Fixed bug when simulation checks generated an error for projected
shapes. Issue #94
Enhancements
Updated web site links in package documentation.
dsims 1.0.5
Bug Fixes
Fixed bug which generated NA’s as scale parameters when factor
covariates were included. Issue #89
Simulation validation checks: consistency in truncation distances
(Issue #76), consistency in region (Issue #88)
dsims 1.0.4
Bug Fixes
Fixed a bug when generating the simulation summary which meant that
only the first value of mean.k and n.miss.dists was repeated rather than
including all values in the summary tables. Issue #84
The make.simulation function now throws an error if the P2 ER
variance estimator is used with line transects designs (rather than
after the simulation has completed). Issue #61
dsims 1.0.3
Bug Fixes
Simulations were crashing if there were zero detections - now fixed
and warnings displayed instead. Issue #77
Errors were also occurring when there were no individuals generated
in a stratum, now fixed. Issue #80
Detections are no longer permitted across stratum boundaries - this
was causing errors due to NA area values in the data. This is inline
with expected protocols on surveys. Issue #81
Remove dependence on sp and rgeos. Issue #42
dsims 1.0.2
Bug Fixes
Fixed transparency issue with detection distance histograms when
saving to wmf (generated a warning in Distance for Windows)
Only print summary table for individuals if animals occur as
individuals (and not as clusters)
Updated references to examples
Fixed grouped strata bugs
Can now read transect shapefiles in from file and will convert all
to one strata if global region used. This allows regional simulations
from stratified designs in distance for windows.
dsims 1.0.1
New Features
Added save.sim.results function so that simulation results can be
written to .txt files. This is mainly useful for Distance for Windows
users as R users would probably prefer to just save the whole simulation
object to file.
Can write the simulation progress to file - this allows the
simulation progress to be displayed when simulations are being run from
Distance for Windows using dsims.
Add segmented trackline design as an option in simulation summary
(currently these design can only be generated inside Distance for
Windows for use in simulations).
Bug Fixes
Partial fix to the bug relating to grouping strata at the analysis
stage. Strata grouping should now work when detections are of
individuals. Still needs to be fixed for when clusters are present.
dsims 1.0.0
New Features
Reading transects from file - this functionality is primarily
envisioned for use from within Distance for Windows.
Enhancements
New routine which will generate covariate values from a
zero-truncated Poisson distribution for non integer values.
There is now no lower limit on the number of detections in
simulations as this was introducing bias. There is now a warning system
in place. Very low numbers of detections may cause issues fitting. There
must be more detections than there are parameters in the model for the
model to have a chance of fitting successfully. Note that distance
sampling good practice recommends minimum of 60-80 detections for
estimating the detection function for line transects and more for
points.
Improved histogram.N.ests function will now plot either a histogram
of estimates of individuals or clusters. It also provides the
use.max.reps argument so that the plot can be consistent with the option
selected for the simulation summary.
Bug Fixes
Fixed simulations where cluster size was included - there was a
formatting change in mrds output tables.
Added a check for repeat model definitions.
Add code to deal with equal model criteria values.
Fixed bug when no simulation repetitions had been successful
AICc method fixed
Warning indexes from parallel runs are now fixed
dsims 0.2.2 / 0.2.3
Bug Fixes
Minor modifications to stay CRAN compliant.
dsims 0.2.1
New Features
Now interfaces with new syntax in Distance >= 1.0.5 (it will
remain backwards compatible with older versions of Distance for this
release)
Bug Fixes
Plus sampling simulations now issue a warning and modify to minus
sampling - these should not have run in previous versions.
Fixed default simulation truncation distance to 50 in the analyses
(will fix dssd to be consistent with this in release 0.3.2)
Fixed the recording of warning / error indexing in parallel
simulations
dsims 0.2.0
New Features
Delta selection criteria is now recorded as the difference in
information criteria between the top 2 best fitting models as determined
by the information criteria.]
The iteration numbers generating warnings or errors are now stored
and displayed so user can choose what to do with these results.
Bug Fixes
Fixed missing RMSE values
Fix strata re-ordering for cluster size
Models with -Inf information criteria no longer selected
Models with dht = NULL are no longer selected
Models which predict detection values < 1 no longer cause errors
and are correctly excluded.
Detectibility parameters for continuous covariates are now checked
and validated.
Fix situation where all reps are to be excluded due to problematic
model fitting.
There was a bug in the underlying code on windows machines that
meant that segmented lines were not being clipped properly. The
dependencies of sf have not been updated and the issue fixed. Please
update sf if you run into missing segment transects.
dsims 0.1.0
Enhancements
Introducing the new Distance Sampling Simulation package. # dsims is
our latest simulation package which interfaces with dssd so designs can
be generated within R, thus making the simulation process a lot easier.
# dsims also makes use of ggplot to produce cleaner looking
graphics.
Region and Design: # dsims can make use of the region creation and
all the designs currently in dssd.
Density: # dsims can generate density objects from constant values
for each strata, from fitted mgcv gam objects with x and y as explantory
covariates and from formulas of x and y.
Density: Density grids are stored as sf polygons with their
associated x, y central coordinates and density value
Population Description: Populations can either be created with fixed
population sizes or based on the densities in the density grid.
Population Description: Both discrete and continuous individual
level covariates can be included in the population
Detectablity: The detectability of the population can be described
by either half normal, hazard rate or uniform detection shapes.
Parameters can vary by stratum
Detectablity: Covariate parameters can be included to modify the
scale parameter for each individual based on their covariate
values.
Analyses:A number of detection function analyses can be incorporated
in a simulation and the model with the lowest criterion (AIC / AICc /
BIC) will be selected.
Analyses:Defining analyses is based on the arguments which are
passed to our Distance R library.
Simulations: Simulations can be run in serial or parallel and their
progress is output.
Simulations: The function run.survey can be used to create a single
instance of a survey and check the simulation setup.