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CHANGELOG
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CHANGELOG
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Changes from version 0.5.10 to 0.5.11
* Changed the scaling factor of Winf from 10000 to 1000
Changes from version 0.5.11 to 0.5.12
* Changed the scaling factor of Winf from 1000 to 10000
Changes from version 0.5.11 to 0.5.12
* Changed the scaling factor of Winf from 1000 to 10000
* The default value for Winf is now 20000
Changes from version 0.5.12 to 0.5.13
* The cdf has as a right y limit the correct value 1 (it had 0)
Changes from version 0.5.13 to 0.5.14
*
Changes from version 0.5.13 to 0.5.14
*
Changes from version 0.5.14 to 0.5.15
*
Changes from version 0.5.15 to 0.5.16
*
Changes from version 0.5.16 to 0.5.17
*
Changes from version 0.5.17 to 0.5.18
* Added calculation for Fmsy
Changes from version 0.5.18 to 0.5.19
* Corrected calculation for Fmsy
* Added F/Fmsy
Changes from version 0.5.19 to 0.5.20
* Corrected calculation for Fmsy
* Added F/Fmsy
Changes from version 0.5.20 to 0.5.21
* Corrected calculation for Fmsy
* Added YpR
Changes from version 0.5.21 to 0.5.22
* Corrected calculation for Fmsy
* Added YpR -- corrected
Changes from version 0.5.22 to 0.5.23
* Corrected calculation for Fmsy
* SampleData3 return a list containing the data and the parameter values used
Changes from version 0.5.22 to 0.5.23
* Corrected calculation for Fmsy
* SampleData3 return a list containing the data and the parameter values used
Changes from version 0.5.23 to 0.5.24
* Corrected calculation for Fmsy
* SampleData3 returns a list containing also Fmsy for the given parameters
Changes from version 0.5.24 to 0.5.25
* estimateParam accepts now the parameter values not their log
* getParams doesn't return N.approx any more
Changes from version 0.5.24 to 0.5.25
* estimateParam accepts now the parameter values not their log
* getParams doesn't return N.approx any more
Changes from version 0.5.25 to 0.5.26
* in estimateParam the default value of fixed.vals is now numeric(0) instead of c()
Changes from version 0.5.26 to 0.5.27
* the estimateParam function simulates data correctly using the simulateData3 function
Changes from version 0.5.27 to 0.5.28
* the estimateParam function has default value for fixed.names c() again
Changes from version 0.5.28 to 0.5.29
* the estimate param does not use lower bounds any more (they are not really needed because of the minimiser uses the log of the params)
Changes from version 0.5.29 to 0.5.30
* scaled all parameters to 1, using the efault value as scaling factor
Changes from version 0.5.29 to 0.5.30
* scaled all parameters to 1, using the efault value as scaling factor
Changes from version 0.5.30 to 0.5.31
* small typo corrected in Parameters class
Changes from version 0.5.31 to 0.5.32
* bug corrected in Parameters class
Changes from version 0.5.32 to 0.5.33
* parameters function accepts normal parameter values, ie not scaled and not logged
Changes from version 0.5.33 to 0.5.34
* parameters function accepts 'again' log scaled values
Changes from version 0.5.34 to 0.5.35
* getParams returns also the paramters object
Changes from version 0.5.35 to 0.5.36
* The mortality at Winf is now Inf and the scaling parameter N1 is returned
Changes from version 0.5.36 to 0.5.37
* corrected pdfN in getParams
Changes from version 0.5.37 to 0.5.38
* corrected cdf in getParams
Changes from version 0.5.38 to 0.5.39
* returned cdf and pdfN into previous correct state in getParams
Changes from version 0.5.39 to 0.5.40
* pdfN.approx is now approximated using pdfN in getParams
Changes from version 0.5.40 to 0.5.41
* N is equal to 0 at Winf in getParams
Changes from version 0.5.41 to 0.5.42
* in estimateParam the optimisation has now a lower bound = 0.01
Changes from version 0.5.42 to 0.5.43
* getParams shows the parameter list and return all other variables invisibly
Changes from version 0.5.43 to 0.5.44
