Canoco 5 Issues

This page lists the presently known issues with the actual release, followed by the issues fixed since the first release (5.00). Note that the issues reported here include both bugs (corresponding to incorrect software functionality) and features (software functionality that might be implemented in a more useful or easier-to-use way).

How to update to the latest Canoco version

To update your present Canoco 5 installation to the latest maintenance version, select the Help | Check for updates menu command and follow the instructions displayed in the dialog box. Please note that the trial versions, provided by Canoco distributor for evaluating the software cannot be updated.

Issues fixed and improvements added in version 5.10

  • Improvement [510-01]: When computing community-weighted means (CWM) of trait data, allow for pre-standardization of trait values to unit variance, including also an option for a weighted unit variance
  • Fixed bug [510-02]: changes in transformation during analysis setup, caused by clicking the "Re-advise" button, were not transferred properly to following steps, producing inconsitent results in multistep analysis, e.g. in variation partitioning
  • Improvement [510-03]: added a "Transpose compositional table" command into the Data | Add new table(s)submenu. Identity of new table' rows is that of the source table' columns. Transposed community table is needed to use the new double-constrained CA and double-constrained PCA templates.
  • Improvement [510-04]: added multiple analysis templates for the newly supported double-constrained CA (dc-CA) method. These templates are available whenever user submits four data table to New Analysis Wizard: community table, transposed community table, environmental data table, and species trait data table. One template expects the user to choose proper sets of environmental variables and functional traits to use, while the other offers interactive stepwise selection from both sets of predictors. Both templates also perform appropriate two-stage testing, combining tests based on CWM scores and on species responses to environmental variables. Additionally, two templates were added for testing individual constrained axes of dc-CA, one with the case-based permutation test, the other with the response-variable based permutation tests.
  • Improvement [510-05]: implemented a linear counterpart to dc-CA, namely dc-PCA, again with the same four versions (including stepwise selection of predictors from the two sets) as in the case of dc-CA.
  • Fixed bug [510-06]: use local decimal point separator when exporting results onto Clipboard or into text format files, as well as local list separator when exporting into files with CSV format. This new behaviour can be overriden, though, with a new option "Export data with local separator" at the Data Sheets | Actions page of the dialog box shown by the Edit | Settings | Canoco5 options menu command.
  • Fixed bug [510-07]: non-zero values were generated from zero values or missing (NA) values during the extended log(A*x+B) transformation, overflowing data storage for response data.
  • Improvement [510-08]: enabled stepwise selection of explanatory variables and overview of simple and conditional effects for a CCA method with active detrending.
  • Fixed bug [510-09]: when calculating NMDS or PCO (or db-RDA) on a compositional data table with preset centering/standardization by rows or columns, these operations were (incorrectly) applied to data before calculating distance matrix.
  • Improvement [510-10]: added Shepard diagram to NMDS analysis template, which is now shown (together with STRESS criterion value) in a dialog shown by the Details button in Summary page of the analysis notebook for the first (NMDS) step. The graph can be copied to the Clipboard.
  • Improvement [510-11]: Canoco 5 became A LITTLE more obtrusive towards its users and now checks on its start and it will inform *once* the user about new version availability. This would be done, however, for every separate user account on the computer where C5 is installed. If user skips a version (e.g. stays with 5.10 even after version 5.11 became available), the update about the existence of a new version is repeated for the following ones (e.g. when version 5.12 becomes available).
  • Improvement [510-12]: the corrections of significance (P) values now uses more appropriate penalty when testing, during stepwise selection or evaluation of simple and conditional effects, a factor, where only k-1 sensible tests are done for a factor with k levels. This reduction of penalty also extends to analysis-defined interaction terms, at least the simple ones.
  • Improvement [510-13]: percentages of explained variation for individual explanatory variables are now shown in the summary of simple and conditional effects with adaptive display precision (depending on how many small values are present) - with one to three decimal places for the percentage (0-100) scale.
  • Feature [510-14]: fill style can be now set for enclosing envelopes when editing global visual attributes (using the Edit | Settings | Visual attributes command).
  • Improvement [510-15]: added possibility to create - in a data table - new numeric variables representing together an interaction between one factor and one numeric variable. The new "Create numeric-factor interaction" command is available both from the Edit menu and from the context-sensitive popup menu.
  • Improvement [510-16]: Canoco 5.10 now warns with a (suppressable) message box when cases are omitted from the analysis due to their emptiness (CA/DCA/CCA methods but also some distance-based analysis cases).
