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Changelog

Version 0.8-0 – February 22, 2024

  • All plots are downloadable using the download button.

Version 0.7-3 – February 7, 2024

  • Hurdle models added as HP and HNB options for the dist argument.
  • The weighted and robust options removed from the Shiny app UI.
  • Hurdle model based PI calculation implemented with 0-truncated P and NB distributions.
  • The new loo function calculates the leave-one-out error as blended Chi-square distance in $chi2.
  • The blended Chi2 based GoF metric is added to the mc_models_total table.

Version 0.7-2 – February 6, 2024

  • Shiny app improvements (#21): Crosstalk-like behavior for univariate plots, Histogram binning, Total Prediction map/summary subsets, Export data checks.

Version 0.7-1 – May 10, 2023

  • Add option to remove intercept(s) in regression to allow regression through the origin.

Version 0.7-0 – March 24, 2023

  • Add robust regression option.

Version 0.6-3 – February 21, 2023

  • Bootstrap setting is now a numeric input, not a slider, to allow high numbers.
  • Composition analysis can be performed by using the cell level stats and by reusing an existing PI object.
  • CPI calculations do not exclude rows with unknown ages.
  • CPI summaries return Mean and Median besides PI.
  • Unknown age classed individuals are distributed randomly according to comp model.
  • The Shiny app uses the PI object when available.

Version 0.6-2 – December 17, 2022

  • Added Residual tab for composition analysis to show model summaries and AIC table.
  • More columns are allowed to be treated as filters/subsetters with 2 levels (usually 0/1).
  • Print abundance/density summaries for subsets under Summary tab.
  • Added Total_Bulls and Bulls_per_Cow to the composition summaries.
  • Yearling cows now calculated as min(adult_cows, yearling_bulls) to avoid negative mature cows values.
  • Total Calves / Total Cows is now part of the mc_summarize_composition output.

Version 0.6-1 – December 14, 2022

  • Composition table contains BIC and coefficients.
  • Composition checks fixed: don’t include unknown ages.
  • mc_plot_univariate has the ability to return ggplot2 objects and their interactive versions.
  • New function: mc_plot_predfit to check model fit.
  • Shiny app: predictions can now be subsetted independent of the training data.

Version 0.6-0 – March 14, 2022

  • Composition analysis added to R package and Shiny app.

Version 0.5-0 – October 4, 2021

  • Total moose estimation is tested and ready to be used in the field.
  • Added run_app() function to launch a Shiny app.

Version 0.4-0 – August 19, 2021

  • Package renamed from DeducerPlugInMoose to moosecounter, with the intention of dropping the rJava/Deducer GUI features in favor of a Shiny app. Version numbering is continuous.

Version 0.3-3 – March 24, 2020

  • Composition analysis fix: vglm failed when input matrix rowsum was 0. Now it is treated as missing and omitted.

Version 0.3-1 – July 2, 2019

  • Added nobs.zeroinfl method.

Version 0.3-0 – March 24, 2019

  • Fixing Non-ZI model summaries.
  • Increment version.

Version 0.2-16 – January 10, 2019

  • Non-ZI versions of count models (P and NB) added by introducing a hacked version of zeroinfl: zeroinfl2.

Version 0.2-15 – December 19, 2018

  • Global option wscale added to tune weighting scale.

Version 0.2-14 – November 10, 2018

  • Dual (weighted & unweighted) prediction added to composition PI calculations.

Version 0.2-13 – November 1, 2018

  • Dual (weighted & unweighted) prediction is performed depending on survey area (unsurveyed gets predicted under unweighted model to better represent the high end of PI, surveyed area gets predicted under weighted model because high values are already captured within surveyed cells).

Version 0.2-12 – October 21, 2018

  • Write down PI/CPI algorithm
  • Accumulate issues and report as part of the summaries

Version 0.2-11 – October 15, 2018

  • Error catching fixes in CPI calculation.

Version 0.2-10 – October 14, 2018

  • Error catching fixes in PI calculation.

Version 0.2-9 – October 2, 2018

  • Exposed optim method through options, might be a good idea to set it to Nelder-Mead (because of weighting instability using BFGS).

Version 0.2-8 – August 30, 2018

  • Fixed issue with plotResiduals and plot_predPI: failed when there were no outliers with error zero-length 'labels' specified.

Version 0.2-7 – April 18, 2018

  • PI distribution plot is tweaked to display sensible results for the case when the distribution has only one unique value (i.e. 0s).

Version 0.2-6 – April 4, 2018

  • ZIP added as option beside ZINB (univariate exploration and model fitting).
  • Weighted modeling option added to minimize influence on predictions.
  • Histograms show % instead of density (%=100*density).
  • Residual plot labels +/- 1.5*SD points and uses symmetric divergent coloring.

Version 0.2-5 – March 17, 2018

  • Cell level stats now include Mode as well.

Version 0.2-4 – March 15, 2018

  • ZI prediction did not use covariate coefs, only the intercept that led to biased simulations.
  • Model averaging now uses selected models from dialog instead of all model in the ModelTab
  • Explicitly imports fitted and model.frame methods from VGAM for composition analysis to avoid scoping issues with formula
  • Number of hist bins in PlotPiDistr can be set by the user.
  • Added AIC weights to composition model table.
  • Composition PI now has the option for model selection similar to total Moose PI.

Version 0.2-3 – March 12, 2018

  • Fixed alpha level: was not available for some functions from options.
  • Null ZINB model in model dialogue fixed (length=0, not ==““)

Version 0.2-2 – February 28, 2018

  • Allow ZI to vary with covariates, UI and help dialog updated. PI simulations how use the model with ZI covariates as well.
  • Model averaging function tracks the fitted values and uses the model averaged mean as the fit.
  • Started adding Rd files with function documentations.

Version 0.2-1 – February 20, 2018

  • Added multi-model averaging to PI simulation: use weights from model table to select models to refit and the option is added to the UI dialog.
  • Checked and updated help dialogues to reflect updates.
  • Added mode to total moose PI table.
  • Added plot of PI distribution (PI) to UI: called ‘Plot pred. distribution’ in the menu, option to select full or subset PI data.
  • pb option set to “none” (tcltk froze Mac).

Version 0.2-0 – March 31, 2017

  • Bootstrap mean with 2 decimal places added to PiData table.
  • Unknown animals are dropped from compositional analysis with a warning.
  • Sightability correction can be defined up front, defaults to 1.
  • Summary tables print decimal numbers instead of scientific notation.
  • Total adult cows can be used as response for total models.
  • Calf/cow ratio and related compositional analysis added.

Version 0.1-0: March 11, 2016

Initial release