Add archive of previous releases

ArchivedReleases/1.0-beta/maxent.bat

@@ -0,0 +1 @@
+java -mx512m -jar maxent.jar

ArchivedReleases/1.0-beta/readme.txt

@@ -0,0 +1,174 @@
+Maximum Entropy Modeling of Species Geographic Distributions
+============================================================
+
+INSTRUCTIONS FOR DOWNLOADING AND GETTING STARTED
+
+Miro Dudik          ([email protected])
+Steven Phillips     ([email protected])
+Rob Schapire        ([email protected])
+
+July, 2004
+
+This file outlines the steps you should take to begin using maxent to
+model species geographic distributions.  To download the program, or
+for background on maxent and its application to species distribution
+modeling, please see http://www.cs.princeton.edu/~schapire/maxent.
+
+
+Terms and Conditions
+--------------------
+This software may be freely downloaded and used for all educational
+and research activities.  This software may not be used for any
+commercial or for-profit purposes.  The software is provided "as-is",
+and does not come with any warranty or guarantee of any kind.  The
+software may not be further distributed.
+
+
+Downloading the Software
+------------------------
+The software consists of a jar file, maxent.jar, which can be used on
+any computer running Java version 1.3 or later.
+
+If you are using Microsoft Windows, you should also download the file
+maxent.bat, and save it in the same directory as maxent.jar.
+
+Maxent.bat assumes that your computer has at least 512 megabytes of
+memory.  If this is not the case, you should edit the file (for
+example, using Notepad) to reduce amount of memory it requests.  Just
+replace the number "512" with the amount of memory your computer has.
+You also can increase the amount of memory available to the program in
+this fashion.
+
+
+Getting Started
+---------------
+If you are using Microsoft Windows, simply click on the file
+maxent.bat.  Otherwise, enter "java -mx512m -jar maxent.jar" in a
+command shell (where "512" can be replaced by the amount of memory you
+want made available to the program).  The program will start up, and
+further instructions can be obtained by pressing the "help" button.
+Maxent.jar can be followed by command line arguments, which is
+especially useful when running maxent in a batch (non-interactive)
+mode using the argument "-a".  See a list of command line options
+below.
+
+
+Input Formats
+-------------
+Input files can be specified through the user interface, or on a
+command line.  The format is as follows:
+
+* Samples: Given by a file in comma-separated value format.  The
+  first line is a header line (ignored by the program), while later
+  lines have the format: species, longitude, latitude.
+
+  For example:
+
+  Species, Long, Lat
+  Blue-headed Vireo, -89.9, 48.6
+  Loggerhead Shrike, -87.15, 34.95
+  ...
+
+* Environmental layers: Given by a directory containing the layers.
+  The layers must be in ESRI ASCII grid format, and their filenames
+  must end in ".asc".
+
+  The ASCII grid file consists of a set of keywords, followed by cell
+  values in row-major order.  The file format is
+
+  ncols xxx
+  nrows xxx
+  xllcorner xxx
+  yllcorner xxx
+  cellsize xxx
+  NODATA_value xxx
+  row 1
+  row 2
+  ...
+  row n
+
+  For example:
+
+  ncols         386
+  nrows         286
+  xllcorner     -128.66338
+  yllcorner     13.7502065
+  cellsize      0.2
+  NODATA_value  -9999
+  -9999 -9999 -123 -123 -123 -9999 -9999 -9999 -9999 -9999 ...
+  -9999 -9999 -123 -123 -123 -9999 -9999 -9999 -9999 -9999 ...
+  -9999 -9999 -117 -117 -117 -119 -119 -119 -119 -119 -9999 ...
+  ...
+
+* Projection layers (optional): Given by a directory containing a
+  second set of environmental layers.  The layers must have the same
+  names as those in the "Environmental layers" directory, though they
+  might describe a different geographic area.
+
+Output files
+------------
+* maxentResults.csv For each species, the number of training samples
+  used for learning, values of training loss and test loss, and an
+  average contribution of individual features is given.  Training loss
+  includes regularization, test loss is given only when a test sample
+  file is provided.
+
+In addition, maxent produces several files for every species. For a
+species called "mySpecies", it produces files
+
+* mySpecies.asc
+  containing the predicted probabilities in ESRI ASCII grid format
+
+* mySpecies.lambdas
+  describing the computed model
+
+* mySpecies.thr
+  describing feature profiles (if threshold features are used)
+
+* mySpecies_projDir.asc
+  containing the projected weights (if the projection directory
+  projDir is specified)
+
+The output format for probabilities and projected weights is either
+raw, with the actual probabilities (weights) of each cell given, or
+cumulative, with the output value at a grid cell being the sum of the
+probabilities (weights) of all grid cells with no higher probability
+(weight) than the grid cell, times 100 (rescaled for projected weights
+so that the maximum is 100).  For example, the grid cell that is
+predicted as having the best conditions for the species, according to
+the model, will have cumulative value 100, while cumulative values
+close to 0 indicate predictions of unsuitable conditions.
+
+
+Command Line Arguments
+----------------------
+  -p   use product, quadratic and linear features
+  -q   use quadratic and linear features
+  -l   use linear features
+  -h   use threshold features
+  -V   print the version number
+  -a   automatically start running, and terminate when done
+  -r   redo species if ".asc" output file already exists
+  -k   skip species if ".asc" output file already exists
+  -s<sample_file>
+       set sample file to <sample_file>
+  -e<layers_directory>
+       set environmental layers directory to <layers_directory>
+  -j<projection_directory>
+       set projection directory to <projection_directory>
+  -o<output_directory>
+       set output directory to <output_directory>
+  -m<max_iters>
+       set the maximum number of iterations to <max_iters>
+  -b<beta>
+       set the regularization constant to <beta>
+  -c<threshold>
+       set the convergence threshold to <threshold>
+  -t<variable>
+       make <variable> a categorical variable
+  -T<test_sample_file>
+       use samples in test_sample_file to evaluate test loss
+  -C   don't do clamping while projecting
+  -Q   don't use "cumulative" output format
+  -K   minimize memory usage, but run approximately half as fast
+  -W   write outputs in a compressed (.mxe) format, to save disk space

