Relocate wiki from trac
parent
36146893e6
commit
d52dbbd9be
|
|
@ -0,0 +1,57 @@
|
|||
|
||||
|
||||
# Laydi
|
||||
|
||||
## Look At Your Data Interactively
|
||||
|
||||
Laydi is an acronym for look at your data interactively, which is what the program is aimed at. It is a lightweight data analysis program for bilinear modeling (PCA and PLS) with a strong focus on interactive use. Laydi is released under the GNU GPL and the latest development snapshot can be downloaded from https://git.pvv.ntnu.no/Projects/laydi.git
|
||||
|
||||
|
||||
|
||||
## Features
|
||||
|
||||
- Principal Component Analysis (PCA)
|
||||
- Partial Least Squares Regression (PLS)
|
||||
- L-shaped PLS regression (L-PLS)
|
||||
- Easy mapping of variables between plots, selections in one plot propagates to other plots.
|
||||
|
||||
## Nonfeatures
|
||||
|
||||
- Does not import arbitrary files. Files must be prepared in a (simple) file format prior to import.
|
||||
- Saving and loading of projects is not implemented. (Datasets can be saved and loaded, though, and plots can be exported)
|
||||
- Not very stable
|
||||
|
||||
## Installation requirements
|
||||
|
||||
Laydi currently requires the following extra packages, available from apt on Debian and Ubuntu.
|
||||
|
||||
- python2.4 or python2.5
|
||||
- python-glade2
|
||||
- python-gnome2
|
||||
- python-gtk2
|
||||
- python-matplotlib
|
||||
- python-scipy
|
||||
- python-numpy
|
||||
|
||||
Partially needed
|
||||
|
||||
- python-networkx
|
||||
- python-pygraphviz
|
||||
|
||||
## Download laydi
|
||||
|
||||
Laydi is not debianized. To download it, use the clone the git repo.
|
||||
|
||||
```console
|
||||
git clone https://git.pvv.ntnu.no/Projects/laydi.git
|
||||
```
|
||||
|
||||
## User documentation
|
||||
|
||||
- [Frequently Asked Questions](./wiki/faq.md)
|
||||
- [Laydi help](./wiki/help.md) (the same as available through the help menu in the application.)
|
||||
- [Terminology](./wiki/Terminology.md)
|
||||
|
||||
## Developer documentation
|
||||
|
||||
- [Developer tips and tricks](./wiki/development/hints.md)
|
||||
|
|
@ -0,0 +1,20 @@
|
|||
# Terminology
|
||||
As most software projects, the Laydi system has its own terms to describe objects and elements. Where possible, we have tried to be somewhat consistent with the terms used in other similar software such as Pathway Assist, Array Assist and Unscrambler. The most important terminology of Laydi is listed here.
|
||||
|
||||
## User Interface
|
||||
|
||||
|
||||
|
||||
- The **Navigator** is where the data and plots for the current project are visually located on the screen. It is usually empty until you load some datasets. Datasets and plots are arranged in a hierarchy.
|
||||
- A **Project** is where the data for an analysis are stored. The data and plots for a project are shown in the navigator window.
|
||||
- A **Workflow** is a set of stages with functions you might want to use to accomplish some task.
|
||||
- Each **Stage** in a workflow has a name like preprocessing or regression, and contain the functions needed to do that part of the analysis.
|
||||
- In the center of the application (marked Plots in the picture) are a set of **viewframes** that can display plots. Drag and drop a plot from the navigator to the viewframe where you want to see it.
|
||||
- In the **Information pane**, two tabs are always visible: Log and Selections. Additional tabs can be made in the workflows.
|
||||
- The **log** contains informational messages from the program.
|
||||
- The **selections** tab shows what is selected in a specific dimension.
|
||||
|
||||
## Implementation Details
|
||||
|
||||
- **Dataset** is the basis class of the data in the program. A dataset is similar to a dataframe in GNU R in that it is a matrix with labels along the axes. Unlike R, each dimension in a dataset contains a globally unique name for the dimensions in the problem domain.
|
||||
- **Annotations** are textual tables that describe the identifiers along an axis in some way.
