Case studies

Over time we have developed a number of examples, or case studies to help users experience how to use the R packages we have developed to perform a number of common tasks. Feel free to use the code provided as templates forming the starting point for your own analysis.

Buttons (e.g. Line transect) can be clicked to filter the examples. Reload the page to remove filter.

Analysing indirect surveys
multipliers
line transects
analysis
Estimation of Sika deer density based upon deer pellet distance sampling data. Includes estimation of decay rate using logistic regression and multiplier based on dung…

Analysis of camera trap data using distance sampling
camera traps
point transects
analysis
Replicates analyses of duiker data presented by Howe et al. (2017) including model selection methods in presence of overdispersion (Howe et al. 2019)

Analysis of cue count surveys
cue counts
line transects
analysis
Cue counting example based on line transect data of winter wrens from Buckland (2006). Incorporating song rate in analysis.

Analysis of double observer data
mark-recapture distance sampling
line transects
analysis
Full independence and point independence analysis of golf tee data from multiple observers.

Analysis of line transect data
line transects
songbirds
analysis
Line transect data of winter wrens in Scotland. An example of model fitting, model selection, goodness of fit assessment. Basic analysis skills required for any distance…

Analysis of point transect data
point transects
songbirds
analysis
Point transect analysis of savannah sparrow data set from Knopf et al. (1988)

Analysis of stratified surveys
stratification
point transects
analysis
Analysis of stratified survey design, including model selection to determine whether stratum-specific detection functions are necessary. Uses point transect analysis of…

Assessing analysis decision effects via simulation
truncation
line transects
simulation
Simulate distance sampling surveys examining the effect of truncation distance and pooling robustness upon estimates of animal density (when true density is known).

Combating the effects of size bias
group size
analysis
Because of the detection process, average group size in sample is a positively biased estimate of average group size in population. This bias can be compensated by employing…

Data formatting for dsm analysis
spatial model
line transects
analysis
Manipulating spatial data with sf to segment effort

Density surface model of dolphins
spatial model
line transects
analysis
Line transect survey of pantropical spotted dolphins in the Gulf of Mexico.

Detection function models including covariates
line transects
design
dssd
Bringing covariates into detection function, using amakihi data from Marques et al. (2007).

Estimates from a multi-species survey
point transects
songbirds
covariates
analysis
Use of species covariate to produce species-specific density estimates when number of detections for some species is small.

Getting started with dsims
line transects
simulation
Simulation of a marine mammal survey

Getting started with dssd
line transects
design
dssd
Create a survey design within a study-area, and examine properties of the design such as how well it covers the study area and average transect lengths. The example uses a…

Inference regarding differences in density between strata
stratification
inference
line transects
analysis
Statistical comparison of density estimates between strata. Uses formulation provided in Buckland et al. (2001) Sect. 3.6.5

Multiple strata in dssd
line transects
design
dssd
stratification
An example of how to create a design in dssd that contains multiple strata, with different design characteristics in each stratum.

Simulation of combining strata
grouped strata
line transects
simulation
Simulations using grouped strata for analysis when the region has been divided into sub-strata for design optimisation.

Software choices for fitting detection functions
camera traps
line transects
analysis
Demonstrating the mcds.exe alternative optimization engine for fitting single platform detection functions in the Distance and mrds packages

Take care when subsetting flatfiles by species
multi-species
line transects
analysis
Adding additional information to flatfiles when subsetting analysis by species

Variance estimation for line transects
bootstrap
variance
analysis
Variance estimation examining three approaches: delta-method, bootstrap and bootstrap incorporating model uncertainty. Based on line transect data of winter wrens from…
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In addition to these, there are several more case studies not associated with specific R packages. Those case studies can be found at the website associated with the book Buckland et al. (2015)

Buckland et al. (2015)