  • Improvement [510-17]: added command to double-center (horizontally as well as vertically) selected label(s) in a graph. This is now offered both in context menu and in the Edit menu.
  • Improvement [510-18]: default export format is now CSV when exporting a data table.
  • Fixed bug [510-19]: CSV and TSV export now always presents missing value as "NA" and zero values as "0", rather than as an empty string.
  • Improvement [510-20]: Canoco 5.10 supports import of condensed data in a text format (CSV or TSV). Ordering and identity of rows and columns can be derived either from file codes (if they are integer values) or from optional files coding for row and/or column labels. Example files can be found in the Samples\ImportCondensedData folder.
  • Fixed bug [510-21]: the dialog box offering statistics to compute from a compositional data table did not update its offer when changing to another data table (if more than one was available within a project)
  • Improvement [510-22]: added alternative way to calculate "enclosing" ellipses for classes of objects; the new ones approximate 2D-Normal spread of positions, based on variance-covariance of X and Y coordinates, and display for the estimated bivariate Gaussian distribution either 95% or 66% confidence areas.
  • Improvement [510-23]: added two new analysis templates for Aitchison's weighted log-ratio PCA and its constrained form (log-ratio RDA)
  • Fixed bug [510-24]: tooltips for the choice of permutation test on the first constrained axis vs. on all constrained axes were swapped in the corresponding page of analysis setup wizard.
  • Improvement [510-25]: Canoco 5 adviser now gives more specific advices (in the ordination method page of the Analysis Setup Wizard) concerning the choice of ordination method for the usual unconstrained and constrained analyses. Most of changes happen for the case where - for a compositional response data table - test DCA can be calculated and the lengths of ordination axes (in SD units) estimated (but there is also an extension of advice for purely binary data, where the linear method is mentioned as an alternative). For intermediate and short gradients, the advice also depends on the percentage of zeros. For the case of short gradient and very few zero values, log-ratio analysis is suggested as a viable alternative to a normal linear model (and unimodal method is not mentioned).
  • Improvement [510-26]: Canoco 5 adviser now informs during analysis setup (in the textual advice about ordination model or when leaving the page with ordination method options, depending on method type) about the impact of chosen method (unimodal) or chosen standardization by cases (linear methods) on the existing empty cases (i.e. just with zero values in the response data).
  • Fixed bug [510-27]: Predicted or fitted response variable values (via the Data | Add new table(s) | Predict from constrained ordination) were not precise. Now it gives a correct fit and predicts exact values when the amount of explained variation is 100%.
  • Improvement [510-27]: New method implemented is PRC (principal response curves) based on CCA, i.e. on a weighted averaging algorithm. This is implemented again as two templates, one focusing on the first set of principal response curves, the other allowing to test and display up to four such sets, corresponding to the first four axes of partial CCA
  • Improvement [510-28]: The two sets of analysis templates focused on relating species attributes (aka functional traits) to plot attributes (aka environmental descriptors) were reworked. First one is now called Double Constrained Ordinations and contain the eight templates implementing (with various specific tasks) the two new methods in Canoco 5.10 - dc-CA and dc-PCA. The other group (set) of templates is now called Interpreting by Traits and the five analysis templates present in it uses trait data table as explanatory or supplementary variables in analyses, in which as response variables serve the species scores from analysis (analyses) either unconstrained or constrained by environmental predictors. Analyses from both groups of templates are illustrated by the revised example project Traits.c5p. All analyses now use just a simple approach to focal data table: community data table is always the focal one.
  • Improvement [510-29]: We have changed the way the pseudo-F value is calculated for the test on first constrained axis. This corresponds to a change in formula (3.13), where lambda-1 (numerator) is now divided by q, the number of DFs for explanatory variables. This makes new pseudo-F values for a test on first axis look usually smaller than they used to be, but no effect on p-values and their scale is now compatible with the pseudo-F values for the test on all constrained axes.
  • Fixed bug [510-30]: Canoco engine no longer reports "Axis is null, so cannot be turned into covariate" in the scenario where we ask for calculating too many axes (based on the count of explanatory variables), but the count of axes with non-zero eigenvalues is much more restricted by the number of response variables (this happens particularly in the trait-related analyses where the response variables are Resp.x scores from a previous analytical step).
  • Improvement [510-31]: Canoco no longer asks the user whether to store project' data tables in a condensed form. This is now decided internally.
  • Fixed bug [510-32]: Canoco was copying scores and/or data tables to Clipboard an excesivelly long time when there were many rows of them (> ca 10 000).