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
# The basic design concepts
|
||||
|
||||
The design is based around two fundamental (and related) concepts; *datasets* and *dimensions*. A dataset is a matrix with a list of identifiers for each row and another list of identifiers for each column. The dimension for rows and columns are also stored.
|
||||
|
||||
## Dimension
|
||||
|
||||
A dimension is just a name of a domain that your data contain. Each element along a dimension is identified by a name that is defined to be unique across every dataset, plot and other program elements that contains that dimension.
|
||||
|
||||
So, if we have a dimension named `samples`, which contains an identifier `patient1`, whenever this identifier is used in the `samples` dimension, it is assumed to refer to the same entity.
|
||||
|
||||
This allows the program to do mapping between different plots and datasets, so that when <`patient1` in the `samples` dimension> is selected in one plot, this selection can propagate to all other places in the program that displays some kind of information on samples.
|
||||
|
||||
## Dataset
|
||||
|
||||
A dataset is a matrix where both columns and rows are associated with dimension. For example, a gene analysis study may have a dataset where the rows are tissue samples associated with the `samples` dimension and the columns are all the measured genes in the `genes` dimension.
|
||||
|
||||
## Annotations
|
||||
|
||||
Sometimes we want additional information associated with the identifiers along a dimension for display purposes. A gene is often represented by an identifier that is not very meaningful without being looked up in a database. So if we also want some extra information, like the name of the gene, this is stored in *annotations* along the `genes` dimension.
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
# Development hints
|
||||
|
||||
## Terminology
|
||||
|
||||
Read terminology for the conventions used in the program. This ensures a consistent use of terms within the program. New terminology should be described on the that page, and should be introduced only when needed. Too much terminology clutters the namespace.
|
||||
|
||||
## Logging
|
||||
Log output is very easy. Import the logger module, and use the singleton Logger instance inside it. The logger has four different debug levels, debug, notice, warning and error. A simple example follows:
|
||||
|
||||
```python
|
||||
import logger
|
||||
|
||||
logger.log('debug', 'This should appear in the log window as a debug message')
|
||||
```
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
## Recommended names
|
||||
|
||||
### Variables
|
||||
|
||||
- fn for filenames.
|
||||
- fd for files.
|
||||
- dim for a dimension.
|
||||
- it for iterators.
|
||||
- ids for a list of identifiers.
|
||||
- indices
|
||||
- func for functions
|
||||
|
||||
### Function handlers
|
||||
|
||||
Function handlers should generally be named _on_<signal>. This makes them private and easy to follow. This is not an absolute rule, as there can be several functions in the same namespace listening to the same signal, but on different objects.
|
||||
|
||||
## Unrecommended names
|
||||
- iter
|
||||
- dimname, dim_name etc.
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
# User documentation ¶
|
||||
|
||||
- [Frequently Asked Questions](./faq.md)
|
||||
- [Installing Laydi](./installing.md)
|
||||
- [Program help](./help.md)
|
||||
- [Terminology](./Terminology.md)
|
||||
|
||||
# Developer documentation
|
||||
|
||||
- [Developer tips and tricks](./development/hints.md)
|
||||
- [Fluents CSV file format description.](./help/format/fcsv.md)
|
||||
- [Naming conventions for variables and methods](./development/names.md)
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
# Frequently Asked Questions
|
||||
|
||||
## 1. General questions
|
||||
|
||||
### 1.1 What is Laydi?
|
||||
|
||||
Laidy is an acronym for look at your data interactively, and that is what the program is designed for. More specifically, bilinear analysis methods like principal component analysis (PCA) and partial least squares regression (PLS) are the two core methods used.