* getParams shows the parameter list and return all other variables invisibly
Changes from version 0.5.44 to 0.5.45
* getParams does not show the parameter list and return all other variables invisibly
Changes from version 0.5.45 to 0.5.46
* the optimisation for Winf is bounded using the biggest caught fish as lower bound
Changes from version 0.5.45 to 0.5.46
* the optimisation for Winf is bounded using the biggest caught fish as lower bound
Changes from version 0.5.46 to 0.5.47
* corrected typo
Changes from version 0.5.47 to 0.5.48
* fixed bug in estimateParam
Changes from version 0.5.48 to 0.5.49
* corrected another typo in estimateParam
Changes from version 0.5.49 to 0.5.50
* the lower bound for Winf is set to 1 gram more than the largest fish in the data
Changes from version 0.5.50 to 0.5.51
* added plotGrowth and plotMortality methods to the Parameters class
Changes from version 0.5.51 to 0.5.52
* added plotGrowth and plotMortality methods to the Namespace of the package
Changes from version 0.5.52 to 0.5.53
* changed the estimation of Fmsy including SSB and Relative recruitment
Changes from version 0.5.53 to 0.5.54
* changed h to A
Changes from version 0.5.54 to 0.5.55
* changed h to A (part 2)
Changes from version 0.5.55 to 0.5.56
* changed h to A (part 3)
Changes from version 0.5.56 to 0.5.57
* changed h to A (part 4)
Changes from version 0.5.57 to 0.5.58
* addedd w_egg parameter, equal to w_r
Changes from version 0.5.58 to 0.5.59
* changed h to A (part 5)
Changes from version 0.5.59 to 0.5.60
* changed h to A (part 6)
Changes from version 0.5.59 to 0.5.60
* changed h to A (part 7)
Changes from version 0.5.59 to 0.5.60
* changed h to A (part 8)
Changes from version 0.5.60 to 0.5.61
* Corrected the Yield calculation
Changes from version 0.5.61 to 0.5.62
* made getY available in the namespace
Changes from version 0.5.62 to 0.5.63
* changed the plotMortality function, the fishing mortality is shown as dotted line instead of grey area
Changes from version 0.5.62 to 0.5.63
* changed the plotMortality function, the fishing mortality is shown as dotted line instead of grey area
Changes from version 0.5.63 to 0.5.64
* Added the alternative approximation of N with the cumulative product and less supporting points
Changes from version 0.5.63 to 0.6.0
* Added the alternative approximation of N with the cumulative product and less supporting points
Changes from version 0.5.63 to 0.6.0
* Added the alternative approximation of N with the cumulative product and less supporting points
Changes from version 0.6.0 to 0.6.1
* Fixed typo in the getParams2 and getY2
Changes from version 0.6.1 to 0.6.2
* Delta shouldn't be deleted in getY2
Changes from version 0.6.2 to 0.6.3
* Changed the default M for getParams2 to 200 (from 100)
Changes from version 0.6.3 to 0.6.4
* Changed the default M for getParams2 to 300 (from 200)
Changes from version 0.6.4 to 0.6.5
* The bootstrap option returns the mean of all estimations for each parameter
Changes from version 0.6.5 to 0.6.6
* The bootstrap option returns the mean of all estimations for each parameter (correction)
Changes from version 0.6.6 to 0.6.7
* The bootstrap option returns the mean of all estimations for each parameter (fixed)
Changes from version 0.6.7 to 0.7.0
* Added the option of estimating using survey data
Changes from version 0.7.0 to 0.7.1
* Fixed the estimation with fixed parameter values when bootstrap is greater than 1
Changes from version 0.7.1 to 0.7.2
* The mean values are fixed in the estimation with bootstrap
Changes from version 0.7.2 to 0.7.3
* The Fmsy is calculatd in getParams only if calcFmsy is TRUE
Changes from version 0.7.3 to 0.7.4
* Estimation using multiple data is possible
* Parameter objects 'show' better now
Changes from version 0.7.4 to 0.7.5
* Exported function estimateMultidata and method difference
Changes from version 0.7.5 to 0.7.6