Issues fixed and improvements added in version 5.04

  • Improvement [504-01]: Improved Canoco 5 performance by parallelizing the bottle-neck computations on multi-core computers using OpenMP library.
  • Improvement [504-02]: Switching between brief and non-brief versions of analysis notebooks was made more easy, by adding toolbar button switching the brief display state on and off for each notebook separately.
  • Improvement [504-03]: Canoco 5 now adapts more readily to user's idea about the required number of permutations: specifying new value in the Analysis Setup Wizard leads to it being accepted as a new default in the analyses defined afterwards.
  • Fixed bug [504-04]: Sorting response variables in the score page of an analysis notebook did not always work in linear ordination methods. This is because the sorting order was based on the default scaling option, but division by response variable' standard deviation could change the order.
  • Improvement [504-05]: Increased the number of case (and response variable) classes and improved their visual consistency (e.g. series line should use same colour as used by the corresponding class symbols, the types of symbols used for cases shall not overlap (much) with the types used for response variables or explanatory variables, etc.)
  • Improvement [504-06]: The cases made supplementary during the analysis execution (e.g. because the explanatory variable or supplementary variable values are missing) are no longer permanently marked as supplementary in the analysis settings. This makes easy - after replacement of missing values - to reexecute the analysis with all the cases active.
  • Fixed bug [504-07]: The Help button in the Define Grouping dialog box (invoked from the role pages of the Analysis Setup Wizard) did not display corresponding help topic.
  • Improvement [504-08]: The Create New Analysis wizard was too small to allow seeing properly the offered analysis templates in its last page.
  • Improvement [504-09]: The error message shown when the TAKE/SKIP rule is incorrectly specified in the Analysis Setup Wizard was confusing (about the number of expected units). Improved the message and the corresponding help topic.
  • Improvement [504-10]: In the db-RDA analysis templates, user choice of omitted (or weighted) cases made in the first step (performing PCO) are now carried over to the second step (performing RDA with PCO scores).
  • Feature [504-11]: The Compare-constrained-unconstrained analysis templates (optionally with covariates) matched CCA with CA method, instead of DCA and detrending could not be even set.
  • Fixed bug [504-12]: The dialog box shown during stepwise selection when the R2(adj) of selected predictors is about to exceed the R2(adj) of the whole pool of predictors could interrupt the automatic selection of all levels of a factor.
  • Fixed bug [504-13]: Cases with missing values in explanatory variables were not detected if these variables are represented in the model just by their interaction.
  • Fixed bug [504-14]: Canoco 5 crashed on GAM models where one of the predictors has just three distinct values.
  • Improvement [504-15]: Allow the choice of Citation button in the About dialog box using keyboard short-cut, Alt-C.
  • Fixed bug [504-16]: The dialog box shown by the Graph | Attribute plots | In ordination space did not allow explanatory variable for plotting when there is just one, producing single constrained axis.
  • Fixed bug [504-17]: The labelling of levels for a nominal explanatory variable in the co-inertia analysis was wrong (level labels are mismatched).
  • Improvement [504-18]: Made the choice of analysis templates in the last page of the New Analysis Wizard easier by adding +/- buttons allowing to open/close a group of templates with a single click, instead of double-clicking group name.
  • Improvement [504-19]: When user closes Log pane of a project, this is now remembered when opening the project file in a new session.
  • Fixed bug [504-20]: Case symbols in ordination diagrams of db-RDA analyses, as offered by Graph Wizard, now represent the CaseE, not CaseR scores for constrained axes.
  • Fixed bug [504-21]: When re-executing already defined analysis, the execution failure led to a complete restoration of the original analysis state, so that no error messages, explaining the reasons for failure could be found in the analysis log.
  • Improvement [504-22]: Changed Canoco 5 so that it supports simple topology-based eigenvector maps (sensu Griffith & Peres-Neto 2006, Ecology) in spatial analyses. Square connectivity matrices (with 0 for disconnected sites and 1 for connected ones) can be specified as similarity matrices (with 1-S transformation to distances) in PCNM analyses, but only if the PCNM threshold value is specified to be computed so that (N-1) nearest neighbours are covered, where N is the total number of sites.
  • Improvement [504-23]: Support optionally the "permutational form of adjustment" of the explained variation in constrained analyses (including variation partitioning), as suggested by Peres-Neto et al. (2006, Ecology). This is based on estimating the amount of explained variation when the explanatory variables are randomised (during Monte Carlo permutation test).
  • Fixed bug [504-24]: when creating a copy of existing analysis (using Modify button) with Hellinger standardisation specified for cases, this option was not copied.
  • Fixed bug [504-25]: the "CopyVarSelection" helper was not properly replicated when creating a copy of analysis (e.g. the PCNM-FS-covariates type).
  • > Fixed bug [504-26]: When executing menu commands affecting data table contents, cell being presently edited was not correctly changed and further it was locked into editing mode.
  • Fixed bug [504-27]: After changing font settings for data table editor, column labels disappeared during scrolling.
  • Fixed bug [504-28]: Popup menu for graph objects was not correctly positioned after horizontally splitting analysis notebook.
  • Improvement [504-29]: Many help topics needed language/contents improvement.