|
||||
|
||||
### 1.2 Could you rephrase that?
|
||||
|
||||
## 2. Usage
|
||||
|
||||
## 3. Internals and development
|
||||
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 25 KiB |
|
|
@ -0,0 +1,215 @@
|
|||
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||
<!-- Created with Inkscape (http://www.inkscape.org/) -->
|
||||
<svg
|
||||
xmlns:ns="http://creativecommons.org/ns#"
|
||||
xmlns:dc="http://purl.org/dc/elements/1.1/"
|
||||
xmlns:cc="http://web.resource.org/cc/"
|
||||
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
|
||||
xmlns:svg="http://www.w3.org/2000/svg"
|
||||
xmlns="http://www.w3.org/2000/svg"
|
||||
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
|
||||
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
|
||||
width="744.09448819"
|
||||
height="1052.3622047"
|
||||
id="svg2"
|
||||
sodipodi:version="0.32"
|
||||
inkscape:version="0.45.1"
|
||||
sodipodi:docname="gui-overview.svg"
|
||||
inkscape:output_extension="org.inkscape.output.svg.inkscape"
|
||||
sodipodi:docbase="/home/einarr/src/laydi/doc"
|
||||
inkscape:export-filename="/home/einarr/src/laydi/doc/gui-overview.png"
|
||||
inkscape:export-xdpi="115"
|
||||
inkscape:export-ydpi="115">
|
||||
<defs
|
||||
id="defs4">
|
||||
<inkscape:perspective
|
||||
sodipodi:type="inkscape:persp3d"
|
||||
inkscape:vp_x="0 : 526.18109 : 1"
|
||||
inkscape:vp_y="0 : 1000 : 0"
|
||||
inkscape:vp_z="744.09448 : 526.18109 : 1"
|
||||
inkscape:persp3d-origin="372.04724 : 350.78739 : 1"
|
||||
id="perspective10" />
|
||||
<filter
|
||||
inkscape:collect="always"
|
||||
x="-0.010937911"
|
||||
width="1.0218758"
|
||||
y="-0.25053026"
|
||||
height="1.5010605"
|
||||
id="filter3210">
|
||||
<feGaussianBlur
|
||||
inkscape:collect="always"
|
||||
stdDeviation="2.1921397"
|
||||
id="feGaussianBlur3212" />
|
||||
</filter>
|
||||
<filter
|
||||
inkscape:collect="always"
|
||||
id="filter3266">
|
||||
<feGaussianBlur
|
||||
inkscape:collect="always"
|
||||
stdDeviation="2.1921397"
|
||||
id="feGaussianBlur3268" />
|
||||
</filter>
|
||||
<filter
|
||||
inkscape:collect="always"
|
||||
id="filter3306">
|
||||
<feGaussianBlur
|
||||
inkscape:collect="always"
|
||||
stdDeviation="2.4541485"
|
||||
id="feGaussianBlur3308" />
|
||||
</filter>
|
||||
<filter
|
||||
inkscape:collect="always"
|
||||
id="filter3200">
|
||||
<feGaussianBlur
|
||||
inkscape:collect="always"
|
||||
stdDeviation="2.6375546"
|
||||
id="feGaussianBlur3202" />
|
||||
</filter>
|
||||
<filter
|
||||
inkscape:collect="always"
|
||||
id="filter3240">
|
||||
<feGaussianBlur
|
||||
inkscape:collect="always"
|
||||
stdDeviation="2.5502183"
|
||||
id="feGaussianBlur3242" />
|
||||
</filter>
|
||||
</defs>
|
||||
<sodipodi:namedview
|
||||
id="base"
|
||||
pagecolor="#ffffff"
|
||||
bordercolor="#666666"
|
||||
borderopacity="1.0"
|
||||
gridtolerance="10000"
|
||||
guidetolerance="10"
|
||||
objecttolerance="10"
|
||||
inkscape:pageopacity="0.0"
|
||||
inkscape:pageshadow="2"
|
||||
inkscape:zoom="1.4"
|
||||
inkscape:cx="472.59664"
|
||||
inkscape:cy="577.79368"
|
||||
inkscape:document-units="px"
|
||||
inkscape:current-layer="layer1"
|
||||
showgrid="false"
|
||||
inkscape:window-width="1280"
|
||||
inkscape:window-height="693"
|
||||
inkscape:window-x="0"
|
||||
inkscape:window-y="25">
|
||||
<inkscape:grid
|
||||
type="xygrid"
|
||||
id="grid3171" />
|
||||
</sodipodi:namedview>
|
||||
<metadata
|
||||
id="metadata7">
|
||||
<rdf:RDF>
|
||||
<ns:Work
|
||||
rdf:about="">
|
||||
<dc:format>image/svg+xml</dc:format>
|
||||
<dc:type
|
||||
rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
|
||||
</ns:Work>
|
||||
<cc:Work
|
||||
rdf:about="">
|
||||
<dc:format>image/svg+xml</dc:format>
|
||||
<dc:type
|
||||
rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
|
||||
</cc:Work>
|
||||
</rdf:RDF>
|
||||
</metadata>
|
||||
<g
|
||||
inkscape:label="Layer 1"
|
||||
inkscape:groupmode="layer"
|
||||
id="layer1">
|
||||
<rect
|
||||
style="fill:#e3e6ff;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
|
||||
id="rect2383"
|
||||
width="500"
|
||||
height="350"
|
||||
x="140"
|
||||
y="302.36218" />
|
||||
<rect
|
||||
