Creates georeferenced data for spatial
pedigree representation form the output of plot_table() function.
Arguments
- plottable
Data frame. Output of
plot_table()function.- na.rm
Logical (
TRUE/FALSE). Remove samples with missing coordinates and/or dates.- 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
"geopackage"or"shapefile". Default is"geopackage"- time.limits
Vector of two
Datevalues as the time window.- time.limit.rep
Logical (
TRUE/FALSE). Apply time limits to reference samples of reproductive animals.- time.limit.offspring
Logical (
TRUE/FALSE). Apply time limits to reference samples of offspring.- time.limit.moves
Logical (
TRUE/FALSE). Apply time limits to movement data.
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,fatherMoveLinesandoffspringMoveLines).Movement lines connect all '...MovePoints' of a specific animal in chronological order.
Movement Polygons (
motherMovePolygons,fatherMovePolygonsandoffspringMovePolygons):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).
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.
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)
#> $motherRpoints
#> Simple feature collection with 1 feature and 15 fields
#> Geometry type: POINT
#> Dimension: XY
#> Bounding box: xmin: 14.14495 ymin: 45.71833 xmax: 14.14495 ymax: 45.71833
#> Geodetic CRS: WGS 84
#> Sample AnimalRef GeneticSex Date SType FirstSeen LastSeen IsDead
#> 20 M2AMA M200F F 2018-08-22 Scat 2015-07-27 2018-08-22 FALSE
#> rep later_rep isPolygamous dead first_sample last_sample IsReference
#> 20 TRUE FALSE TRUE FALSE FALSE TRUE FALSE
#> geometry
#> 20 POINT (14.14495 45.71833)
#>
#> $fatherRpoints
#> Simple feature collection with 1 feature and 15 fields
#> Geometry type: POINT
#> Dimension: XY
#> Bounding box: xmin: 14.15404 ymin: 45.67033 xmax: 14.15404 ymax: 45.67033
#> Geodetic CRS: WGS 84
#> Sample AnimalRef GeneticSex Date SType FirstSeen LastSeen IsDead
#> 58 M2C36 M228J M 2018-02-09 Tissue 2016-09-30 2018-02-09 TRUE
#> rep later_rep isPolygamous dead first_sample last_sample IsReference
#> 58 TRUE FALSE FALSE TRUE FALSE TRUE FALSE
#> geometry
#> 58 POINT (14.15404 45.67033)
#>
#> $offspringRpoints
#> Simple feature collection with 8 features and 18 fields
#> Geometry type: POINT
#> Dimension: XY
#> Bounding box: xmin: 14.04242 ymin: 45.67397 xmax: 14.1563 ymax: 45.71845
#> Geodetic CRS: WGS 84
#> Sample AnimalRef GeneticSex Date SType FirstSeen LastSeen IsDead
#> 1 M10XC M10XC M 2017-11-16 Scat 2017-11-16 2017-12-22 FALSE
#> 8 M1XA7 M1YP0 F 2017-01-25 Scat 2017-01-25 2017-01-25 TRUE
#> 43 M2C2F M220J M 2017-11-10 Saliva 2017-11-10 2018-02-17 FALSE
#> 59 M22AM M22AM M 2017-01-26 Scat 2017-01-26 2017-08-07 FALSE
#> 71 M2772 M2772 M 2017-11-12 Scat 2017-11-12 2020-09-29 FALSE
#> 77 M28LU M28LU F 2017-09-18 Saliva 2017-09-18 2021-01-19 FALSE
#> 125 M275E M2AXE F 2017-12-16 Scat 2017-12-16 2019-11-06 FALSE
#> 131 M277F M2C1T F 2017-10-31 Scat 2017-10-31 2018-01-26 FALSE
#> plottingID FamID hsGroup rep later_rep isPolygamous dead first_sample