Issues fixed and improvements added in version 5.03

  • Fixed Bug [503-01]: The 32-bit version of Canoco 5 crashed when executing (D)CA on a data set with 'perfect split' of the data table into two disjunct sub-tables, i.e. when the first eigenvalue is >= 0.999.
  • Improvement [503-02]: Allow custom aggregation of cases of a compositional data table (via the Project | Create derived project | Aggregate cases). Instead of averaging, data tables (particularly the compositional ones) can be aggregated using sum, median, variance or inter-quartile range.
  • Improvement [503-03]: Added possibility to "unlock" the analyses created by Canoco Adviser, so that they can be further customized (using new Clone unlocked command in the Analysis menu). This is useful particularly if you want either change the type of permutation testing in advanced analysis templates (e.g. to calculate simple and conditional effects in discriminant analysis) or when you want to replace existing data table by another one. This is an advanced feature not recommended for less experienced Canoco 5 users.
  • Fixed Feature [503-04]: Improved user apprehension of program interface when specifying interaction terms in analysis templates using the same data table for explanatory variables and covariates. These two are specified on separate setup wizard pages, shown in non-QuickWizard mode, and when a user checked for interaction definition for explanatory variables at the earlier page, (s)he might have been surprised to see, on the later page, that the definition of interactions was pre-checked also for covariates. Unchecking this box, however, switched off the interaction definition for explanatory variables as well. The fix was to disable the checked box at the later page and allow the change of state only through the explanatory variables area, in this particular context.
  • Improvement [503-05]: Changed wording of the Do not draw symbols on the curves for the specialized page of Graph Wizard used for principal response curves (PRC) diagram. The new wording is positive (Draw symbols on the curves) and the option meaning (and default value) is therefore flipped.
  • Improvement [503-06]: Changed wording of the second page of the New analysis wizard ("Select table focal for"... to "Select focal table for"...).
  • Improvement [503-07]: Better support for automated labelling of ordination axes with the ordination method name and axis number: when user asks for the dialog for axis labelling and transformation to be shown each time a diagram is created, these axes labels are not only be generated (as they already were) but also selected for plotting by default. Note that this was already the case for XY(Z) diagrams.
  • Improvement [503-08]: Made the second page of Excel import wizard more clever by suggesting the number of imported data tables, depending on how many source sheets were selected.
  • improvement [503-09]: Added support for silent installer (and uninstaller) execution.
  • Fixed Bug [503-10]: Few of the registry data (concerning the automated opening of .c5p and .c5g files in Canoco 5 application) were left uninstalled on 32-bit Windows platform when Canoco 5 package was unistalled.
  • Fixed Bug [503-11]: Fixed error in discriminant analysis (CVA) template, where the Setup Wizard, when executed in non-QuickWizard mode, did not offer the selection of response variables and hence all the variables present in the table with case classification factor were used, leading to an incorrect analysis.
  • Fixed Feature [503-12]: The Downweighting rare <response-variables> option in the Analysis Setup Wizard had no tooltip shown.
  • Fixed Feature [503-13]: When right-clicking a centroid (or, less usually, an arrow) of explanatory (or supplementary) factor variable in an ordination diagram, creation of attribute plots is no longer offered. While this submenu was originally offered, no attribute plot was, in fact, created for such non-numeric variables.
  • Improvement [503-14]: Made use of Excel import wizard easier in a situation, where second or later imported data table is transposed (90 degree rotated) relatively to the first data table, and the user forgets to check the corresponding option before entering the spreadsheet area preview. This context often led to difficulties, as the user tried to get back (to check the corresponding option on the preceding page), but the wizard prevented the return based on its check of matching row numbers. Now, only the progress in forward direction from the spreadsheet preview page is prevented on row mismatch.
  • Fixed Feature [503-15]: Canoco Adviser was too hesitant in offering suggestions for response data transformation in circumstances where the type of ordination method (linear vs. unimodal) was preset in the analysis template (e.g. for PRC analysis) or it was implied by data nature (e.g. only a single response variable entering the analysis). This resulted, e.g., in a situation where the log transformation was never recommended for PRC analysis, even where this was appropriate, given data properties.
  • Fixed Feature [503-16]: CoCA analysis template with specified supplementary variables claimed in the Summary page of the analysis notebook that these variables explain 0% of the variation in the CoCA ordination space, but this was due to the fact this statistic is not computed. Changed the way of reporting.
  • Fixed Bug [503-17]: When an attribute plot was created with attribute values coded only by a colour gradient (colour ramp), the request to label the symbols by attribute values was not respected.
  • Improvement [503-18]: Provided better visual feedback when complex diagrams are re-created or re-drawn. An hourglass cursor is now shown also when re-creating or re-drawing an existing diagram.
  • Fixed Feature [503-19]: When importing from an Excel worksheet multiple tables and their case labels disagreed and they were imported as full labels, Canoco 5 incorrectly reported the total number of labels being imported as 0,in a message box.
  • Improvement [503-20]: Allowed silent execution also for a binary patcher of older Canoco 5 versions.
  • Improvement [503-21]: Binary patcher for older Canoco 5 versions made more robust in finding the folder with installed Canoco 5.
  • Fixed Bug [503-22]: Fixed Canoco crashing when one of the envelopes could not be computed and also made the envelope calculation more robust.
  • Fixed Bug [503-23]: Contours in attribute plots were not always properly scaled, namely when combined with different ordination items and therefore forced to be re-scaled.
  • Improvement [503-24]: Users can now specify that the legend section layout wraps after more than four sections.