style="fill:#eaf0ed;stroke:#000000;stroke-opacity:1;fill-opacity:1;filter:url(#filter3306)"
|
||||
id="rect3163"
|
||||
width="480"
|
||||
height="80"
|
||||
x="150"
|
||||
y="562.36218" />
|
||||
<rect
|
||||
style="fill:#eaf0ed;stroke:#000000;stroke-opacity:1;fill-opacity:1;filter:url(#filter3200)"
|
||||
id="rect3165"
|
||||
width="90"
|
||||
height="210"
|
||||
x="150"
|
||||
y="342.36218" />
|
||||
<rect
|
||||
style="fill:#eaf0ed;stroke:#000000;stroke-opacity:1;fill-opacity:1;filter:url(#filter3240)"
|
||||
id="rect3167"
|
||||
width="80"
|
||||
height="210"
|
||||
x="550"
|
||||
y="342.36218" />
|
||||
<rect
|
||||
style="fill:#eaf0ed;stroke:#000000;stroke-opacity:1;fill-opacity:1;filter:url(#filter3266)"
|
||||
id="rect3169"
|
||||
width="290"
|
||||
height="210"
|
||||
x="250"
|
||||
y="342.36218" />
|
||||
<rect
|
||||
style="fill:#eaf0ed;stroke:#000000;stroke-opacity:1;fill-opacity:1;filter:url(#filter3210)"
|
||||
id="rect3173"
|
||||
width="480"
|
||||
height="20"
|
||||
x="150"
|
||||
y="312.36218" />
|
||||
<text
|
||||
xml:space="preserve"
|
||||
style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans"
|
||||
x="336.85547"
|
||||
y="326.83582"
|
||||
id="text3175"><tspan
|
||||
sodipodi:role="line"
|
||||
id="tspan3177"
|
||||
x="336.85547"
|
||||
y="326.83582">Menus & Toolbars</tspan></text>
|
||||
<text
|
||||
xml:space="preserve"
|
||||
style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans"
|
||||
x="562.50488"
|
||||
y="362.36218"
|
||||
id="text3179"><tspan
|
||||
sodipodi:role="line"
|
||||
id="tspan3181"
|
||||
x="562.50488"
|
||||
y="362.36218">Workflow</tspan></text>
|
||||
<text
|
||||
xml:space="preserve"
|
||||
style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans"
|
||||
x="165.0498"
|
||||
y="362.36218"
|
||||
id="text3187"><tspan
|
||||
sodipodi:role="line"
|
||||
id="tspan3189"
|
||||
x="165.0498"
|
||||
y="362.36218">Navigator</tspan></text>
|
||||
<text
|
||||
xml:space="preserve"
|
||||
style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans"
|
||||
x="380.26953"
|
||||
y="442.36218"
|
||||
id="text3191"><tspan
|
||||
sodipodi:role="line"
|
||||
id="tspan3193"
|
||||
x="380.26953"
|
||||
y="442.36218">Plots</tspan></text>
|
||||
<text
|
||||
xml:space="preserve"
|
||||
style="font-size:12px;font-style:normal;font-weight:normal;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;font-family:Bitstream Vera Sans"
|
||||
x="303.29297"
|
||||
y="602.36218"
|
||||
id="text3195"><tspan
|
||||
sodipodi:role="line"
|
||||
id="tspan3197"
|
||||
x="303.29297"
|
||||
y="602.36218">Log, Selections & Extensions</tspan></text>
|
||||
</g>
|
||||
</svg>
|
||||
|
After Width: | Height: | Size: 7.0 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 6.3 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 116 KiB |
|
|
@ -0,0 +1,11 @@
|
|||
# Fluents help index ¶
|
||||
|
||||
- [Invocation and command line parameters.](./help/cmdline.md)
|
||||
- [Configuration files and settings.](./help/config.md)
|
||||
- [Keyboard shortcuts.](./help/shortcuts.md)
|
||||
- [Fluents CSV file format description.](./help/format/fcsv.md)
|
||||
|
||||
## Functions
|
||||
|
||||
- [PCA](./tasks/PCA.md)
|
||||
- [PLS](./tasks/PLS.md)
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
Fluents takes the following command line options:
|
||||
| | |
|
||||
|----------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------|
|
||||
| `-h` or `--help` | Displays help index, which is probably more updated than what is documented on the web. |
|
||||
| `-l` or `--workflow-list` | Lists the available workflows. Available workflows must be in the workflows package and must load on your system. |
|
||||
| `-w workflow` or `--workflow=workflow` | Creates a new project using the given workflow. Use -l to get a list of workflows. The workflow parameter is the identifier of the workflow. |
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
# Configuration
|
||||
|
||||
Laydi reads configuration from two types of configuration files. The main configuration is read from `/etc/laydirc/` and `$HOME/.laydi`. The possible variables in this configuration are described in the section Laydi configuration below.
