# “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As a follow-up to my post about major changes to FSA and that some of the “old” vignettes are now out-of-date, here is a brief summary of new material in the draft book chapters (linked to below) that replaced the vignettes.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=`

and`row.lab=`

arguments to`ref.lab=`

and`nref.lab=`

(easier to remember which one represents the reference data) in`ageBias()`

, added a`what="numbers"`

to`plot()`

to plot the number of fish at each point, and the correction of a bug in`agePrecision()`

that occurred when two ages agreed for an age-0 fish. Minor changes included adding`what="n"`

to get the sample size for the age-agreement table, adding the ability to use multiple`what=`

arguments in`summarize()`

after`ageBias()`

, adding`nYpos=`

to`plot()`

to allow control of the position of the sample size values on the plot, changing the default color of the confidence intervals in`plot()`

to black, changing`col.err=`

and`col.err.sig=`

to`col.CI=`

and`col.CIsig=`

, and changing the defaults of the agreement line in`plot()`

. 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, changing`tFrancis=`

to`ages2use=`

, changing the Schnute method to use the ages in`ages2use=`

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 if`ages2use=NULL`

, changing`Schnute`

parameterization to use t3 and L3 instead of t2 and L2 (allows for simplicity in explanation with Francis model). The`growthModelSim()`

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 the`extraSS()`

and`lrt()`

functions for performing extra sum-of-squares and likelihood ratio tests when comparing nested models (these are more useful when comparing several nested models than`anova()`

or`lrtest()`

). 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 to`method=`

in`mrClosed()`

and major changes to`capHistConvert()`

(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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