#> 1 3 1 1 FALSE FALSE FALSE FALSE TRUE
#> 8 4 1 1 FALSE FALSE FALSE FALSE TRUE
#> 43 5 1 1 FALSE FALSE FALSE FALSE TRUE
#> 59 6 1 1 FALSE FALSE FALSE FALSE TRUE
#> 71 7 1 1 FALSE TRUE FALSE FALSE TRUE
#> 77 8 1 1 FALSE TRUE FALSE FALSE TRUE
#> 125 9 1 1 FALSE FALSE FALSE FALSE TRUE
#> 131 10 1 1 FALSE FALSE FALSE FALSE TRUE
#> last_sample IsReference geometry
#> 1 FALSE TRUE POINT (14.12922 45.70766)
#> 8 FALSE FALSE POINT (14.12954 45.71845)
#> 43 FALSE FALSE POINT (14.04242 45.7131)
#> 59 FALSE TRUE POINT (14.12501 45.70004)
#> 71 FALSE TRUE POINT (14.1563 45.69639)
#> 77 FALSE TRUE POINT (14.11112 45.67397)
#> 125 FALSE FALSE POINT (14.14771 45.71293)
#> 131 FALSE FALSE POINT (14.1357 45.71323)
#>
#> $motherMovePoints
#> Simple feature collection with 11 features and 15 fields
#> Geometry type: POINT
#> Dimension: XY
#> Bounding box: xmin: 14.03169 ymin: 45.68138 xmax: 14.14653 ymax: 45.7525
#> Geodetic CRS: WGS 84
#> First 10 features:
#> Sample AnimalRef GeneticSex Date SType FirstSeen LastSeen IsDead
#> 10 EX.1JH0 M200F F 2015-07-27 Saliva 2015-07-27 2018-08-22 FALSE
#> 11 EX.1JJ5 M200F F 2015-08-14 Saliva 2015-07-27 2018-08-22 FALSE
#> 12 M20A4 M200F F 2016-10-11 Saliva 2015-07-27 2018-08-22 FALSE
#> 13 M200F M200F F 2017-01-11 Scat 2015-07-27 2018-08-22 FALSE
#> 14 M1TU6 M200F F 2017-01-25 Scat 2015-07-27 2018-08-22 FALSE
#> 15 M1XPY M200F F 2017-01-25 Scat 2015-07-27 2018-08-22 FALSE
#> 16 M1YH8 M200F F 2017-03-20 Scat 2015-07-27 2018-08-22 FALSE
#> 17 M1T7L M200F F 2017-04-21 Scat 2015-07-27 2018-08-22 FALSE
#> 18 M2ATF M200F F 2018-07-04 Scat 2015-07-27 2018-08-22 FALSE
#> 19 M2ATC M200F F 2018-07-19 Scat 2015-07-27 2018-08-22 FALSE
#> rep later_rep isPolygamous dead first_sample last_sample IsReference
#> 10 TRUE FALSE TRUE FALSE TRUE FALSE FALSE
#> 11 TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> 12 TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> 13 TRUE FALSE TRUE FALSE FALSE FALSE TRUE
#> 14 TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> 15 TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> 16 TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> 17 TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> 18 TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> 19 TRUE FALSE TRUE FALSE FALSE FALSE FALSE
#> geometry
#> 10 POINT (14.14653 45.7525)
#> 11 POINT (14.03169 45.69501)
#> 12 POINT (14.04434 45.71347)
#> 13 POINT (14.08802 45.71602)
#> 14 POINT (14.12843 45.69746)
#> 15 POINT (14.08937 45.71062)
#> 16 POINT (14.07037 45.70856)
#> 17 POINT (14.11843 45.68138)
#> 18 POINT (14.07282 45.70502)
#> 19 POINT (14.09111 45.70253)
#>
#> $fatherMovePoints
#> Simple feature collection with 5 features and 15 fields
#> Geometry type: POINT
#> Dimension: XY
#> Bounding box: xmin: 14.01201 ymin: 45.67033 xmax: 14.15404 ymax: 45.7114
#> Geodetic CRS: WGS 84
#> Sample AnimalRef GeneticSex Date SType FirstSeen LastSeen IsDead
#> 54 M20AP M228J M 2016-09-30 Saliva 2016-09-30 2018-02-09 TRUE