|
||||
|
||||
The other file is the settings file for the matplotlib plotting package that is used in Laydi. This package has a lot of settings on its own, and instead of incorporating it into the general laydi configuration file it is distributed as a separate `matplotlibrc` file with options suitable for use in Laydi.
|
||||
|
||||
## Laydi configuration
|
||||
|
||||
### Directories
|
||||
|
||||
#### datadir
|
||||
|
||||
datadir is a directory for datasets. There are helper functions that makes it easy for a workflow to load data from this directory.
|
||||
|
||||
#### cachedir
|
||||
|
||||
cachedir is a directory where laydi can write cached data at will.
|
||||
|
||||
#### workflowdir
|
||||
|
||||
workflowdir is a path of directories where Laydi should look for workflows. When Laydi is started the `-w ''workflow''` option, these are the directories that will be searched for workflows. Note that *all* directories in `workflowdir` are added to the python path. If you add your own workflow directory, make sure that no files in the directory interfere with Laydi modules or standard Python modules.
|
||||
|
||||
## Matplotlib configuration
|
||||
|
||||
Matplotlib is configured with a matplotlib configuration file included with laydi. Documentation for the various options are included as comments in the file itself.
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
# Fluents Comma Separated Values file format description
|
||||
|
||||
This is the documentation of the textual (and primary) Fluents data file format. The other way to store a dataset is as a pickled Dataset object. The main differences between these methods are:
|
||||
|
||||
- Text based file formats are easier to read, easier to browse throgh, running commands on etc.
|
||||
- Text based files are better suited for svn.
|
||||
- Picled files are faster.
|
||||
|
||||
## File headers
|
||||
|
||||
Header lines must begin on the first line in the file. Header lines are of the form:
|
||||
|
||||
```
|
||||
# keyword : value
|
||||
#keyword:value
|
||||
# keyword :value
|
||||
```
|
||||
|
||||
Where an optional number of whitespace characters can be put between the different units on the line. The # sign at the start of the line is a traditional UNIX comment sign, and makes it easier for other programs to ignore those lines.
|
||||
|
|
@ -0,0 +1,20 @@
|
|||
Keyboard shortcuts in Fluents, written in Emacs syntax. I.e. C-x means "press control and x". Equivalently M-x is "meta x".
|
||||
|
||||
## Main:
|
||||
|
||||
| | |
|
||||
|----------|-----------------------------------------------------------------|
|
||||
| C-+ | Show only current plot. |
|
||||
| C-- | Show four plots. |
|
||||
| C-arrows | Move focus between views. |
|
||||
| C-n | Create new project. This brings up a workflow selection window. |
|
||||
| C-q | Quit |
|
||||
| M-l | Activate "Log" tab. |
|
||||
| M-s | Activate "Selections" tab. |
|
||||
|
||||
## Selections:
|
||||
|
||||
| | |
|
||||
|---------|--------------|
|
||||
| shift | Union |
|
||||
| control | Intersection |
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
# Principal Component Analysis
|
||||
|
||||
The principal component analysis (PCA) task.
|
||||
|
||||
## Input
|
||||
|
||||
## Options
|
||||
|
||||
## Output
|
||||
|
||||
- Score matrix
|
||||
- Loadings matrix
|
||||
|
||||
## Plots
|
||||
|
||||
- Score plot
|
||||
- Loadings plot
|
||||
- Profiles
|
||||
|
|
@ -0,0 +1,23 @@
|
|||
# Principal Component Analysis
|
||||
|
||||
The principal component analysis (PCA) task.
|
||||
|
||||
## Input
|
||||
|
||||
- X
|
||||
- Y
|
||||
|
||||
## Options
|
||||
|
||||
|
||||
## Output
|
||||
|
||||
- Score matrix
|
||||
- Loadings matrix
|
||||
|
||||
## Plots
|
||||
|
||||
- Score plot
|
||||
- X loadings plot
|
||||
- Y loadings plot
|
||||
- Profiles
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
# Installing Laydi
|
||||
|
||||
Installing Laydi is (by far) easiest on computers running [Ubuntu](https://www.ubuntu.com/) or [Debian](https://www.debian.org/) because that is what we use when developing it, and hence it is where the program is best tested.
|
||||
|
||||
## Requirements
|
||||
|
||||
## Subversion checkout
|
||||
|
|
@ -0,0 +1,280 @@
|
|||
```
|
||||
GNU GENERAL PUBLIC LICENSE
|
||||
Version 2, June 1991
|
||||
|
||||
Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
|
||||
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
|
||||
Everyone is permitted to copy and distribute verbatim copies
|
||||
of this license document, but changing it is not allowed.