Issues fixed and improvements added in version 5.02

  • Bug [502-1]: Change of label text could not be undone and did not raise the "project changed" state.
  • Feature [502-02]: The decision which predictors (explanatory/supplementary variables) have their centroid scores (CenE/CenS) computed was based on positive value of their average and for those variables where calculation was not done, zero value was returned, leading to symbols presence in graphs. Now are the centroid scores computed for all predictors with no negative values and when not calculated, missing (NA) values are used.
  • Improvement [502-03]: Within Analysis Setup Wizard, pre-defined group of items (e.g. cases or response variables) can be used to quickly select a set of items used or excluded from an analysis or a set of items to be weighted.
  • Improvement [502-04]: Created a simple utility (C5CleanReg) that removes user settings for Canoco 5 from the Windows registry. This utility is provided mainly for user support, but can be downloaded from here.
  • Improvement [502-05]: Removing typo in the message informing user about available Canoco 5 update (redundant closing parenthesis character).
  • Improvement [502-06]: Progress bar shown during analysis execution now progresses more smoothly, being updated during permutation test (in each analysis step, for multi-step analyses).
  • Bug [502-07]: For some of the example projects (e.g. Grid.c5p project in Samples/Permutio folder), limiting number of response variables shown in graph had no effect (both when specified in Graph Wizard or by Analysis | Plot settings dialog box before creating the graph).
  • Improvement [502-08]: AIC calculation changed: Canoco 5.02 no longer uses the "AIC-proportional" statistic, but rather the true statistic value. The finite-sample correction is also applied (calculating AICc values) by default, but this can be switched off.
  • Bug [502-09]: There was a problem with permutation test settings propagating to new analyses, when in a partial constrained ordination, covariate Z was used to define permutation blocks and then a new variation partitioning analysis was created, where one of the groups contained variable Z.
  • Improvement [502-10]: When user chooses to limit the set of plotted response variables to N best fitting ones in Graph Wizard, this choice is propagated to analysis' plot settings (unless the user already selected a different value there). This has the nice consequence (in most types of use) that the number of plotted variables does not increase after recreating the diagram created with Graph Wizard.
  • Improvement [502-11]: There is a new scroll-button above the upper right corner of the list of analyses, allowing to move currently selected analysis upwards or downwards in the list. This complements the existing possibilities of renaming or deleting an analyses, so that the user has a complete control over the arrangement of analyses in the project. Change of analysis order is persistent (stored in the project file).
  • Improvement [502-12]: All submenus of the main menu can be opened by a keyboard shortcut. In the previous versions, this was not possible for Data and Analysis submenus, where Alt-D and Alt-A shortcuts applied to the controls of the project pane. With this improvement, one can easily characterize the required menu command choice, such as "Alt-A P" for opening Analysis | Plot creation options dialog.
  • Improvement [502-13]: In the dialog for the response curves command (in the Graph | Attribute plots submenu), the response variables available for plotting can be either kept in their table order or sorted alphabetically, for an easier lookup.
  • Improvement [502-14]: Improved the wording on specialized setup wizard pages shown when working with distances (NMDS, PCO, PCNM, db-RDA analyses): the direct input of distances from an existing table is now described in less confusing way
  • Bug [502-15]: Canoco 5 stopped redrawing user interface (analysis notebook contents and usually also the main menu) when more than ca 30 analysis notebooks were open in a project.
