nondecreasing_length_sampler {Xcertainty} | R Documentation |
Build an MCMC sampler that uses calibration data to estimate measurements that are assumed to be non-decreasing in time. This sampler is well suited for when individuals have replicate measurements across time points but do not have age information. The model estimates changes in unique combinations of Subject/Measurement pairs over Timepoints.
nondecreasing_length_sampler(data, priors, package_only = FALSE)
data |
Photogrammetric data formatted for Xcertainty models, required to
be an object with class |
priors |
|
package_only |
|
outputs a function to run a sampler, the function arguments are:
set the number of iterations
set the number samples to discard
set the thinning rate
# load example wide-format data
data("calibration")
data("whales")
data("whale_info")
# parse calibration study
calibration_data = parse_observations(
x = calibration,
subject_col = 'CO.ID',
meas_col = 'Lpix',
tlen_col = 'CO.L',
image_col = 'image',
barometer_col = 'Baro_Alt',
laser_col = 'Laser_Alt',
flen_col = 'Focal_Length',
iwidth_col = 'Iw',
swidth_col = 'Sw',
uas_col = 'uas'
)
# parse field study
whale_data = parse_observations(
x = whales,
subject_col = 'whale_ID',
meas_col = 'TL.pix',
image_col = 'Image',
barometer_col = 'AltitudeBarometer',
laser_col = 'AltitudeLaser',
flen_col = 'FocalLength',
iwidth_col = 'ImageWidth',
swidth_col = 'SensorWidth',
uas_col = 'UAS',
timepoint_col = 'year'
)
# build sampler
sampler_data = nondecreasing_length_sampler(
data = combine_observations(calibration_data, whale_data),
priors = list(
image_altitude = c(min = 0.1, max = 130),
altimeter_bias = rbind(
data.frame(altimeter = 'Barometer', mean = 0, sd = 1e2),
data.frame(altimeter = 'Laser', mean = 0, sd = 1e2)
),
altimeter_variance = rbind(
data.frame(altimeter = 'Barometer', shape = .01, rate = .01),
data.frame(altimeter = 'Laser', shape = .01, rate = .01)
),
altimeter_scaling = rbind(
data.frame(altimeter = 'Barometer', mean = 1, sd = 1e1),
data.frame(altimeter = 'Laser', mean = 1, sd = 1e1)
),
pixel_variance = c(shape = .01, rate = .01),
object_lengths = c(min = .01, max = 20)
),
# set to false to return sampler function
package_only = TRUE
)