# Version Control

The table describes the changes that have been made to InVivoStat since the first release in 2010. Earlier versions of InVivoStat are available upon request from invivostat@hotmail.co.uk.

Version number |
Date |
Description of change |

1.1 | 17/02/2010 | Initial version |

1.2 | 16/07/2010 | Initial website version |

1.3 | 01/09/2010 | Inclusion of Nested Design Analysis module |

Inclusion of Paired t-test/within-subject Analysis module | ||

Inclusion of Incomplete Factorial Parametric Analysis module | ||

Bug fix: if the user defines an X-axis title then it is not included in the plot | ||

Bug fix: to stop InVivoStat crashing when running complex operations | ||

Additional functionality: Allow dataset entries to include + and – symbols | ||

Additional functionality: Rank transformation added to list of transformations | ||

Non-parametric Analysis module: Dialogue to include “Mann-Whitney” as well as “Kruskal-Wallis” | ||

Bug fix: Improvements to Excel data import | ||

Non-parametric Analysis module: Warning messages to only include ‘Mann-Whitney’ rather than ‘Wilcoxon’ to tie in with interface | ||

Power Analysis module: Rename ‘MS error’ to ‘MS residual’ to tie in with the rest of InVivoStat | ||

Additional functionality: Inclusion of Normal probability plot in Summary Statistics module | ||

Inclusion of Unpaired t-test Analysis module | ||

Single and Repeated Measures Parametric Analysis modules: QQ plot title changed to Normal probability plot to tie in with interface | ||

Repeated Measures Parametric Analysis Module: ‘Animal’ label on GUI replaced with the more general ‘Subject’ label | ||

1.4 | 01/03/2011 | Bug fix: In the Repeated Measures Parametric Analysis module Overall Effects Table, the Lowest p-value is not formatted properly |

Additional functionality: In the Repeated Measures Parametric Analysis module no analysis performed if Animal factor level has replication of 1 | ||

Repeated Measures Parametric Analysis Module: Decision to use the within-animal variability when Studentising the residuals that are used in the predicted vs. Residuals plot | ||

Bug fix: Trailing spaces in variable names causes analyses to fall over | ||

For consistency, all p-values formatted to 3 decimal places | ||

Bug fix: Tukey’s test in Single Measures Parametric Analysis module does not give unique results due to a random seed (seed now fixed) | ||

2.0 | 19/07/2011 | Bug fix: Problem with user defined formulas involving brackets |

Additional functionality: Ability to print analysed data in the output | ||

2.1 | 01/08/2011 | Bug fix: In the Single and Repeated Measures Parametric Analysis module, if the covariate has a zero value and the covariate is log transformed, the analysis stops. |

Bug fix: When plotting two continuous variables (in the Graphics module or as part of the output when fitting a covariate in Single and Repeated Measures modules) if all the x-axis values in one group are the same then the slope is infinite and InVivoStat halts. | ||

2.2 | 13/10/2011 | Bug fix: In the Non-parametric Analysis module, the treatment group labels in the all pairwise comparisons table were not always correct |

Inclusion of Fishers Exact and Chi-squared tests module | ||

Additional functionality: all means and differences to be quoted to 3 decimal places | ||

Bug fix: Warning message about missing data incorrectly generated when log transformation applied to the covariate | ||

2.3 | 13/03/2012 | Inclusion of R-runner module |

Change to interfaces to make them consistent across modules | ||

Bug fix: Change to Unpaired t-test as the analysis does not proceeded if the response variable is called “Response” in the dataset | ||

2.4 | 07/08/2012 | Inclusion of Correlation module |

Inclusion of Survival Analysis module | ||

Additional functionality: Update to Excel reader | ||

Update to Nested Design Analysis interface (Effects now called Factors) | ||

2.5 | 26/11/2013 | Additional functionality to all modules: ability to create black and white plots |

Additional functionality to all modules: ability to create pdf versions of the plots | ||

Bug fix: Remove limit of 2 decimal place format of data printout in Output window | ||

Bug fix: In Single Measures Parametric Analysis module, drop Planned Comparisons terminology from LSD tests | ||

Bug fix: Align y-axis on the Predicted vs. residual plots | ||

Bug fix: Align all p-values to 4 decimal places | ||

3.0 | 14/08/2015 | Additional functionality: Update all plots to use the GGPlot2 R graphics package |

Additional functionality: Allow user to manipulate appearance of graphics using a new interface | ||

Additional functionality: Allow user to manipulate various global parameters and output options | ||

