“Vignettes” Update
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As a follow-up to my post about major changes to FSA and that some of the “old” vignettes are now out-of-date, here is a brief summary of new material in the draft book chapters (linked to below) that replaced the vignettes.
- Age Comparisons – Major changes are the addition of two more tests of symmetry (McNemar’s and Evans-Hoenigs), changed the
col.lab=
androw.lab=
arguments toref.lab=
andnref.lab=
(easier to remember which one represents the reference data) inageBias()
, added awhat="numbers"
toplot()
to plot the number of fish at each point, and the correction of a bug inagePrecision()
that occurred when two ages agreed for an age-0 fish. Minor changes included addingwhat="n"
to get the sample size for the age-agreement table, adding the ability to use multiplewhat=
arguments insummarize()
afterageBias()
, addingnYpos=
toplot()
to allow control of the position of the sample size values on the plot, changing the default color of the confidence intervals inplot()
to black, changingcol.err=
andcol.err.sig=
tocol.CI=
andcol.CIsig=
, and changing the defaults of the agreement line inplot()
. Several other internal changes were made but should be transparent to the user. The vignette is built upon a more interesting (and completely real) data set. All results were tested against published sources or results from other validated softwares.
- Weight-Length – No major changes. The vignette also serves as an introduction to simple linear and dummy variable regression so the vignette is longer to accommodate the general introduction to these methods.
- Growth – Major changes include the following to
vbStarts()
: forcing the use of a formula, changingtFrancis=
toages2use=
, changing the Schnute method to use the ages inages2use=
rather than being hard-wired to use the minimum and maximum observed age, allowing both the Schnute and Francis methods to use the minimum and maximum observed ages ifages2use=NULL
, changingSchnute
parameterization to use t3 and L3 instead of t2 and L2 (allows for simplicity in explanation with Francis model). ThegrowthModelSim()
had similar changes relative to the Schnute parameterization and the user is forced to use a formula. Changed"vbGallucciQuinn"
to"vbGQ"
, changed all"Gomp"
versions to"Gompertz"
, and added a"Weisberg"
parameterization to all functions. Add theextraSS()
andlrt()
functions for performing extra sum-of-squares and likelihood ratio tests when comparing nested models (these are more useful when comparing several nested models thananova()
orlrtest()
). Tested all output against verified sources. Greatly improved (in my opinion) the description for comparing two growth models. This chapter also serves as an introduction to non-linear model fitting and, thus, is longer than the original vignette.
- Mark-Recapture – I have not finished the changes here (will likely be a while), but the major change thusfar has been changing the
type=
argument tomethod=
inmrClosed()
and major changes tocapHistConvert()
(too many changes to detail here … should treat this as a new function if updating your code).
Filed under: Administration, R Tagged: Abundance, Age, Age Bias, Age Comparisons, FSA, Growth, Mark-Recapture, Precision, R, von Bertalanffy
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