LEFKO3 NEWS

CHANGES IN VERSION 3.2.0 (2021-01-03)
-------------------------------------
  NEW FEATURES
    1. Function cond_hmpm() added to create conditional hMPMs
    2. Function slambda3() added to estimate the log stochastic growth rate
    3. Function summary.lefkoElas() added to summarize elasticities by kind of
       transition
    4. Added citation() data for package
    5. Added NEWS section, using package lme4 NEWS as a template
    
  USER-VISIBLE CHANGES
    1. Corrected inconsistent stage name variable in stage frame creation and
       manipulation functions
    2. Updated and reorganized vignettes
    3. Modified stageframes exported by matrix creation functions now include
       entry status variable
    4. Objects of class lefkoElas now include the original A, U, and F matrices
    5. Elasticity and sensitivity outputs for lefkoMat objects now include the
       original A, U, and F matrices used as input
  
  BUG FIXES
    1. Matrix estimation function now create loy tables treating pop and patch
       as strings by default, eliminating possible conversion errors
    2. Corrected incorrect overwrite() call in lathyrus example used in function
       flefko3() and all population dynamics analysis functions


CHANGES IN VERSION 3.1.2 (2020-11-16)
-------------------------------------
  BUG FIXES
    1. Corrected auto-conversion of characters to factors occurring on R 3.6.3,
       which affected the creation and interpretation of the $labels element in
       matrix estimation


CHANGES IN VERSION 3.1.1 (2020-11-13)
-------------------------------------
  BUG FIXES
    1. Fixed bug in lmean() function resulting from an implicit cast and
       affecting users operating lefko3 on Solaris systems


CHANGES IN VERSION 3.1.0 (2020-11-08)
-------------------------------------
  NEW FEATURES
    1. Added function sfdistrib() to test whether mean = var and the level of
       zero-inflation in count variable data to be used for size and fecundity
    2. Added zero-inflated Poisson and negative binomial distributions
       as choices for the underlying distribution of size and fecundity
    3. Added individual and environmental covariates to function-based
       MPM estimation functions

  USER-VISIBLE CHANGES
    1. Corrected, updated, and reorganized vignettes

  BUG FIXES
    1. Corrected parameterization of negative binomial distribution in
        function modelsarch()



CHANGES IN VERSION 3.0.0 (2020-10-22)
-------------------------------------
  NEW FEATURES
    1. Added function aflefko2() function to estimate age x stage MPMs
    2. Added function sensitivity3() to estimate sensitivity matrices of
       historical and ahistorical MPMs
    3. Added Function elasticity3() to estimate elasticity matrices of
       historical and ahistorical MPMs

  USER-VISIBLE CHANGES
    1. Increased consistency of output variable names across functions
    2. Corrected, updated, and reorganized vignettes
    3. Eliminated faulty parameterization of matrix geometric mean in lmean()
       function

  \subsection{BUG FIXES}{
    1. Corrected core kernel underlying lmean(), and redeveloped in C++ to yield
       faster results
    2. Corrected parameterization of negative binomial distribution
    3. Function summary.lefkoMat() now shows which vital rate models were not
       estimated



CHANGES IN VERSION 2.4.2 (2020-09-12)
-------------------------------------
  USER-VISIBLE CHANGES
    1. All matrix estimators sped up through lapply()-based calls to C++ kernels
    2. Function lmean() now keeps the original names of populations and patches
    3. Corrected incorrect reference links in vignettes

  BUG FIXES
    1. Fixed memory leak in kernel behind function historicalize3()
    2. Fixed faulty indexing affecting all matrix estimators under certain
       conditions
    3. Bugs in Cypripedium candidum vignettes and examples caused by incomplete
       overwrite tables fixed


CHANGES IN VERSION 2.3.0 (2020-08-18)
-------------------------------------
  USER-VISIBLE CHANGES
    1. Major speed up to flefko2() and flefko3() through the
       incorporation of C++ core kernels

  BUG FIXES
    1. Bug fixed that could lead to the erroneous incorporation of mature
       stages as immature in flefko3() under certain rare circumstances
    2. Bug fixed that could fit proxy rates into the wrong elements in all
       matrix construction under certain rare circumstances
    3. Bug fixed that could, under some circumstances, lead to individuals
       being treated as dead when not observed for a period of more than a year


CHANGES IN VERSION 2.2.2 (2020-07-28)
-------------------------------------
  USER-VISIBLE CHANGES
    1. Revised vignettes
    2. Improved default handling of reproductive ratio and fecundity ratio

  BUG FIXES
    1. Fixed calculation of observed lifespan in functions verticalize3() 
       and historicalize3()