ArchivedReleases/1.6.2/maxent.bat

@@ -0,0 +1 @@
+java -mx512m -jar maxent.jar

ArchivedReleases/1.6.2/readme.txt

@@ -0,0 +1,175 @@
+Maximum Entropy Modeling of Species Geographic Distributions
+============================================================
+
+INSTRUCTIONS FOR DOWNLOADING AND GETTING STARTED
+
+Miro Dudik          ([email protected])
+Steven Phillips     ([email protected])
+Rob Schapire        ([email protected])
+
+Version 1.6.2 (beta)
+August, 2004
+
+This file outlines the steps you should take to begin using maxent to
+model species geographic distributions.  To download the program, or
+for background on maxent and its application to species distribution
+modeling, please see http://www.cs.princeton.edu/~schapire/maxent.
+
+
+Terms and Conditions
+--------------------
+This software may be freely downloaded and used for all educational
+and research activities.  This software may not be used for any
+commercial or for-profit purposes.  The software is provided "as-is",
+and does not come with any warranty or guarantee of any kind.  The
+software may not be further distributed.
+
+
+Downloading the Software
+------------------------
+The software consists of a jar file, maxent.jar, which can be used on
+any computer running Java version 1.3 or later.
+
+If you are using Microsoft Windows, you should also download the file
+maxent.bat, and save it in the same directory as maxent.jar.
+
+Maxent.bat assumes that your computer has at least 512 megabytes of
+memory.  If this is not the case, you should edit the file (for
+example, using Notepad) to reduce amount of memory it requests.  Just
+replace the number "512" with the amount of memory your computer has.
+You also can increase the amount of memory available to the program in
+this fashion.
+
+
+Getting Started
+---------------
+If you are using Microsoft Windows, simply click on the file
+maxent.bat.  Otherwise, enter "java -mx512m -jar maxent.jar" in a
+command shell (where "512" can be replaced by the amount of memory you
+want made available to the program).  The program will start up, and
+further instructions can be obtained by pressing the "help" button.
+Maxent.jar can be followed by command line arguments, which is
+especially useful when running maxent in a batch (non-interactive)
+mode using the argument "-a".  See a list of command line options
+below.
+
+
+Input Formats
+-------------
+Input files can be specified through the user interface, or on a
+command line.  The format is as follows:
+
+* Samples: Given by a file in comma-separated value format.  The
+  first line is a header line (ignored by the program), while later
+  lines have the format: species, longitude, latitude.
+
+  For example:
+
+  Species, Long, Lat
+  Blue-headed Vireo, -89.9, 48.6
+  Loggerhead Shrike, -87.15, 34.95
+  ...
+
+* Environmental layers: Given by a directory containing the layers.
+  The layers must be in ESRI ASCII grid format, and their filenames
+  must end in ".asc".
+
+  The ASCII grid file consists of a set of keywords, followed by cell
+  values in row-major order.  The file format is
+
+  ncols xxx
+  nrows xxx
+  xllcorner xxx
+  yllcorner xxx
+  cellsize xxx
+  NODATA_value xxx
+  row 1
+  row 2
+  ...
+  row n
+
+  For example:
+
+  ncols         386
+  nrows         286
+  xllcorner     -128.66338