|
||||
|
||||
Preamble
|
||||
|
||||
The licenses for most software are designed to take away your
|
||||
freedom to share and change it. By contrast, the GNU General Public
|
||||
License is intended to guarantee your freedom to share and change free
|
||||
software--to make sure the software is free for all its users. This
|
||||
General Public License applies to most of the Free Software
|
||||
Foundation's software and to any other program whose authors commit to
|
||||
using it. (Some other Free Software Foundation software is covered by
|
||||
the GNU Lesser General Public License instead.) You can apply it to
|
||||
your programs, too.
|
||||
|
||||
When we speak of free software, we are referring to freedom, not
|
||||
price. Our General Public Licenses are designed to make sure that you
|
||||
have the freedom to distribute copies of free software (and charge for
|
||||
this service if you wish), that you receive source code or can get it
|
||||
if you want it, that you can change the software or use pieces of it
|
||||
in new free programs; and that you know you can do these things.
|
||||
|
||||
To protect your rights, we need to make restrictions that forbid
|
||||
anyone to deny you these rights or to ask you to surrender the rights.
|
||||
These restrictions translate to certain responsibilities for you if you
|
||||
distribute copies of the software, or if you modify it.
|
||||
|
||||
For example, if you distribute copies of such a program, whether
|
||||
gratis or for a fee, you must give the recipients all the rights that
|
||||
you have. You must make sure that they, too, receive or can get the
|
||||
source code. And you must show them these terms so they know their
|
||||
rights.
|
||||
|
||||
We protect your rights with two steps: (1) copyright the software, and
|
||||
(2) offer you this license which gives you legal permission to copy,
|
||||
distribute and/or modify the software.
|
||||
|
||||
Also, for each author's protection and ours, we want to make certain
|
||||
that everyone understands that there is no warranty for this free
|
||||
software. If the software is modified by someone else and passed on, we
|
||||
want its recipients to know that what they have is not the original, so
|
||||
that any problems introduced by others will not reflect on the original
|
||||
authors' reputations.
|
||||
|
||||
Finally, any free program is threatened constantly by software
|
||||
patents. We wish to avoid the danger that redistributors of a free
|
||||
program will individually obtain patent licenses, in effect making the
|
||||
program proprietary. To prevent this, we have made it clear that any
|
||||
patent must be licensed for everyone's free use or not licensed at all.
|
||||
|
||||
The precise terms and conditions for copying, distribution and
|
||||
modification follow.
|
||||
|
||||
GNU GENERAL PUBLIC LICENSE
|
||||
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
|
||||
|
||||
0. This License applies to any program or other work which contains
|
||||
a notice placed by the copyright holder saying it may be distributed
|
||||
under the terms of this General Public License. The "Program", below,
|
||||
refers to any such program or work, and a "work based on the Program"
|
||||
means either the Program or any derivative work under copyright law:
|
||||
that is to say, a work containing the Program or a portion of it,
|
||||
either verbatim or with modifications and/or translated into another
|
||||
language. (Hereinafter, translation is included without limitation in
|
||||
the term "modification".) Each licensee is addressed as "you".
|
||||
|
||||
Activities other than copying, distribution and modification are not
|
||||
covered by this License; they are outside its scope. The act of
|
||||
running the Program is not restricted, and the output from the Program
|
||||
is covered only if its contents constitute a work based on the
|
||||
Program (independent of having been made by running the Program).
|
||||
Whether that is true depends on what the Program does.
|
||||
|
||||
1. You may copy and distribute verbatim copies of the Program's
|
||||
source code as you receive it, in any medium, provided that you
|
||||
conspicuously and appropriately publish on each copy an appropriate
|
||||
copyright notice and disclaimer of warranty; keep intact all the
|
||||
notices that refer to this License and to the absence of any warranty;
|
||||
and give any other recipients of the Program a copy of this License
|
||||
along with the Program.
|
||||
|
||||
You may charge a fee for the physical act of transferring a copy, and
|
||||
you may at your option offer warranty protection in exchange for a fee.
|
||||
|
||||
2. You may modify your copy or copies of the Program or any portion
|
||||
of it, thus forming a work based on the Program, and copy and
|
||||
distribute such modifications or work under the terms of Section 1
|
||||
above, provided that you also meet all of these conditions:
|
||||
|
||||
a) You must cause the modified files to carry prominent notices
|
||||
stating that you changed the files and the date of any change.