#> 55 M228J M228J M 2017-01-26 Scat 2016-09-30 2018-02-09 TRUE
#> 56 M28ML M228J M 2017-08-18 Saliva 2016-09-30 2018-02-09 TRUE
#> 57 M28MM M228J M 2017-08-18 Saliva 2016-09-30 2018-02-09 TRUE
#> 58 M2C36 M228J M 2018-02-09 Tissue 2016-09-30 2018-02-09 TRUE
#> rep later_rep isPolygamous dead first_sample last_sample IsReference
#> 54 TRUE FALSE FALSE FALSE TRUE FALSE FALSE
#> 55 TRUE FALSE FALSE FALSE FALSE FALSE TRUE
#> 56 TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> 57 TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> 58 TRUE FALSE FALSE TRUE FALSE TRUE FALSE
#> geometry
#> 54 POINT (14.01201 45.7114)
#> 55 POINT (14.12798 45.70406)
#> 56 POINT (14.1115 45.67397)
#> 57 POINT (14.1115 45.67397)
#> 58 POINT (14.15404 45.67033)
#>
#> $offspringMovePoints
#> Simple feature collection with 35 features and 18 fields
#> Geometry type: POINT
#> Dimension: XY
#> Bounding box: xmin: 13.80997 ymin: 45.52787 xmax: 14.39713 ymax: 46.28649
#> Geodetic CRS: WGS 84
#> First 10 features:
#> Sample AnimalRef GeneticSex Date SType FirstSeen LastSeen IsDead
#> 1 M10XC M10XC M 2017-11-16 Scat 2017-11-16 2017-12-22 FALSE
#> 2 M0PXH M10XC M 2017-11-22 Scat 2017-11-16 2017-12-22 FALSE
#> 3 M0PFL M10XC M 2017-12-22 Scat 2017-11-16 2017-12-22 FALSE
#> 8 M1XA7 M1YP0 F 2017-01-25 Scat 2017-01-25 2017-01-25 TRUE
#> 9 M1YP0 M1YP0 F 2017-01-25 Tissue 2017-01-25 2017-01-25 TRUE
#> 43 M2C2F M220J M 2017-11-10 Saliva 2017-11-10 2018-02-17 FALSE
#> 44 M220J M220J M 2018-02-17 Scat 2017-11-10 2018-02-17 FALSE
#> 59 M22AM M22AM M 2017-01-26 Scat 2017-01-26 2017-08-07 FALSE
#> 60 M28MF M22AM M 2017-08-07 Saliva 2017-01-26 2017-08-07 FALSE
#> 71 M2772 M2772 M 2017-11-12 Scat 2017-11-12 2020-09-29 FALSE
#> plottingID FamID hsGroup rep later_rep isPolygamous dead first_sample
#> 1 3 1 1 FALSE FALSE FALSE FALSE TRUE
#> 2 3 1 1 FALSE FALSE FALSE FALSE FALSE
#> 3 3 1 1 FALSE FALSE FALSE FALSE FALSE
#> 8 4 1 1 FALSE FALSE FALSE FALSE TRUE
#> 9 4 1 1 FALSE FALSE FALSE TRUE FALSE
#> 43 5 1 1 FALSE FALSE FALSE FALSE TRUE
#> 44 5 1 1 FALSE FALSE FALSE FALSE FALSE
#> 59 6 1 1 FALSE FALSE FALSE FALSE TRUE
#> 60 6 1 1 FALSE FALSE FALSE FALSE FALSE
#> 71 7 1 1 FALSE TRUE FALSE FALSE TRUE
#> last_sample IsReference geometry
#> 1 FALSE TRUE POINT (14.12922 45.70766)
#> 2 FALSE FALSE POINT (14.10497 45.71356)
#> 3 TRUE FALSE POINT (14.07907 45.69898)
#> 8 FALSE FALSE POINT (14.12954 45.71845)
#> 9 TRUE TRUE POINT (14.11387 45.71246)
#> 43 FALSE FALSE POINT (14.04242 45.7131)
#> 44 TRUE TRUE POINT (14.15949 45.71823)
#> 59 FALSE TRUE POINT (14.12501 45.70004)
#> 60 TRUE FALSE POINT (13.80997 45.8081)
#> 71 FALSE TRUE POINT (14.1563 45.69639)
#>
#> $maternityLines
#> Simple feature collection with 8 features and 7 fields
#> Geometry type: LINESTRING
#> Dimension: XY
#> Bounding box: xmin: 14.04242 ymin: 45.67397 xmax: 14.1563 ymax: 45.71845
#> Geodetic CRS: WGS 84
#> ID pair fam plyClust relation child parent geometry
#> 1 1 1 1 1 maternity M10XC M200F LINESTRING (14.14495 45.718...
