For more information on each function click here.

For source code for each function click here. 



Functions for data manipulation and statistical
analysis 
arraymax: 
find the maximum value in an array and the associated dim names 
arraymin: 
find the minimum value in an array and the associated dim names 
bcount: 
perform a Boolean count on a vector, i.e., count the number
of TRUEs in the vector. 
calcsignifr: 
Calculate what value of r is significant at the alpha level given the sample size n 
combinep: 
combine the pvalues from a series of independent hypothesis tests to
get an overall significance level. See Sokal and Rohlf, 1981. Biometry, 2^{nd}, ed. p.780. 
combinevar: 
combine k estimates of the sample variance. This is useful in Monte Carlo simulations where one may
wish to run additional simulations to guarantee adequate precision. This function allows one to combine
the estimates of sample variance without having to recalculate the squared deviations. 
cumavg: 
compute the cumulative mean of the elements of a vector. This is useful for monitoring how estimates
from a Monte Carlo simulation are converging as the number of simulations increases.
(See also cumvar and updatevar.) 
cumvar: 
compute the mean and variance of the first n, 2n, 3n, … observations in a vector as well as for all
of the elements of a vector. This is useful for monitoring how results from a Monte Carlo simulation are
converging as the number of simulations increases. (See also cumavg and updatevar.) 
dnelement: 
Get dimnames corresponding to the n'th element of a vector which is also an array filled columnwise
with the vector. This function is called by arraymin() and arraymax() which are available on this site. 
gmean: 
compute the geometric mean of the elements of a vector. 
is.even: 
determine if each element of a vector is even (TRUE) or odd (FALSE) 
is.odd: 
determine if each element of a vector is odd (TRUE) or even (FALSE) 
myprop.table: 
calculate row or column proportions or proportions of the grand total.
This is a more general version of prop.table() in the base R package because
it provides the option of removing NAs from the object being summarized before calculating the proportions. 
same: 
tests whether two vectors are exactly the same. 
tabcounts: 
sort the unique values in a vector and return a count of the number of occurrences of each value. 
updatevar: 
updates the sample variance given the mean, variance, and sample size of a sample and a vector of
additional observations. That is, it is not necessary to have the individual observations from the
first sample in order to update the variance given additional observations. (See also cumavg and cumvar.) 

Functions for graphing. 
ellipse: 
compute (x,y) pairs for plotting an ellipse. 
regpolygon: 
compute (x,y) pairs that define the vertices of a regular polygon with
number of sides specified by the user 
rotate: 
rotate (x,y) coordinates counterclockwise through an angle to obtain new coordinates (x',y') 

Functions for fisheries assessments. 
calcFishMort: 
calculate the instantaneous rate of fishing mortality given the exploitation
rate, u, and natural mortality rate, M. 
M.Pauly: 
Compute Pauly's empirical estimate of natural mortality rate, M, given von Bertalanffy growth
parameters and mean water temperature.

plotagecomparisons: 
plots age readings from 3 readers (or from 3 methods of processing the
hard part) on a hexagon. This allows one to check if the 3 readers (or 3
methods) are interchangeable. In this way one can check if "odd man out"
tends to be higher or tends to be lower than the other readers. 
ya2yc: 
convert a table with rows denoting years and columns denoting age of fish
to one where the rows denote year and the columns denote cohort. This can
be useful for virtual population analysis and other longitudinal studies
of populations 
Z.Hoenig 
compute an estimate of mortality rate given the maximum known age or, optionally,
given the maximum age, the minimum age fully sampled, and the sample size.
