Changes in version 4.0.5 (2025-04-10)

Bug fixes:

• Fixed bug in predict method when type = "density" causing NaN estimates on transects with observations outside the strip.
• Fixed bug in RdistDf when merge parameter by was named. When by was named, and hence we merge on different variables, the names and values in by were reversed because we nest first then merge. Bug did not affect merges on same-named variables.
• Non-bug change: Moved all the examples from README to tutorials on the McDonald Data Science website because we have more control, they are indexed by date and keyword, and they look better.

Changes in version 4.0.3 (2025-03-28)

Version numbers >4.0.0 are substantially different from prior versions.

• BIGGEST CHANGE: Input data frames are now nested tibbles with one row per transect, and detection information in a data frame contained within a list column. Technically, the new data frame format is a grouped tibble with one row per group, and each group is a transect. Survey type, observer system, and name of the effort column are recorded as attributes in the new data frame.
  • RdistDf constructs the new Rdistance data frames from separate transect and detection data frames formatted for use in prior versions. Use this function on old sets of site and detection data frames to construct the new nested data frames. See examples in ?RdistDf.
  • is.RdistDf checks the validity of the new Rdistance data frames.
    
  • summary prints a summary of number of transects, number of groups seen, number of individuals, etc.
• Temporary Functionality Removal: Versions >4.0.0 are a near complete re-write of versions <3.1.3. I felt the re-write was necessary to improve stability of the code and lay the ground work for future functionality improvements. But, to keep from going insane, I am rolling out new versions that build on one another, with core functions first (in 4.0.* versions). As such, I have temporarily removed the following functionality from versions with numbers 4.0.*:
  • Logistic distance function form.
  • Smoothed distance functions.
  • Beta distribution distance functions.
  • Double-observer methods.
  • All vignettes.
• print, summary, and plot methods have been improved.
• Documentation updated and improved.
• Rdistance options can now be assessed by the regular options function. All Rdistance options are prefixed with ‘Rdistance_’ to distinguish them from other options.
• New data frame format is pipe-able through the estimation workflow. For example, the basic workflow is df |> dfuncEstim(dist~1) |> abundEstim(), which will estimate a distance function and density in one go.

Changes in version 3.1.3 (2025-03-11)

Version 3.1.3 contains three patches. Several updates to documentation and one bug fix precipitated by changes to the ‘units’ package.

Changes in version 3.1.0 (2023-08-28)

Version 3.1.0 primarily addresses GitHub issues.

• Summary Methods Implemented: Issue #57. Rdistance did not implement summary methods for dfunc and abund objects prior to version v3.1.0. This version implements both summary and print methods for the main outputs. print.dfunc and print.abund are modeled on print methods for lm and glm objects. New methods summary.dfunc and summary.abund are modeled on the summary methods for lm and glm and will produce fuller (relative to print) outputs.
• Documentation fixes:
  • Added reference to general method in DESCRIPTION as suggested by CRAN editors.
  • Updated and clarified Description field of DESCRIPTION file.
  • Updated numerous links in README and NEWS.
• Bug Fixes:
  • Fixed bug when abundEstim was called with tibbles.

Changes in version 3.0.0 (2023-06-12)

Version 3.0.0 is a substantial change and upgrade.

• BIGGEST CHANGE: Measurement units are now required on all distances (e.g., off-transect distances, strip widths, study area size, etc.), and it is possible to specify output units. Unit conversion makes use of the units package, is internal, and automatic.
• One-sided Transects: Added the ability to analyze single-sided transects by setting singleSided = TRUE in call to abundEstim.
• User Requested: Added computation of bootstrap confidence intervals for effective sampling distances (ESW and EDR).
• NA Length Transects: NA length transects are now allowed. Observations on NA length transects are used to estimate distance functions, but are dropped when estimating density. This allows, for example, off-transect distance observations from one study area or year to estimate a distance function which is then applied to the observations from another study area or year.
• Added calculation of target density (number per unit area) to abundEstim, and it is included in bootstrapping.
• Allowed expansion terms and covariates in the same distance function.
• Renamed uniform likelihood to logistic. Uniform is now deprecated.
• Added covariates to Gamma likelihood estimation.
• Change in default parameter: Changed default value of area in abundEstim from 1 to NULL. NULL now translates to 1 square output unit.
  
• Added color to print methods. Results are in green, if the R terminal allows it (i.e., in Rstudio, but not R gui). Errors are in red.
• Reformatted default output to include target density and abundance when printing an abund object.
• Fixed bug in F.gx.estim that occasionally popped up when sighting function was monotonically decreasing.
• Updated starting values for faster estimation.
• Decreased lower limit of negexp likelihood parameter to achieve more valid fits.
• Warning messages now report which parameters are at their boundary, and which boundary (lower or upper).
• Bug fixes:
  • Fixed issue with contrasts in model.matrix
  • Fixed issue of no observations during bootstrapping
  • Fixed issues with changing scale locations (i.e., x.scl and g.x.sxl)
  • Fixed ESW for w.lo > 0
  • Restricted likelihood values to be positive
• Substantial documentation updates
• Substantial testing facilities added.

Changes in version 2.1.5 (2020-06-17)

• Fixed bug when bootstrap iteration selects zero targets
• Many updates to vignettes
• Updates to testthat files
• Added descriptive error for case when bySite==T and detection level covariates are present (Issue #72)

Changes in version 2.1.4 (2019-06-11)

• Fixed bug caused by empty factor levels
• Included automated testing (testthat)

Changes in version 2.1.3 (2019-01-02)

• Fixed scaling error in the Gamma likelihood causing mode to be less than 1.0
• Fixed inverted plots that occurred when w.lo > 0 (left-truncation)
• Fixed bug in ‘autoDistSamp’ when ‘bySite=TRUE’
• Fixed bug causing bootstrap failure of point transect surveys when ‘siteData’ contained only one column

Changes in version 2.1.2 (2018-08-23)

• Included methods for point transects. Previous version (v1.3.2) allowed only line transects.
• Implemented covariates in the detection functions.
• Implemented non-parametric (smoothed) distance functions
• Enhanced plotting abilities
• Enhanced vignettes
• Many bug fixes