The following list was compiled by Matt Johnson in October 2003.  If you run across a program not on this list that you think may be useful to your fellow animal ecologists, email the information and link to Matt.

 

Program

Description (˜indicates an especially widely used program)

Density Estimation

DISTANCE

˜Provides an analysis of distance sampling data to estimate density and abundance of a population.

TRANSECT

Analyzes line transect data as described by Burnham et al. (1980), analyzing both perpendicular distances and sighting angle and sighting distance data.

WEBSIM

Assists in the optimal design of trapping webs for density estimation.

 

Population Software (survival, density, population size, capture/recapture/resight probabilities, etc.)

BAND2

Computes the number of animals that must be banded in order to achieve a specified level of precision for survival rates estimated using band recovery models. (from USGS Patuxent Software site)

CONTRAST

Compares estimates of survival (or any normally distributed parameter estimates). (from USGS Patuxent Software site)

ESOR

Estimates patch occupancy rates and related parameters. (from USGS Patuxent Software site)

MARK

˜Program MARK, a Windows 95, 98, or NT program, provides parameter estimates from marked animals when they are re-encountered at a later time.

MAYFIELD

Computes estimates of daily survival rate for nest visitation data. (from USGS Patuxent Software site)

PRESENCE

Estimates patch occupancy rates and related parameters. (from USGS Patuxent Software site)

RELEASE

Computes estimates of survival and capture probability for capture-recapture experiments on open animal populations. (from USGS Patuxent Software site)

SCATMAN

Tests the hypothesis of prey-selectivity based on random samples of predator scats.

SURVIV

Computes estimates of survival (or any model parameter) with multinomially distributed data.

PVA_EXT

Population Viability Analysis packaged as an extension to ESRI products.

MICROMORT & SURGE

Alternative survival analysis packages.

 

 

Home Range Estimators

ANIMAL MOVEMENT

˜ESRI Product (extension) that enables home estimation (MCP and fixed kernel), nearest neighbor analyses, path analyses, random point, etc.

HOME RANGER

Calculates fixed or adaptive kernel home ranges of animals from radio-telemetry data.

RANGES6

˜Allows easy analysis of animal movement & locations, including location estimator (see radio telemetry below), various home range estimators, and some resource selection functions (see Habitat Analyses, below).

BIOTAS

˜Calculates various home range estimators, spatial statistics, and integrates with GIS (also performs some resource selection functions, see Habitat Analyses, below).

CALHOME

˜Calculates various home range estimators.

 

 

Community Analyses

SPECRICH

Computes "species richness" or total number of species from empirical species abundance distribution data.

ECOSIM

˜An interactive computer program for null model analysis in community ecology – e.g., co-occurrence, niche overlap, etc.

RAREFACTION CALCULATOR

A quick web-based calculator for rarefaction samples useful with small datasets.

 

Radio telemetry (locations, also see home range)

TRIANG

A simple program to calculate triangulations.

LOAS

˜Location of a signal – allows various methods of location (best biangulation, triangulation, maximum likelihood estimator, etc.).  Also does some home range estimations (see above).

LOCATE

A DOS-based program which replaces manually drawing bearings on maps and guesstimating where animals are located.

 

 

Habitat Analyses

BYCOMP.SAS

A SAS program to perform Compositional Analysis as described in the work by Aebischer et. al. (Ecology 1993).

SELECTION RATIOS

An Excel-based program that calculates otherwise laborious selection ratio analyses.  Written by Ken Gerow and available from Matt Johnson.

PREFER

Performs calculations described in Johnson (1980) to determine the preference of J individuals for I components using availability and usage data.

FRAGSTATS

˜Quantifies landscape structure through numerous metrics including: area, patch density, size and variability metrics; edge, shape, core area, and diversity metrics, and contagion and interspersion metrics. Two separate versions of Fragstats exist, one for vector images and one for raster images.

CWHR

Predicts species occupancy and habitat values based on inputted habitat variables for the state of California. 

ORWHR

Similar to above, but covers Oregon.

HARVEST

A timber harvest simulation model constructed to allow the input of specific rules to allocate forest stands for even-age harvest (clearcuts and shelterwood) and group selection, using parameters commonly found in National Forest Plan standards and guidelines.

RAMAS GIS

Links your GIS with a metapopulation model for population viability analysis and extinction risk assessment. (RAMAS has numerous other ecological/conservation software products).

 

 

General Statistics

SAS

˜ The most “tried & true” and flexible stats package.  If you need to do it, SAS can handle it.  Not, however, the most user friendly.  First designed for business analyses.

SPSS

˜ A menu-driven statistics package; robust and relatively user-friendly.  First designed for social science analyses.

SYSTAT

A menu-driven statistics package; robust and relatively user-friendly; has extensive graphing capabilities.  First designed for psychology analyses.  First written for Macintosh.

NCSS

Not widely used, some questions re: its accuracy.

BMDP

Robust package first designed for biomedical analyses; relatively user friendly.

MINITAB

Robust package first designed for teaching statistics.

SPLUS

Robust package first designed for social sciences.

 

 

General GIS

ArcView (see ESRI for all Arc… products)

˜ Easy-to-use product by ESRI that allows anyone to view, explore, and print published map files, plus some data visualization, query, analysis, and integration capabilities along with the ability to create and edit simple geographic features.

ArcEditor

Includes all the functionality of ArcView and adds the power to create and edit features in a multi-user geodatabase.

ArcInfo

˜ It includes all the functionality of ArcView and ArcEditor and adds the advanced geoprocessing and data conversion capabilities that make ArcInfo the de facto standard for GIS.

ArcGIS

˜ Provides flexibility when configuring a system since it is modular and scalable. It is modular in the sense that you acquire the system in pieces.

SPATIAL ANALYST

˜ An ESRI extension that provides a broad range of powerful spatial modeling and analysis features.

 

 

General Graphing

SIGMAPLOT

˜ The most flexible and complete graphing software package.  User friendly.

EXCEL

˜All hail Bill Gates.  It can meet most basic graphing needs; everyone with Microsoft Office has it.

DELTAGRAPH

Chief competitor to SigmaPlot; best supported for Macintosh.

 


 

Table below shows the % of papers examined (from 2002) that used the listed programs.  Asterisks indicate software that were clearly used much more than indicated in this table because the authors often do not specify which GIS software they used.

 

 

General Statistics

Demographics

Spatial Issues

 

 

Journal

# papers examined

SAS

SPLUS

SPSS

SYSTAT

Not Specified

DISTANCE

MARK

MAYFIELD

MICROMORT

CONTRAST

RANGES6

LOCATE

ARCVIEW/INFO

ANIMAL MOVEMENTS

FRAGSTATS

CALHOME

LOAS

ECOSIM

GENEPOP

J. Wild. Manag.

119

34

3

4

3

49

4

6

3

3

2

2

3

10*

5*

3

4

3

0

2

 

Ecology

 

25

12

0

12

8

60

0

0

0

0

0

0

0

0

0

0

0

0

2

0