# 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 |

4.10 | 26/04/2024 | Bug fix: Update to remove error in Single Measures Parametric Analysis module when response has missing data and user selects factors in an order that is different from the order they appear in the dataset. |

4.9 | 14/03/2024 | Version update: Update to categorisation colour palette |

Bug fix: Update to cluster analysis to allow user defined clustering and also variable standardisation as a default | ||

4.8 | 21/01/2023 | Minor update to installer |

4.7 | 09/12/2022 | Additional functionality: User now has the ability to investigate sample sizes when performing TOST equivalence tests |

Bug fix: In Linear regression module, model parameters now displayed to 2 decimal places | ||

Additional functionality: On the Linear Regression module, clarification that when fitting more complex models, the best-fit regression lines on the scatterplot are not related to the statistical model. | ||

Bug fix: In Repeated Measures module, conclusions not generated when log transformed applied but “geometric means not displayed” output option selected | ||

Bug fix: In Repeated Measures module, the term “Timezzz” has been removed from output when repeated factor is numeric | ||

4.6 | 24/08/2022 | Additional functionality: Allow missing values in continuous factors in the Linear Regression module |

Additional functionality: Inclusion of matrix correlation tables of results in the Correlation module | ||

Additional functionality: Inclusion of the sum summary statistic in the Summary Statistics module | ||

Bug fix: Removed labels from the normal probability plot (when “Display marker labels” has been selected) | ||

Bug fix: Printout of data in original order in the Graphics module | ||

4.5 | 15/06/2022 | Bug fix: Update to libraries for mac version to allow completion of repeated measures and paired t-test analyses |

4.4 | 15/03/2022 | Additional functionality: For the unpaired t-test, with unequal variance, the normal probability plot is presented separately for each treatment group |

Additional functionality: For the Equivalence test module the lower % change equivalence bound can now be numerically larger then the upper % change bound | ||

Additional functionality: Ability within the graphics module to control the X-axis and Y-axis ranges | ||

Additional functionality: Summary Statistics, categorised normal probability plot when categorical factors selected | ||

Bug fix: Update to Equivalence test code to avoid program crashing when % change is greater than 100% | ||

Bug fix: Update to the normal probability plot linear line to give a more accurate line | ||

Bug fix: Pairwise tests not generated in Single and Repeated Measures Analysis on the Mac OS. All versions updated to Version 4.1.2 of R | ||

4.3 | 18/11/2021 | Update: Ability to choose a significance level of 0.025 in the power analysis modules |

New functionality: Addition of a module to allow users to perform Two One-sided Equivalence tests (TOST) | ||

New functionality: Addition of the R-runner module to allow users to run their own R code within InVivoStat | ||

Bug fix: Across modules, conclusions when p<0.0001 was not always accurate | ||

Update: Error message generated in incomplete factorial module when user attempts to run an analysis with only one factor | ||

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 | ||

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 | ||

4.0.2 | 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) | ||

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

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 | ||

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

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

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 | ||

3.4 | 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 |

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

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 | ||

3.1 | 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. |

3.0 | 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) | ||

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 | ||

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) | ||

2.3 | 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 | ||

2.2 | 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 | ||

2.1 | 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. | ||

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

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

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) | ||

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 | ||

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

1.1 | 17/02/2010 | Initial version |