A blog about free research software, alternative to commercial paid software.

One way to help people is to share your knowledge with those who could benefit from it. As a researcher , constant effort to solve scientific problems have exposed me to various scientific resources that can be accessed free of charge. Especially these knowledge is useful to labs and institution unable to access expensive software or novice users due to lack of expertise. In this blog, I have provided a comprehensive list of freely available softwares, alternative to commercial software. I shall share with you all that I have learned, as I make the changes or learn something new, I shall document them. Hope this blog will help those finding the way………….

Research software and books

Showing posts with label Statistics. Show all posts
Showing posts with label Statistics. Show all posts

Dec 25, 2010

Linear regression using Excel

To do advanced statistics in excel you have to make sure that Analysis Toolpak Add-in is installed. Assuming that it is not installed,the following needs to be done;

  • Run Microsoft Office Setup to add components to MS Office
  • Select Analysis Toolpak under the Excel group of software items.
  • Once this is done
  • Run Excel
  • Select Addins in the tool menu. ( In EXCEL 2007 Add-ins tab is in the excel option dialogue box). In the dialogue box select Analysis Toolpak and then click on the OK button.
Now you have an extra command, Data analysis on the Tools Menu and you can do the statistics.To do advanced statistics in excel you have to make sure that Analysis Toolpak Add-in is installed. Assuming that it is not installed,the following needs to be done;

  • Run Microsoft Office Setup to add components to MS Office
  • Select Analysis Toolpak under the Excel group of software items.
          Once this is done
  • Run Excel

Select Addins in the tool menu. ( In EXCEL 2007 Add-ins tab is in the excel option dialogue box). In the dialogue box select Analysis Toolpak and then click on the OK button.

Now you have an extra command, Data analysis on the Tools Menu and you can do the statistics.


Linear, non-weighted regression


Type your data into blank excel spread sheet.




Now select the data analysis command on the tools menu (Data menu in excel 2007). This will give you dialogue box as shown below, listing all the data analysis facilities that are available. Select Regression and click on the OK button. This will give you a dialogue box full of options.


 Place the cursor in the input range control and then use the mouse to select on the spreadsheet the data you want to analyse. This should enter the appropriate cell reference in the control.
 

Label in first row check box tells the tool to use the labels in the top row of the data to label some of the statistical values. If you haven’t used labels leave this unticked.


  • Tick the confidence level check box and enter appropriate values.
  • Select the new worksheet ply.
  • Select residual plot.
  • Click on the OK button.

Excel will do all the calculation and present the results in a new ply.  Lets go through the results step by step:




The slope (m) is the X variable 1 in our case it is 7.05714 x 10-05 . However if you look along the row you will see 95% confidence limits on m- there is 0.95 probability that m lies between 5.85107E x 10 -05 and 8.26322E x 10-05 . The coefficient c in our equation of straight line is 0.002496 with upper and lower 95% confidence limits of 0.00069 and 0.00429.


Correlation coefficient

R = 0.9856. R represents how closely x variable and y variable vary together .

>> continue reading: Excel can also be used for non- linear regression analysis using the solver add in.



Dec 22, 2010

ANOVA with Excel

To do advanced statistics in excel you have to make sure that Analysis Toolpak Add-in is installed. Assuming that it is not installed,the following needs to be done;

  • Run Microsoft Office Setup to add components to MS Office
  • Select Analysis Toolpak under the Excel group of software items.

        Once this is done

  • Run Excel
  • Select Addins in the tool menu. ( In EXCEL 2007 Add-ins tab is in the excel option dialogue box)
  • In the dialogue box select Analysis Toolpak and then click on the OK button.

Now you have an extra command, Data analysis on the Tools Menu and you can do the statistics.

ANOVA

Type your data into blank spread sheet.

Now select the data analysis command on the tools menu (Data menu in excel 2007). This will give you dialogue box as shown below, listing all the data analysis facilities that are available.

Select Anova: Single Factor and clickon the OK button. This will give you a dialogue box full of options.

You have to tell the tool where the data are, where to put the analysis and select various options.

Place the cursor in the input range control and then use the mouse to select on the spreadsheet the data you want to analyse. This should enter the appropriate cell reference in the control.

Depending upon whether the data is grouped as columns or Rows click on the appropriate values.

Label in first row check box tells the tool to use the labels in the top row of the data to label some of the statistical values. If you haven’t used labels leave this unticked.

Alpha refers to critical probability . It makes hardly any difference to the analysis Simply adds to the table of results f statistics.

Select the new worksheet ply and type in appropriate label.

Click on the OK button.

Excel will do all the calculation and present the results in a new ply.



Summary in the table represents summary statistics separately for each column. Following this is table labeled Anova that contains figures used for the significance test.

The P value in the Anova table above which contains the probability that the three column means are due only to random variation is important for coming up with a final conclusion. All the values are intermediate statistics. In single factor Anova the variation categorized into different source. So there is variation owing to imprecision within the group and between the groups.

Between groups

This is the variation between group means. The first step is the sums of squares of deviation of group means from the overall mean (SS=0.0144). Further the table show mean squares (MS=0.00722) which is the sum of squares divided by degrees of freedom (df=2).

Within groups.

This is the variation within group. The sums of squares values is simply the total for each of the individual block sums of squared deviations (SS=0.676).Mean square (MS=0.045) is the sums of squares divided by degrees of freedom (df=15).

Total

Is the sum of squares values that you already have.

f statistic

This is the mean square ration of ‘between’ to ‘within’. If f is big then variation between groups is high compared with within groups. An f value of 1.0 is expected if there is no significant difference between group means.

P Value

This is the probability that the f value could have occurred because of random variation in the replicates. If P is below s chosen threshold (often 0.05), then you accept that there is different accuracy occurring between different sets of measurement . In the above test P = 0.85 which is greater than 0.05 so there is no significant difference between groups.

F crit

This is the critical f value. It is the f value that would give a P value of 0.05.





Dec 20, 2010

STATISTICS

Gnuplot

Gnuplot is a portable command-line driven graphing utility for linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow researchers and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986.Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types.
Website to download: http://www.gnuplot.info/

R

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed by researchers at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.


Website to Download: http://www.r-project.org/

GNU Octave


GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.

Website to Download:
http://www.gnu.org/software/octave/