* estimParam return the hessian of the likelihood function as an attribute
Changes from version 0.7.6 to 0.7.7
* the numDeriv package is now imported by the package in the NAMESPACE
Changes from version 0.7.7 to 0.7.8
* The estimateParam returns the 95% confidence interval for the parameter estimates
Changes from version 0.7.7 to 0.7.8
* The estimateParam returns the 95% confidence interval for the parameter estimates
Changes from version 0.7.8 to 0.7.9
* In estimateParam the matrix containing the estimated parameter, se, and confidence limits is printed only if verbose = TRUE
Changes from version 0.7.9 to 0.7.10
* The standard error is not returned any more from estimateParam because it only calculated for the untransformed paramter
Changes from version 0.7.10 to 0.7.11
* In estimParam the inversion of the hessian is done in a 'try' statement. NAs are returned for the standard error and confidence limits if the hessian is not invertible
Changes from version 0.7.11 to 0.7.12
* Corrected typo in estimParam
Changes from version 0.7.12 to 0.7.13
* In estimateParam a bug was fixed, the function that return the class of a variable is 'class', not 'typeof'
Changes from version 0.7.13 to 0.7.14
* In estimateParam removed 'browser'
Changes from version 0.7.14 to 0.7.15
* estimParam returns the value of the 'objective' function
Changes from version 0.7.15 to 0.7.16
* estimParam returns the convergence status from nlminb
Changes from version 0.7.16 to 0.8.0
* New parameter Wfs was introduced
Changes from version 0.8.0 to 0.8.1
* Fixed bug in parameters function
Changes from version 0.8.1 to 0.8.2
* Changed the y label of the growth plot produced by plotGrowth
Changes from version 0.8.2 to 0.8.3
* In estimParam removed the lower bound of all parameters except Winf
* estimParam returns the message of nlminb
Changes from version 0.8.2 to 0.8.3
* In estimParam removed the lower bound of all parameters except Winf
* estimParam returns the message of nlminb
Changes from version 0.8.3 to 0.8.4
* estimParam returns its call, as it is returned from match.call
Changes from version 0.8.4 to 0.8.5
* reloadSteadyStateEstimation, new function that reloads the package without restarting R
Changes from version 0.8.4 to 0.8.5
* reloadSteadyStateEstimation, new function that reloads the package without restarting R
Changes from version 0.8.5 to 0.8.6
* reloadSteadyStateEstimation, removed debuging cat
Changes from version 0.8.5 to 0.8.6
* reloadSteadyStateEstimation, removed debuging cat
Changes from version 0.8.6 to 0.9.0
* Changed the filenames to more apropriate ones
* The getParams also returns yield (yield per recruit) in order to be used for finding Fmsy (Fmsyr)
* Weight at recruitment is set to 1mg
* Checked all equations to match with Ken&Beyer(2013)
Changes from version 0.8.6 to 0.9.0
* Changed the filenames to more apropriate ones
* The getParams also returns yield (yield per recruit) in order to be used for finding Fmsy (Fmsyr)
* Weight at recruitment is set to 1mg
* Checked all equations to match with Ken&Beyer(2013)
Changes from version 0.8.6 to 0.9.0
* Changed the filenames to more apropriate ones
* The getParams also returns yield (yield per recruit) in order to be used for finding Fmsy (Fmsyr)
* Weight at recruitment is set to 1mg
* Checked all equations to match with Ken&Beyer(2013)
Changes from version 0.9.0 to 0.9.1
* estimateParam accepts data in a data.frame with columns 'Weight' and 'Freq'
* plotFit plots also data.frames
Changes from version 0.9.1 to 0.9.2
* plotFit does not plot the points of the actual data, only histograms
Changes from version 0.9.2 to 0.9.3
* simulateData3 returns a usable data.frame containing the data. The estimation using the data frame is much faster
* Added parameter u, i.e the width of the sigmoid selectivity curve going from 0 to 1
Changes from version 0.9.3 to 0.9.4
* fixed bug in 'parameters', false warning
Changes from version 0.9.4 to 0.9.5