#> 2 2 2 1 1 maternity M1YP0 M200F LINESTRING (14.14495 45.718...
#> 3 3 3 1 1 maternity M220J M200F LINESTRING (14.14495 45.718...
#> 4 4 4 1 1 maternity M22AM M200F LINESTRING (14.14495 45.718...
#> 5 5 5 1 1 maternity M2772 M200F LINESTRING (14.14495 45.718...
#> 6 6 6 1 1 maternity M28LU M200F LINESTRING (14.14495 45.718...
#> 7 7 7 1 1 maternity M2AXE M200F LINESTRING (14.14495 45.718...
#> 8 8 8 1 1 maternity M2C1T M200F LINESTRING (14.14495 45.718...
#>
#> $paternityLines
#> Simple feature collection with 8 features and 7 fields
#> Geometry type: LINESTRING
#> Dimension: XY
#> Bounding box: xmin: 14.04242 ymin: 45.67033 xmax: 14.1563 ymax: 45.71845
#> Geodetic CRS: WGS 84
#> ID pair fam plyClust relation child parent geometry
#> 1 1 1 1 1 paternity M10XC M228J LINESTRING (14.15404 45.670...
#> 2 2 2 1 1 paternity M1YP0 M228J LINESTRING (14.15404 45.670...
#> 3 3 3 1 1 paternity M220J M228J LINESTRING (14.15404 45.670...
#> 4 4 4 1 1 paternity M22AM M228J LINESTRING (14.15404 45.670...
#> 5 5 5 1 1 paternity M2772 M228J LINESTRING (14.15404 45.670...
#> 6 6 6 1 1 paternity M28LU M228J LINESTRING (14.15404 45.670...
#> 7 7 7 1 1 paternity M2AXE M228J LINESTRING (14.15404 45.670...
#> 8 8 8 1 1 paternity M2C1T M228J LINESTRING (14.15404 45.670...