|
||||
|
||||
b) You must cause any work that you distribute or publish, that in
|
||||
whole or in part contains or is derived from the Program or any
|
||||
part thereof, to be licensed as a whole at no charge to all third
|
||||
parties under the terms of this License.
|
||||
|
||||
c) If the modified program normally reads commands interactively
|
||||
when run, you must cause it, when started running for such
|
||||
interactive use in the most ordinary way, to print or display an
|
||||
announcement including an appropriate copyright notice and a
|
||||
notice that there is no warranty (or else, saying that you provide
|
||||
a warranty) and that users may redistribute the program under
|
||||
these conditions, and telling the user how to view a copy of this
|
||||
License. (Exception: if the Program itself is interactive but
|
||||
does not normally print such an announcement, your work based on
|
||||
the Program is not required to print an announcement.)
|
||||
|
||||
These requirements apply to the modified work as a whole. If
|
||||
identifiable sections of that work are not derived from the Program,
|
||||
and can be reasonably considered independent and separate works in
|
||||
themselves, then this License, and its terms, do not apply to those
|
||||
sections when you distribute them as separate works. But when you
|
||||
distribute the same sections as part of a whole which is a work based
|
||||
on the Program, the distribution of the whole must be on the terms of
|
||||
this License, whose permissions for other licensees extend to the
|
||||
entire whole, and thus to each and every part regardless of who wrote it.
|
||||
|
||||
Thus, it is not the intent of this section to claim rights or contest
|
||||
your rights to work written entirely by you; rather, the intent is to
|
||||
exercise the right to control the distribution of derivative or
|
||||
collective works based on the Program.
|
||||
|
||||
In addition, mere aggregation of another work not based on the Program
|
||||
with the Program (or with a work based on the Program) on a volume of
|
||||
a storage or distribution medium does not bring the other work under
|
||||
the scope of this License.
|
||||
|
||||
3. You may copy and distribute the Program (or a work based on it,
|
||||
under Section 2) in object code or executable form under the terms of
|
||||
Sections 1 and 2 above provided that you also do one of the following:
|
||||
|
||||
a) Accompany it with the complete corresponding machine-readable
|
||||
source code, which must be distributed under the terms of Sections
|
||||
1 and 2 above on a medium customarily used for software interchange; or,
|
||||
|
||||
b) Accompany it with a written offer, valid for at least three
|
||||
years, to give any third party, for a charge no more than your
|
||||
cost of physically performing source distribution, a complete
|
||||
machine-readable copy of the corresponding source code, to be
|
||||
distributed under the terms of Sections 1 and 2 above on a medium
|
||||
customarily used for software interchange; or,
|
||||
|
||||
c) Accompany it with the information you received as to the offer
|
||||
to distribute corresponding source code. (This alternative is
|
||||
allowed only for noncommercial distribution and only if you
|
||||
received the program in object code or executable form with such
|
||||
an offer, in accord with Subsection b above.)
|
||||
|
||||
The source code for a work means the preferred form of the work for
|
||||
making modifications to it. For an executable work, complete source
|
||||
code means all the source code for all modules it contains, plus any
|
||||
associated interface definition files, plus the scripts used to
|
||||
control compilation and installation of the executable. However, as a
|
||||
special exception, the source code distributed need not include
|
||||
anything that is normally distributed (in either source or binary
|
||||
form) with the major components (compiler, kernel, and so on) of the
|
||||
operating system on which the executable runs, unless that component
|
||||
itself accompanies the executable.
|
||||
|
||||
If distribution of executable or object code is made by offering
|
||||
access to copy from a designated place, then offering equivalent
|
||||
access to copy the source code from the same place counts as
|
||||
distribution of the source code, even though third parties are not
|
||||
compelled to copy the source along with the object code.
|
||||
|
||||
4. You may not copy, modify, sublicense, or distribute the Program
|
||||
except as expressly provided under this License. Any attempt
|
||||
otherwise to copy, modify, sublicense or distribute the Program is
|
||||
void, and will automatically terminate your rights under this License.
|
||||
However, parties who have received copies, or rights, from you under
|
||||
this License will not have their licenses terminated so long as such
|
||||
parties remain in full compliance.
|
||||
|
||||
5. You are not required to accept this License, since you have not
|
||||
signed it. However, nothing else grants you permission to modify or
|
||||
distribute the Program or its derivative works. These actions are
|
||||
prohibited by law if you do not accept this License. Therefore, by
|
||||
modifying or distributing the Program (or any work based on the
|
||||
Program), you indicate your acceptance of this License to do so, and
|
||||
all its terms and conditions for copying, distributing or modifying
|
||||
the Program or works based on it.