Additional functionality: Graphics Module – for the scatterplot replace “correlation and p-value” with “Horizontal jitter”. The former now appear automatically. | ||

Bug fix: Align quartile definition Q1 and Q3 across all modules | ||

Additional functionality: User has ability to change plot size | ||

Additional functionality: Repeated measures module, add ability to choose the Selected Effect | ||

Additional functionality: Single and Repeated Measures Parametric Analysis module – ability to choose any model term as the Selected Effect | ||

Additional functionality: Single and Repeated Measures Parametric Analysis module – addition of the LSMeans package so that means are adjusted for blocking factors | ||

Update: For Repeated Measures Parametric Analysis module, use partial (Type III) sums of squares rather than marginal (Type I) to align with other modules | ||

Inclusion of new Multivariate Analysis module (results not verified) | ||

Additional functionality: Ability to import dataset of p-values, generated using the Single and Repeated Measures Parametric Analysis modules, into the P-value adjustment module | ||

Additional functionality: Repeated Measures Parametric Analysis module – following log transformation ability to generate the geometric means and ratios between the means | ||

Additional functionality: Single Measures Parametric Analysis module – following log transformation ability to generate the geometric means and ratios between the means | ||

Additional functionality: Single Measures Parametric Analysis module – If making comparisons back to control, ability to plot the differences from control + 95% CI | ||

Additional functionality: Single and Repeated Measures Parametric Analysis module – Ability to test the treatment by covariate interaction formally rather than just via a plot | ||

Additional functionality: Single and Repeated Measures Parametric Analysis module – Ability to generate the covariate regression coefficient | ||

Update to R V3 | ||

Bug fix: Rename the Predicted vs. residuals plot as the Residuals vs. predicted plot | ||

Bug fix: Update to css file so that background output is always white | ||

Additional functionality: Fishers and Chi-squared test module – Include the Barnard’s test (alternative to Fishers) | ||

3.1 | 23/10/2015 | Bug fix: Change to model parameterisation to correct p-values in the ‘Table of overall tests of model effects’ table in Repeated Measures Parametric Analysis module. |

3.2 | 26/11/2015 | Bug fix: Case selection conditions with re-ordered data corrected |

Additional functionality: Regression lines extend to ends of plot window | ||

Additional functionality: Random seed fixed so that random jitter on plots is consistent across repeated runs | ||

Additional functionality: Difference with 95% confidence interval included in Paired and Unpaired t-test modules | ||

Additional functionality: Output Options GUI re-organised | ||

3.3 | 07/01/2016 | Update to installer |

3.4 | 19/01/2016 | Bug fix: to allow spaces in % changes list in the Power Analysis module and user-defined equation start values in the Dose-Response module |

3.5 | 05/09/2016 | Clarification to Summary stats output: QQplot not adjusted for categorical factors |

Bug fix: Issue with variable length in Dose response module | ||

Output update: Covariate descriptive text amended | ||

Additional functionality: Ability to have continental Windows setup | ||

Interface update: Graphics module Y-axis title relabelled as Response variable | ||

3.6 | 02/02/2017 | Output update: P-value adjustment module to include contrast labels |

3.7 | 14/07/2017 | Update to improve reliability of installation process |

4.0 | 13/02/2020 | Non-parametric Analysis module: Inclusion of Freidman’s test and the Wilcoxon Rank Sum test |

Graphics module: Ability to include labels on scatterplots | ||

Single Measures Parametric Analysis module: Add coefficients from the model if requested | ||

All modules: Inclusion of analysis options at the end of the output | ||

Single and Repeated Measures Parametric Analysis modules: Change label in ANOVA from ‘Residuals’ to ‘Residual’ | ||

One sample t-test module: New module created to perform the one sample t-test | ||

Graphics module: Ability to fit spec line for all plots | ||

Graphics and Non-parametric Analysis modules: Ability to vary transparency of fill of bars/boxes | ||

Power Analysis modules: One-way ANOVA power analysis module added | ||

Correlation Analysis module bug fix: If the dataset contains a ‘y’ variable, then the analysis fails as it internally uses a ‘y’ variable. Update to remove the internal y variable | ||

All modules: Generation of .PNG plots instead of .JPG plots to improve quality | ||

Graphics and correlation modules: Generation of correlation coefficient and p-value which were missing when x-axis contained two distinct values | ||

All modules bug fix: Print of raw data that contains only variables included in the analysis | ||

