CRAN release 2.3.0

mrds 2.3.0

New Features

• The 'P2' estimator is now the default for estimating the encouter rate variance for point transect surveys. (Issue #65)

Bug Fixes

• Re-formatted the format section of the documentation for the book.tee.data (Issue #91)
• Ensure that the MCDS optimizer is not used for double observer models as this was generating errors. (Issue #89)
• Improved the documentation on initial values, lower and upper bounds in both the ddf and mrds_opt documentation (mrds_opt was renamed from mrds-opt which was not accessible via ?mrds-opt). (Issue #90)

CRAN release 2.2.9

mrds 2.2.9

New Features

• Users can now download the fortran MCDS.exe optimiser used in Distance for Windows and fit single observer models with both the optimisers in R via mrds and also MCDS.exe. For some datasets the optimisation with MCDS.exe is superior (giving a better likelihood) than the optimiser in R used with mrds. See ?MCDS for more details.

Bug Fixes

• fix bug where the (true, 2nd derivative) hessian was not calculated during optimisation. This then lead to weird errors later (summary doesn't work etc). Hessians are now calculated in this case. Thanks to Anne Provencher St-Pierre for reporting the issue
• Fix prediction bug (Issue #84) where predicting for hazard rate model with covariates and se.fit= TRUE. Note there may be issues when predicting in this instance for binned data - check results are as expected.
• Fix bug when a uniform model was fitted with no adjustments. This caused an error when looking for the hessian. It also required that the covariance set to 0 when estimating the cluster size standard errors (Issue #79).
• fix bug with using binned data via cutpoints for prediction (#73)

CRAN Release 2.1.18

• fixed bug in parameter rescaling where scales were incorrectly entered as 1 due to an indexing bug
• Quantile-quantile plots now use an aspect ratio of 1
• Bug in half-normal integration code when no adjustments are used lead to likelohood being evaluated incorrectly for models with binned (grouped) distances. This only effected AIC comparisons between models and parameter estimates should have been the same. Thanks to Olivier Devineau for spotting this!
• Fix bug where predict.ds() didn't work with uniform keys. Thanks to Jason Roberts for reporting this bug.
• Correctly specify distbegin/distend for predictions with binned data, thanks to Jason Roberts for spotting this bug.
• Let the user know that int.range was set in summary() results

CRAN Release 2.1.17

This is the CRAN Release to be packages with Distance 7 Release 1

• fixed starting value bug for hazard-rate models when distances are binned. Thanks to Natalia Schroeder and Eric Rexstad for discovering this.
• predict.ds now uses numerical integration to calculate integrals (rather than an approximation). Thanks to Eric Rexstad for spotting an issue with goodness of fit testing that highlighted this.
• plot.ds() now accepts an xlab="" argument to change the x axis label. Thanks to Steve Ahlswede for suggesting this.

CRAN Release 2.1.16

mrds 2.1.16

• improved predict() method now does the Right Thing with factors
• Fixed bug in scaling of histograms for point transect pdf plots and points on those plots. Thanks to Erics Howe and Rexstad for reporting these issues.
• You can now set y axis limits when using plot.ds, defaults should be more sensible for pt+point models. Thanks to Eric Howe for the suggestion.
• Fixed bug when setting initial values that threw many errors. Thanks to Laura Marshall for spotting this.

mrds 2.1.15

• rescaling parameters were not correct, now fixed. Thanks to Laura Marshall for spotting this.
• coefficients are called coefficients (not a mixture of coefficients and parameters) in summary() results
• speed-up in io.fi models (thanks to Winston Chang's profvis, showing many unecessary calls to model.matrix)
• plot.ds now has a pdf= option to plot the probability density function (for point transect models only)
• assign.par, create.ddfobj and detfct are now exported, so it can be used by dsm (though shouldn't be used by anything else!)
• fixed bug in left truncation where probability of detection was not calculated correctly. Thanks to Jason Roberts for pointing this out!