|
||||
|
||||
6. Each time you redistribute the Program (or any work based on the
|
||||
Program), the recipient automatically receives a license from the
|
||||
original licensor to copy, distribute or modify the Program subject to
|
||||
these terms and conditions. You may not impose any further
|
||||
restrictions on the recipients' exercise of the rights granted herein.
|
||||
You are not responsible for enforcing compliance by third parties to
|
||||
this License.
|
||||
|
||||
7. If, as a consequence of a court judgment or allegation of patent
|
||||
infringement or for any other reason (not limited to patent issues),
|
||||
conditions are imposed on you (whether by court order, agreement or
|
||||
otherwise) that contradict the conditions of this License, they do not
|
||||
excuse you from the conditions of this License. If you cannot
|
||||
distribute so as to satisfy simultaneously your obligations under this
|
||||
License and any other pertinent obligations, then as a consequence you
|
||||
may not distribute the Program at all. For example, if a patent
|
||||
license would not permit royalty-free redistribution of the Program by
|
||||
all those who receive copies directly or indirectly through you, then
|
||||
the only way you could satisfy both it and this License would be to
|
||||
refrain entirely from distribution of the Program.
|
||||
|
||||
If any portion of this section is held invalid or unenforceable under
|
||||
any particular circumstance, the balance of the section is intended to
|
||||
apply and the section as a whole is intended to apply in other
|
||||
circumstances.
|
||||
|
||||
It is not the purpose of this section to induce you to infringe any
|
||||
patents or other property right claims or to contest validity of any
|
||||
such claims; this section has the sole purpose of protecting the
|
||||
integrity of the free software distribution system, which is
|
||||
implemented by public license practices. Many people have made
|
||||
generous contributions to the wide range of software distributed
|
||||
through that system in reliance on consistent application of that
|
||||
system; it is up to the author/donor to decide if he or she is willing
|
||||
to distribute software through any other system and a licensee cannot
|
||||
impose that choice.
|
||||
|
||||
This section is intended to make thoroughly clear what is believed to
|
||||
be a consequence of the rest of this License.
|
||||
|
||||
8. If the distribution and/or use of the Program is restricted in
|
||||
certain countries either by patents or by copyrighted interfaces, the
|
||||
original copyright holder who places the Program under this License
|
||||
may add an explicit geographical distribution limitation excluding
|
||||
those countries, so that distribution is permitted only in or among
|
||||
countries not thus excluded. In such case, this License incorporates
|
||||
the limitation as if written in the body of this License.
|
||||
|
||||
9. The Free Software Foundation may publish revised and/or new versions
|
||||
of the General Public License from time to time. Such new versions will
|
||||
be similar in spirit to the present version, but may differ in detail to
|
||||
address new problems or concerns.
|
||||
|
||||
Each version is given a distinguishing version number. If the Program
|
||||
specifies a version number of this License which applies to it and "any
|
||||
later version", you have the option of following the terms and conditions
|
||||
either of that version or of any later version published by the Free
|
||||
Software Foundation. If the Program does not specify a version number of
|
||||
this License, you may choose any version ever published by the Free Software
|
||||
Foundation.
|
||||
|
||||
10. If you wish to incorporate parts of the Program into other free
|
||||
programs whose distribution conditions are different, write to the author
|
||||
to ask for permission. For software which is copyrighted by the Free
|
||||
Software Foundation, write to the Free Software Foundation; we sometimes
|
||||
make exceptions for this. Our decision will be guided by the two goals
|
||||
of preserving the free status of all derivatives of our free software and
|
||||
of promoting the sharing and reuse of software generally.
|
||||
|
||||
NO WARRANTY
|
||||
|
||||
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
|
||||
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
|
||||
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
|
||||
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
|
||||
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
|
||||
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
|
||||
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
|
||||
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
|
||||
REPAIR OR CORRECTION.
|
||||
|
||||
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
||||
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
|
||||
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
|
||||
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
|
||||
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
|
||||
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
|
||||
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
|
||||
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
|
||||
POSSIBILITY OF SUCH DAMAGES.
|
||||
```
|
||||
|
|
@ -0,0 +1 @@
|
|||
# Principal Component Analysis
|
||||
|
|
@ -0,0 +1 @@
|
|||
# Partial Least Squares Regression
|
||||
Loading…
Reference in New Issue