MVA analysis module: Module validated | ||

Graphics module: Ability to control categorised factor levels on plots | ||

All modules: Ability to have ‘?’ in variable name | ||

Summary Statistics module: %CV now positive when mean is negative | ||

Correlation Analysis module: Update to matrix plot axis range to make them more sensible | ||

All modules: Ability to generate a pdf of the output | ||

Bug fix: Correction to code to deal with p<0.0001 in output | ||

Non-parametric Analysis module: Information about continuity correction and whether tests are exact or asymptotic | ||

Non-parametric Analysis module: Exact tests used when there are no ties in the data and sample size if less than 50 | ||

All parametric modules: Ability to include multiple covariates in the statistical model | ||

All parametric modules: Alignment of statistical models when interactions are selected | ||

Bug fix in T-test modules: Title on Predicted Means plot corrected – Confidence interval title fixed at 95% | ||

Single Measures Parametric Analysis module: Remove line connecting means from Predicted Means plot by default (ability to switch on in options tab) | ||

Paired t-test module: Addition of ability to define control group (to compare back to) | ||

Unpaired t-test module: Addition of ability to define control group (to compare back to) | ||

Paired t-test module: Inclusion of plot comparing one response to the other (paired t-test only) | ||

Graphics module: removal of default line comparing means in line plot of means with SEM | ||

Graphics module: Removal of box around symbol in legend | ||

Graphics module: Ability to fit a spec line in all plots | ||

Graphics module: Ability to change ordering of levels in categorical x-axis and categorical factors | ||

Ability to use InVivoStat on a max and linux platform | ||

Ability to generate a pdf of all plots in output | ||

4.0.1 | 13/02/2020 | Bug fix to allow use on computer with continental European regional settings |

4.0.2 | 18/03/2020 | Bug fix to allow control group names to have spaces |

Change pdf output to a more flexible HTML format | ||

Update to R version 3.6 so that all packages can be installed (solves issue with Repeated Measures Analysis module) | ||

4.1 | 13/07/2020 | Graphics module: Legend included on the case profiles plot |

Interface update: Removal of redundant post-hoc test option in unpaired t-test module | ||

New module to perform logistic regression | ||

Bug fix: When displaying back transformed pairwise comparisons (following log transformation) the effect size column was labelled ‘Ratio’ rather than ‘Difference’ | ||

Bug fix: In the P-value adjustment module, when using an existing dataset that contains the unadjusted p-values, the headers were not selected correctly | ||

Bug fix: In the P-value adjustment module, p-values of the form p<0.001 were not analysed correctly | ||

Bug fix: Datasets containing commas were not imported correctly | ||

Mac edition: Update to instructions and R script for library installation | ||

4.2 | 08/04/2021 | New functionality: For repeated measures analyses, the AIC, BIC and log likelihood have been included to allow users to compare different correlation structures |

New functionality: A new module created to allow users to transform “short-fat” repeated measures datasets into the “long-thin” format required by InVivoStat’s repeated measures analysis tools | ||

New functionality: Back and Forward navigation arrows included on the InVivoStat interfaces | ||

New functionality: For all parametric modules, when the blocking factor has only one level, an error message is generated | ||

Bug fix: In Graphics module, legend containing Animal ID’s can now be included on the case profiles plot | ||

New functionality: In Graphics module, new functionality to allow users to plot confidence intervals or standard errors in the means with error bar plots | ||

New functionality: A new module to generate the Area Under Curve (AUC) summary measure for repeatedly measured responses. Original data can be in either long-thin or short-fat formats | ||

Bug fix: the incorrect error bars that appear underneath the columns on the Means with Error bar plots have now been removed | ||

New functionality: Plot axis titles reflect any transformation applied to the variables | ||

Bug fix: When data is log transformed, for SMPA the plot of pairwise comparisons y-axis label changed to “Ratio of geometric means” rather than “Difference of geometric means” | ||

Update: When data is log transformed, p-values now included in table of back transformed ratio of the geometric means in Single Measures, Repeated Measures Parametric Analysis modules, Paired and unpaired t-test modules | ||

Update: When the log transformation is used, the mean column in the table of back-transformed means has been renamed to “Geometric Mean” | ||

Update: For Single Measures and Repeated Measures Parametric Analysis modules, the order of output has been changed so that table of predicted means is presented before the corresponding plot | ||

Update to output options: User can choose to display back-transformed geometric means with or without the log transformed results | ||

Update: The user output option to change the angle of the labels is not applied to the x-axis and y-axis labels on the diagnostic plots |