* simulateData3 returns more reasonable data.frame with weight classess of 5 grams
Changes from version 0.9.4 to 0.9.5
* simulateData3 returns more reasonable data.frame with weight classess of 5 grams
Changes from version 0.9.5 to 0.9.6
* getParams returns the vonBertalanffy parameters M and K, and the ratio M/K
Changes from version 0.9.6 to 0.9.7
* some code optimizations
* simulateData3 produces better data.frames
Changes from version 0.9.6 to 0.9.7
* some code optimizations
* simulateData3 produces better data.frames
Changes from version 0.9.7 to 0.9.8
* getParams has now less arguments
* simulateData3 was change to accomodate the changes in getParams
Changes from version 0.9.8 to 0.9.9
* getParams, the ranges where the biological reference points are searched were increased
Changes from version 0.9.9 to 0.9.10
* getParams, biological reference points are only returned if no error is occured while serching for them
Changes from version 0.9.10 to 0.9.11
* removed Frasier selectivity
Changes from version 0.9.11 to 0.9.12
* removed Frasier selectivity
Changes from version 0.9.12 to 0.9.13
* fixed typo in the show method of Parameters
Changes from version 0.9.13 to 0.9.14
* simulateData3 returns a data.frame keeping also the weight classes that have frequency 0
Changes from version 0.9.14 to 0.9.15
* simulateData3 has argument wcw to change the weight class width, this is also returned as an attribute on the data.frame
Changes from version 0.9.15 to 0.9.16
* Added helper function 'sample2df' that takes a sample and returns a data.frame with Weight and Freq(uencies)
Changes from version 0.9.16 to 0.9.17
* sample2df returns a data.frame as it should
* simulateData3 asks if multicore is available and uses sapply if not
* simulateData3 has boolean argument 'retDF' about returning a data.frame
Changes from version 0.9.16 to 0.9.17
* sample2df returns a data.frame as it should
* simulateData3 asks if multicore is available and uses sapply if not
* simulateData3 has boolean argument 'retDF' about returning a data.frame
Changes from version 0.9.17 to 0.9.18
* simulateData3 has boolean argument 'retDF' about returning a data.frame
Changes from version 0.9.18 to 0.9.19
* estimateParam accepts also upper bounds for the parameters
Changes from version 0.9.19 to 0.9.20
* estimateParam accepts also upper bounds for the parameters
Changes from version 0.9.20 to 0.9.21
* added method 'as.list' for Parameters objects
Changes from version 0.9.21 to 0.9.22
* added method 'as.list' for Parameters objects
Changes from version 0.9.22 to 0.9.23
* 'parameters' accepts now non-transformed parameters using the boolean argument 'transformed'
Changes from version 0.9.23 to 0.9.24
* added method 'as.list' for Parameters objects
Changes from version 0.9.24 to 0.9.25
* added method 'as.list' for Parameters objects, also in the NAMESPACE
Changes from version 0.9.25 to 0.9.26
* plotGrowth has ... argument
Changes from version 0.9.26 to 0.9.27
* plotGrowth and plotMortality had been changed, cex were removed and margins were adjusted
Changes from version 0.9.27 to 0.9.28
* added tmclapply function, i.e. timed mclapply
* added getRandomParameters function that returns a 'Parameters' object with random parameters
Changes from version 0.9.28 to 0.9.29
* tmclapply shows estimated time to completion
Changes from version 0.9.29 to 0.9.30
* estimateParam: cleaner return structure
Changes from version 0.9.30 to 0.9.31
* estimateParam: verbose=getOption('verbose')
Changes from version 0.9.31 to 0.9.32
* tmclapply has a nicer ETC
* getRandomParameters has two new arguments to return only parameter vectors with a minimum Rrel and Fmsy
Changes from version 0.9.32 to 0.9.33
* implemented method 'setlogWinf<-' that changes the asymptotic weight and changing Wfs accordingly
Changes from version 0.9.33 to 0.9.34
* fixed small typo in 'setlogWinf'
Changes from version 0.9.34 to 0.9.35
* fixed small typo in 'setlogWinf'