+  yllcorner     13.7502065
+  cellsize      0.2
+  NODATA_value  -9999
+  -9999 -9999 -123 -123 -123 -9999 -9999 -9999 -9999 -9999 ...
+  -9999 -9999 -123 -123 -123 -9999 -9999 -9999 -9999 -9999 ...
+  -9999 -9999 -117 -117 -117 -119 -119 -119 -119 -119 -9999 ...
+  ...
+
+* Projection layers (optional): Given by a directory containing a
+  second set of environmental layers.  The layers must have the same
+  names as those in the "Environmental layers" directory, though they
+  might describe a different geographic area.
+
+Output files
+------------
+* maxentResults.csv For each species, the number of training samples
+  used for learning, values of training loss and test loss, and an
+  average contribution of individual features is given.  Training loss
+  includes regularization, test loss is given only when a test sample
+  file is provided.
+
+In addition, maxent produces several files for every species. For a
+species called "mySpecies", it produces files
+
+* mySpecies.asc
+  containing the predicted probabilities in ESRI ASCII grid format
+
+* mySpecies.lambdas
+  describing the computed model
+
+* mySpecies.thr
+  describing feature profiles (if threshold features are used)
+
+* mySpecies_projDir.asc
+  containing the projected weights (if the projection directory
+  projDir is specified)
+
+The output format for probabilities and projected weights is either
+raw, with the actual probabilities (weights) of each cell given, or
+cumulative, with the output value at a grid cell being the sum of the
+probabilities (weights) of all grid cells with no higher probability
+(weight) than the grid cell, times 100 (rescaled for projected weights
+so that the maximum is 100).  For example, the grid cell that is
+predicted as having the best conditions for the species, according to
+the model, will have cumulative value 100, while cumulative values
+close to 0 indicate predictions of unsuitable conditions.
+
+
+Command Line Arguments
+----------------------
+  -p   use product, quadratic and linear features
+  -q   use quadratic and linear features
+  -l   use linear features
+  -h   use threshold features
+  -V   print the version number
+  -a   automatically start running, and terminate when done
+  -r   redo species if ".asc" output file already exists
+  -k   skip species if ".asc" output file already exists
+  -s<sample_file>
+       set sample file to <sample_file>
+  -e<layers_directory>
+       set environmental layers directory to <layers_directory>
+  -j<projection_directory>
+       set projection directory to <projection_directory>
+  -o<output_directory>
+       set output directory to <output_directory>
+  -m<max_iters>
+       set the maximum number of iterations to <max_iters>
+  -b<beta>
+       set the regularization constant to <beta>
+  -c<threshold>
+       set the convergence threshold to <threshold>
+  -t<variable>
+       make <variable> a categorical variable
+  -T<test_sample_file>
+       use samples in test_sample_file to evaluate test loss
+  -C   don't do clamping while projecting
+  -Q   don't use "cumulative" output format
+  -K   minimize memory usage, but run approximately half as fast
+  -W   write outputs in a compressed (.mxe) format, to save disk space

ArchivedReleases/1.8.1/maxent.bat

@@ -0,0 +1 @@
+java -mx512m -jar maxent.jar