  • Improvement [502-16]: The action performed by the "Add table..." button in the project pane was changed: it no longer offers creation of a new empty data table, but rather adding one or multiple data tables via import from Excel, which is a more frequented path for Canoco 5 users.
  • Improvement [502-17]: The Log page of each analysis notebook now displays the list of covariates used in each analysis step. Note that for factors, the active covariate levels are shown in the list.
  • Improvement [502-18]: The analysis formula shown in the third page of the New Analysis Wizard now makes obvious that a priori covariates can be added to PRC analyses (with QuickWizard mode switched off). This information was also added to topics describing the PRC analysis templates.
  • Improvement [502-19]: The execution of an analyses with more than 100 explanatory or supplementary variables was substantially speeded by omitting the calculation of the matrix of correlations among individual predictors. The matrix calculation (and storage in the Log page) can be still switched on using an option in the Edit | Settings | Canoco5 Options dialog box, on its Analyses / Actions page.
  • Improvement [502-20]: The main (left-hand) plot in the specialized PRC diagram now labels the horizontal axis with "Time" rather than the less clear "PRC.Time".
  • Improvement [502-21]: The axes of an XY diagram (or of one-dimensional X-diagram or Y-diagram) referring to ordination scores now respect the "Flip axes" options in the dialog shown by the Analysis | Plot creation options menu command. Note that the choices are interpreted with respect to horizontal vs. vertical direction, not with respect to the order of currently active ordination axes. Practical implication of this new feature is that the vertical axis of PRC diagram (and of its supplementary plot with response variable scores) can be now reverted. On the other hand, the horizontal (time) axis of the PRC diagram is protected against the reversal.
  • Improvement [502-22]: Implementation of the "average of table weights" choice in the specialized setup wizard page of co-correspondence (CoCA) analysis template has changed. Now the relative case weights are averaged, rather than the original row totals that were dependent on the average value magnitude and number of response variables in both compared data tables.
  • Improvement [502-23]: When importing factor variables from Excel data sources, a warning message is shown. When this happens for non-compositional data tables, this is rather an informative message box and its display can be suppressed by the user. For compositional data tables, however, the user is advised that the imported factors should be (likely) transformed to numeric values before analysing the data.
  • Improvement [502-24]: Added a new analysis template for a partial unconstrained analysis (PCA or CA or DCA with covariates).
  • Improvement [502-25]: Implementation of PCNM spatial eigenvectors calculation is now up-to-date with the recommendations of the Dray et al. (2006) paper in Ecological Modelling, namely in (a) zero distances on the main diagonal are now replaced with the 4 * threshold value, so that the points are not auto-correlated with themselves; (b) the spatial eigenvectors corresponding to negative eigenvalues can be not only computed but also used in the PCNM analysis template to model spatial autocorrelation with negative Moran's I values. Additionally, the algorithm for calculating the adjusted distance matrix for PCNM eigenvectors was improved so that it now handles correctly simple connectivity matrices (with 0 and 1 values), even when they are non-symmetrical.
  • Improvement [502-26]: Another improvement for PCNM method is the addition of a new analysis template where a priori covariates are added to PCNM variation partitioning, so that for example a global spatial trend (defined by X and Y coordinates and optionally their polynomial terms) can be removed from the response data.
  • Improvement [502-27]: Further change to PCNM method is the suppression of the global permutation test on PCNM eigenvector pool before their stepwise selection. This suppression takes place when the corresponding constrained ordination model is too much determined, with the number of eigenvectors approaching the number of cases, or when their count is generally large (over 100).