#>
#> $motherMoveLines
#> Simple feature collection with 1 feature and 2 fields
#> Geometry type: LINESTRING
#> Dimension: XY
#> Bounding box: xmin: 14.03169 ymin: 45.68138 xmax: 14.14653 ymax: 45.7525
#> Geodetic CRS: WGS 84
#> # A tibble: 1 × 3
#> AnimalRef no_mvPoints geometry
#> <chr> <int> <LINESTRING [°]>
#> 1 M200F 11 (14.14653 45.7525, 14.03169 45.69501, 14.04434 45.71347…
#>
#> $fatherMoveLines
#> Simple feature collection with 1 feature and 2 fields
#> Geometry type: LINESTRING
#> Dimension: XY
#> Bounding box: xmin: 14.01201 ymin: 45.67033 xmax: 14.15404 ymax: 45.7114
#> Geodetic CRS: WGS 84
#> # A tibble: 1 × 3
#> AnimalRef no_mvPoints geometry
#> <chr> <int> <LINESTRING [°]>
#> 1 M228J 5 (14.01201 45.7114, 14.12798 45.70406, 14.1115 45.67397,…
#>
#> $offspringMoveLines
#> Simple feature collection with 8 features and 2 fields
#> Geometry type: LINESTRING
#> Dimension: XY
#> Bounding box: xmin: 13.80997 ymin: 45.52787 xmax: 14.39713 ymax: 46.28649
#> Geodetic CRS: WGS 84
#> # A tibble: 8 × 3
#> AnimalRef no_mvPoints geometry
#> <chr> <int> <LINESTRING [°]>
#> 1 M10XC 3 (14.12922 45.70766, 14.10497 45.71356, 14.07907 45.6989…
#> 2 M1YP0 2 (14.12954 45.71845, 14.11387 45.71246)
#> 3 M220J 2 (14.04242 45.7131, 14.15949 45.71823)
#> 4 M22AM 2 (14.12501 45.70004, 13.80997 45.8081)
#> 5 M2772 6 (14.1563 45.69639, 14.1013 46.2444, 14.0529 46.23509, 1…
#> 6 M28LU 9 (14.11112 45.67397, 14.07135 45.73484, 14.39713 45.6606…
#> 7 M2AXE 6 (14.14771 45.71293, 14.07355 45.7183, 14.06085 45.70965…
#> 8 M2C1T 5 (14.1357 45.71323, 14.22777 45.57041, 14.22777 45.57041…
#>
#> $motherMovePolygons
#> Simple feature collection with 1 feature and 2 fields
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: 14.03169 ymin: 45.68138 xmax: 14.14653 ymax: 45.7525
#> Geodetic CRS: WGS 84
#> # A tibble: 1 × 3
#> AnimalRef no_mvPoints geometry
#> <chr> <int> <POLYGON [°]>
#> 1 M200F 11 ((14.03169 45.69501, 14.11843 45.68138, 14.14495 45.718…
#>
#> $fatherMovePolygons
#> Simple feature collection with 1 feature and 2 fields
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: 14.01201 ymin: 45.67033 xmax: 14.15404 ymax: 45.7114
#> Geodetic CRS: WGS 84
#> # A tibble: 1 × 3
#> AnimalRef no_mvPoints geometry
#> <chr> <int> <POLYGON [°]>
#> 1 M228J 5 ((14.01201 45.7114, 14.1115 45.67397, 14.15404 45.67033…
#>
#> $offspringMovePolygons
#> Simple feature collection with 8 features and 2 fields
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: 13.80997 ymin: 45.52787 xmax: 14.39713 ymax: 46.28649
#> Geodetic CRS: WGS 84
#> # A tibble: 8 × 3
#> AnimalRef no_mvPoints geometry
#> <chr> <int> <POLYGON [°]>
#> 1 M10XC 3 ((14.07907 45.69898, 14.12922 45.70766, 14.10497 45.713…
#> 2 M1YP0 2 ((14.11387 45.71246, 14.12954 45.71845, 14.12171 45.715…
#> 3 M220J 2 ((14.10095 45.71568, 14.15949 45.71823, 14.04242 45.713…
#> 4 M22AM 2 ((13.80997 45.8081, 14.12501 45.70004, 13.96764 45.7541…
#> 5 M2772 6 ((13.97469 46.24017, 14.1563 45.69639, 14.1013 46.2444,…
#> 6 M28LU 9 ((14.07135 45.73484, 14.11112 45.67397, 14.27129 45.598…
#> 7 M2AXE 6 ((14.06085 45.70965, 14.02367 45.52787, 14.14771 45.712…
#> 8 M2C1T 5 ((14.18179 45.64183, 14.22777 45.57041, 14.1357 45.7132…
#>