CRAN release 2.1.14

New from 2.1.12 (previous CRAN release)

mrds 2.1.14

• updated initialvalues calculation for hazard-rate -- now uses Beavers & Ramsay method to scale parameters for hazard-rate
• automatic parameter rescaling for covariate models when covariates are poorly scaled. Now default for nlminb method
• minor speed-up to logistic code when distance is a covariate

mrds 2.1.13

• link to distance sampling Google Groups in help
• duplicate non-convergence warning/error removed
• warning of singular Hessian is now a warning()
• re-wrote the debug output to be easier to read
• dht now has an option (ci.width) to specify confidence interval width in output (thanks to David Pavlacky for the suggestion)
• monotonicity now operates over left->right truncation for models that are left truncated and will fail with an error message if many integration intervals are used. Thanks to Tiago Marques for highlighting this issue.

pre-CRAN release 2.1.13

mrds 2.1.13

• link to distance sampling Google Groups in help
• duplicate non-convergence warning/error removed
• warning of singular Hessian is now a warning()
• re-wrote the debug output to be easier to read
• dht now has an option (ci.width) to specify confidence interval width in output (thanks to David Pavlacky for the suggestion)
• monotonicity now operates over left->right truncation for models that are left truncated and will fail with an error message if many integration intervals are used. Thanks to Tiago Marques for highlighting this issue.

mrds vesion 2.1.11

This release works around a bug in the Rsolnp package that made uniform+cosine(1) models fail in mrds and Distance. Thanks to Nathalie Cavada for spotting this.

File mrds_2.1.11.zip is a binary package for Windows.

From the NEWS file:

mrds 2.1.11

• Bug in unif+cos(1) models when using monotonicity constraints and randomised starting points. Since the model only has 1 parameter, there is a bug in selecting columns in Rsolnp starting value code that makes the result be a vector, which then doesn't work with an apply later. Workaround of not using randomised starting values in mrds for that model. Thanks to Nathalie Cavada for finding this bug.

CRAN release 2.1.10

This is mrds version 2.1.10, as uploaded to CRAN.

Windows binary: mrds_2.1.10.zip
OS X Mavericks binary: mrds_2.1.10.tgz

Changes from 2.1.6:

mrds 2.1.10

• added testing directory to .Rbuildignore, tests are now not included in built packages and are not run on CRAN, for test use the source packages on github.

mrds 2.1.9

BUG FIXES

• removed test that failed on CRAN's testing

mrds 2.1.8

CHANGES

• removed doeachint/cgftab code, which used a spline approximation to the effective strip width/effective area when a half-normal detection function was used. This has been replaced with exact calculation via the error function (erf).
• tests updated accordingly
• monotonically constrained models now use a bunch of random start points -- uses gosolnp() from Rsolnp
• re-fitting by jiggling parameters refined to multiply by a uniform variable with limits set as the upper and lower bounds (+/-1) so jiggling can go either way, on approximately the same scale as the parameters
• corrected documentation for predict methods, which incorrectly stated what is returned for point transect models. Thanks to Thibault Dieuleveut for spotting this.

BUG FIXES

• fixed 2 bugs in create.varstructure; the first was for removal method which was being treated as a trial method. The second was when obs.table was not specified (Region and sample labels in dataframe for each obs) and there was dual observers. In that case it was doubling the number of observations.
• fixed a bug in dht.deriv which had not been setup for removal; thanks to John Boulanger for noticing and reporting both of these bugs

mrds 2.1.7

BUG FIXES

• Standardisation was being applied to detection functions (such that g(0)=1) when there were no adjustments (which is uneccesary) but also caused issues when using gamma detection functions as this should be calculated at g(apex) instead. Standardisation code has been removed for when there are no adjustments and the correct scaling used for the gamma when there are. Thanks to Thomas Doniol-Valcroze for alerting us to this bug.
• Partial name-matching in dht was fixed. Produced warning but not error.

NEW FEATURES

• Tests for gamma detection functions
• Observations are automatically ordered by object and observer fields (if included) in ddf as expected by double observer analysis. A erroneous error message can be created if they are not ordered correctly or worse. Thanks to Ainars Aunins for bringing this to our attention.
• Added function create_document() which will run a shiny application interface to mrds and will create a knitr document from a template. The template currently is only for a single observer analysis and is behind on all of the features for the app which is fairly complete.

Distance 6.2 Patch Release 1

This version of mrds fixes a bug with plot.det.tables where histograms were created on separate pages, rather than overlayed.

.zip file should be installable in Windows.

.tar.gz for other platforms.