Changes from version 0.9.35 to 0.9.36
* Added simplify2dataframe function for use with tmclapply
Changes from version 0.9.36 to 0.9.37
* Renamed the reload function to reloadS6modelPackage
Changes from version 0.9.37 to 0.9.38
* 'tmclapply' has FALSE as default value for 'simplify' argument
Changes from version 0.9.38 to 0.9.39
* 'parameters' accepts a base parameters object, makes it easier to change few parameter values of existing objects
Changes from version 0.9.39 to 0.9.40
* 'tmclapply' has new argument 'progressbar' that shows(TRUE, default) or hides (FALSE) the progress bar
Changes from version 0.9.39 to 0.9.40
* 'tmclapply' has new argument 'progressbar', TRUE(default) shows a progress bar while running
Changes from version 0.9.39 to 0.9.40
* Added imports numderiv in the DESCRITPION file
Changes from version 0.9.40 to 0.9.41
* Added imports numderiv in the DESCRITPION file
Changes from version 0.9.41 to 0.9.42
* Added imports numderiv in the DESCRITPION file
Changes from version 0.9.42 to 0.9.43
* pdfN.approx is equal to .Machne$double.xmin instead of zero for values larger than Winf
* difference returns the percent difference for each variable
* minimizeme assumes data.frame with Weight column of class numeric
* Winf has maximum observed as starting value, not as lower bound
Changes from version 0.9.43 to 0.10.0
* Removed unused functions, like getY, getYR, reloads6model, simulateData, simulateData2
* Removed bootstrap argument from estimateParam
* Added roxygen comments
* Changed from multicore to parallel
* estimateParam default names are Fm, Winf and Wfs
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Changes from version 0.10.0 to 0.10.1
* Added documentation for more functions
Changes from version 0.10.1 to 0.10.2
* Added argument fixed.transformed to estimatParam
* Exported Winf
Documented rest of methods
Changes from version 0.10.2 to 0.10.3
* minimizeme and estimateParam accept the list returned by simulateData3 as data input
Fixed tmclapply, exported, documented
Changes from version 0.10.3 to 0.10.4
* Not (ab)using ifelse to select btw mclapply and lapply
Changes from version 0.10.4 to 0.10.5
* Added some tests for Parameters
* parameters initialization using Winf respects default eta_F and changed Wfs accordingly
as.list(Parameter): added documentation, returns also u
Changes from version 0.10.5 to 0.10.6
* Fixed bug where Wfs was wrong if eta_F and Wfs were not estimated
Changes from version 0.10.6 to 0.10.7
* Added warning in getParams with mismatched Wfs/eta_F Parameters object
Show includes u in the printout of a Parameters object
Wrong check for mismatch btw etaF/Wfs in getParams
Changes from version 0.10.7 to 0.10.8
* TMB code for Fmsy and parameter estimation
* removed unnecessary numDeriv:: when using the imported hessian and jacobian functions
Changes from version 0.10.8 to 0.10.9
* argument `wcw` is now binsize
* added version to results and plots
* added estimate_TMB and calcFmsy functions
* removed numderiv::
* styled output
* documentation fixes
* S3 methods for as.list, lines and plot
Changes from version 0.10.9 to 0.10.10
* added observation error
Changes from version 0.10.10 to 0.10.11
* makeAssessment function that accepts time series of size distributions
* new class s6modelResults
* print function for s6modelResults
* plot function for s6modelResults
* relative recruitment is calculated and reported from estimate_TMB
Changes from version 0.10.11 to 0.10.12
* Observation error, independent poisson or gaussian errors
* Rmax calculation - SSB, Y, R, N are returned as absolute values, not scaled
* function for DATRAS input and manipulation
* findLatest file in directory and specific pattern
* better makeAssessment and plot functions
* bounded phys.mortality
Changes from version 0.10.12 to 0.10.13
* Poisson estimation has one parameter for the level
* Confidence interval results are saved
* Seed is saved
* Small plotting changes