These points represent all the samples of the respective animals.
Movement Lines (
motherMoveLines
,fatherMoveLines
andoffspringMoveLines
).Movement lines connect all '...MovePoints' of a specific animal in chronological order.
Movement Polygons (
motherMovePolygons
,fatherMovePolygons
andoffspringMovePolygons
):Movement polygons represent a convex hull that encloses all the samples of an individual.
An individual must have more than two samples for this representation.
Besides that the function also produces lines that connect mothers and
their offspring (maternityLines
), fathers and their offspring
(paternityLines
), and if fullsibdata
parameter is specified,
full siblings (FullsibLines
).
Examples
# Prepare the data for usage with ped_spatial() function.
# Get animal timespan data using the anim_timespan() function.
animal_ts <- anim_timespan(wolf_samples$AnimalRef,
wolf_samples$Date,
wolf_samples$SType,
dead = c("Tissue")
)
# Add animal timespan to the sampledata
sampledata <- merge(wolf_samples, animal_ts, by.x = "AnimalRef", by.y = "ID", all.x = TRUE)
# Define the path to the pedigree data file.
path <- paste0(system.file("extdata", package = "wpeR"), "/wpeR_samplePed")
# Retrieve the pedigree data from the get_colony function.
ped_colony <- get_colony(path, sampledata, rm_obsolete_parents = TRUE, out = "FamAgg")
# Organize families and expand pedigree data using the org_fams function.
org_tables <- org_fams(ped_colony, sampledata, output = "both")
# Prepare data for plotting.
pt <- plot_table(plot_fams = 1,
org_tables$fams,
org_tables$ped,
sampledata,
deadSample = c("Tissue")
)
# Run the function
# Get files for spatial pedigree representation in list format.
ped_spatial(plottable = pt)
Prepares pedigree data for plotting and spatial representation
Description
Combines extended pedigree (obtained by org_fams()
function)
and sample metadata data for visual (ped_satplot()
) and spatial
(ped_spatial()
) representation of the pedigree.
Usage
plot_table(
plot_fams = "all",
all_fams,
ped,
sampledata,
datacolumns = c("Sample", "AnimalRef", "GeneticSex", "Date", "SType", "lat", "lng",
"FirstSeen", "LastSeen", "IsDead"),
deadSample = c("Tissue")
)
Arguments
plot_fams |
Character string or numeric vector. FamID numbers from |
all_fams |
Data frame. Family ( |
ped |
Data frame. Organized pedigree ( |
sampledata |
Data frame. Metadata for all genetic samples that belong
to the individuals included in pedigree reconstruction analysis.
For description of |
datacolumns |
Vector of column names included |
deadSample |
Single value or vector of different lethal sample types. Defaults to c("Tissue"). |
Details
-
sampledata
has to include columns that contain information on:unique identifier of each sample; character or numeric (default column name =
Sample
, seecheck_sampledata()
function),date of sample collection in
Date
format (default =Date
),assignment of sample to particular individual; character or numeric (default =
AnimalRef
, seecheck_sampledata()
function),sex of the animal coded as
F
,M
orNA
; character (default =GeneticSex
, seecheck_sampledata()
function),longitude and latitude coordinates of sample collection location; numeric (default =
lng
andlat
, seecheck_sampledata()
function),type of particular sample eg. scat, tissue, saliva; character (default =
SType
, seecheck_sampledata()
function),date of first and last sample of individual in
Date
format (default =FirstSeen
andLastSeen
, seeanim_timespan()
function),value identifying if if the individual is dead; logical (default =
IsDead
, seeanim_timespan()
function).
Value
Extended sampledata
data frame that includes all columns defined in datacolumns
parameter and adds information needed for visual and spatial representation of
pedigree:
-
plottingID
: Numeric. Identifier number for temporal pedigree plotped_satplot()
. In case of polygamous animals same individual can be included in more than one family. -
FamID
: Numeric. Identifier number of family that individual belongs to. -
hsGroup
: Numeric. Identifier number for the half-sib group of individual. -
rep
: Logical. Is individual reproductive in current family, (current family defined withFamID
for a particular entry). -
later_rep
: Logical. Is individual reproductive in any other (later) families. -
isPolygamous
: Logical. Does the individual have more than one mate. -
dead
: Logical. Is individual dead. -
first_sample
: Logical. Is this particular sample the first sample of the individual. -
last_sample
: Logical. Is this particular sample the last sample of the individual. -
isReference
: Logical. Is this particular sample reference sample of individual.
Examples
# Prepare the data for usage with plot_table() function.
# Get animal timespan data using the anim_timespan() function.
animal_ts <- anim_timespan(wolf_samples$AnimalRef,
wolf_samples$Date,
wolf_samples$SType,
dead = c("Tissue")
)
# Add animal timespan to the sampledata
sampledata <- merge(wolf_samples, animal_ts, by.x = "AnimalRef", by.y = "ID", all.x = TRUE)
# Define the path to the pedigree data file.
path <- paste0(system.file("extdata", package = "wpeR"), "/wpeR_samplePed")
# Retrieve the pedigree data from the get_colony function.
ped_colony <- get_colony(path, sampledata, rm_obsolete_parents = TRUE, out = "FamAgg")
# Organize families and expand pedigree data using the org_fams function.
org_tables <- org_fams(ped_colony, sampledata, output = "both")
# Run the function
# Prepare data for plotting.
plot_table(plot_fams = "all",
org_tables$fams,
org_tables$ped,
sampledata,
deadSample = c("Tissue")
)
Wolf monitoring genetic samples metadata
Description
Metadata of selected genetic samples of wolves collected between 2015 and 2021, in the scope of Slovenian National Wolf Monitoring
Usage
wolf_samples
Format
A data frame with 407 rows and 7 columns:
- Sample
Sample unique identifier code
- Date
Date of sample collection (format:
YYYY-MM-DD
)- AnimalRef
Identification string for particular animal
- GeneticSex
Sex of animal to which the sample belong (format:
M
= male,F
= female)- lat
latitude (N-S) of the sample (CRS: WGS84; EPSG: 4326)
- lng
longitude (W-E) of the sample (CRS: WGS84; EPSG: 4326)
- SType
Type of the sample. (
Direct Saliva, Scat, Urine, Saliva, Tissue, Decomposing Tissue, Blood
)
Source
Slovenian National Wolf Monitoring