withr::local_par
.relax
and tcltk
.catchCurveSim()
: Modified. Used withr::local_par
to handle par()
changes.cohortCurveSim()
: Modified. Used withr::local_par
to handle par()
changes.growthModelSim()
: Modified. Used withr::local_par
to handle par()
changes.lengthWeightSim()
: Modified. Used withr::local_par
to handle par()
changes.lelsieSim()
: Modified. Used withr::local_par
to handle par()
changes.mrClosed1Sim()
: Modified. Used withr::local_par
to handle par()
changes.simAgeBias()
: Modified. Used withr::local_par
to handle par()
changes.simLenSelect()
: Modified. Used withr::local_par
to handle par()
changes.srCobWeb()
: Modified. Changed how par()
was handled.srSim()
: Modified. Replaced dependency on relax
with manipulate
. Removed formula
and data
arguments and, thus, the functionality to plot with data as this was used to find reasonable starting values for the model fitting which is better accomplished with srStartsDP()
. Used withr::local_par
to handle par()
changes.srStartsDP()
: Modified. Replaced dependency on relax
with manipulate
.vbComp()
: Modified. Changed how par()
was handled.vbStartsDP()
: Modified. Replaced dependency on relax
with manipulate
. Used withr::local_par
to handle par()
changes.::
to functions in many functions..onAttach()
: Removed.mrClosed1Sim()
: Modified. Fixed bug in plot when an infinite population was estimated. Tried to streamline code some (did not seem to make faster).sample4ALK()
: Modified. Fixed misuse of df
where should have been data
.simLenSelectP()
: Modified. Changed plot with show=TRUE
and actual probabilities so that they actually represent the beta distribution over the range of values. Removed an unnecessary catch for max.height=
. Minor spelling corrections.srStartsDP()
: Added from FSA
.vbDataGen()
: Modified. Changed ouput variable ageFrac
to ageFracG
and added ageFracY
. Fixed a bug related to repeating the lengths-at-capture (appeared only when the sampling season was the whole year and a fish happened to be sampled on the first day). Streamlined some code and updated the documentation.vbStartsDP()
: Added from FSA
. Fixed a bug related to call to vbStarts()
and how type=
worked with vbStarts()
(thanks to Jake Lowe for pointing this out).manipulate
, relax
, graphics
, and stats
. Added Suggests for tcltk
(ultimately want to get rid of this and relax
).catchCurveSim()
: Modified. Major overhaul including changing to use manipulate
rather than relax
, removed Zsteady=
and NoSteady=
in favor of a checkbox (but must be the same for both Z and No), removed ZDeltaAge=
and NoDeltaAge=
in favor of one deltaAge=
to be used for both Z and No. Moved legend to bottomleft. Changed lines such that including randomness in Z or No is considered an assumption violation.cohortSim()
: Modified. Changed to use manipulate
rather than relax
.growthModelSim()
: Modified. Changed to use manipulate
rather than relax
. Removed the ability to plot actual data (see vbStarts
) for this functionality. Changed parameter limits for most models. Fixed links to functions in FSA
that had changed names.lengthWeightSim()
: Modified. Changed to use manipulate
rather than relax
.leslieSim()
: Modified. Major overhaul including changing to use manipulate
rather than relax
, moved removals
to an argument rather than a slider bar, chagned type=
to sim=
, and dramatically changed the plot for sim="montecarlo"
.lwModelSim()
: Deleted. Same as lengthWeightSim()
.mrClosed1Sim()
: Modified. Changed to use manipulate
rather than relax
. Removed the type=
argument and put it as a dynamic choice. Added the sim=
argument which allows simulations of the distribution
or for assessing assumptions
violations. Changed look of the histogram (more like hist()
from FSA
). Force more bins in the histogram. Modified the legend look. Changed default number of rsmpls=
. Streamlined code some.vbComp()
: Modified. Reorganized code and deleted bad fishR links in documentation.vbDataGen()
: Modified. Removed bad link to gReshape()
in FSA
, which no longer exists.tidyr
(for spread()
in vbDataGen()
).growthModelSim()
: Modified. Changed links to FSA
in the help file.vbDataGen()
: A complete rebuild. See help file.growthModelSim()
: Added.leslieSim()
: Modified. Updated for changes to depletion()
in FSA
.simAgeBias()
: Modified. Updated for changes to ageBias()
in FSA
.srSim()
: Added. Still needs work to add functionality for "Shepherd" and "SailaLorda" methods.catchCurveSim()
: Added.cohortSim()
: Added.lengthWeightSim()
: Added.leslieSim()
: Added.lwModelSim()
: Added.sample4ALK()
: Added.simAgeBias()
: Added.simAges()
: Added.simLenFromAge()
: Added.simLenSelect()
: Added.mrClosed1Sim()
: Added.srCobWeb()
: Added.vbComp()
: Added.VBGMlit
: Added.vbDataGen()
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