Issues fixed in version 5.01

  • Feature [501-01]: to display classified symbols in a XY diagram, one had to check the Use inclusion rules in the Create XY(Z) Plot dialog.
  • Bug [501-02]: after selecting the Compare-constrained-unconstrained-* analysis template, the Canoco Adviser might recommend using unimodal ordination method. If user rejected this suggestion and changed to linear method, the unconstrained method of the second step was correctly changed, but the detrending option was not switched off. Consequently, the helper suggesting calculation of more than 4 axes (so that all constrained axes are computed) did not work and displayed message box.
  • Bug [501-03]: when displaying an ordination diagram with the scatter of explanatory / supplementary variables including both arrows and centroids, for a DCA or DCCA with detrending by segments, and there were neither case nor response variable scores in the diagram, the centroids and arrows were mis-aligned, as the arrows were not shifted by the values of coordinate origin.
  • Bug [501-04]: when you have defined in Analysis Setup Wizard a third order interaction (e.g. A:B:C) with a help of previously defined second-order interaction (e.g. B:C combined with A) and then asked for second-order interaction removal, this did not happen: the Canoco engine used both B:C and A:B:C interaction terms.
  • Bug [501-05]: model DFs used in the warning about model DFs exceeding total DFs were calculated incorrectly, using number-of-levels as DFs for each factor, without decreasing their count by one. The interactions among factors were affected in the same way.
  • Bug [501-06]: after creating attribute plot with contour lines, the restriction of axes range so that not all original contour lines are included lead to contour lines being drawn outside the axes rectangle.
  • Feature [501-07]: Canoco engine did not compute CenE/CenS scores for explanatory / supplementary variables with average (weighted average for unimodal methods) smaller or equal to 0.001. Such a case could happen for example, when cases belonging to particular category represented less than 0.1% of the total number of cases (or even more, if such cases have below-average weight in unimodal methods). Now the threshold is at 0.000001.
  • Bug [501-08]: when exporting a graph in PDF format to a folder with insufficient rights for file creation, Canoco application crashed. When exporting in EMF format under same circumstances, the failure to store the file went unnoticed.

Canoco 5 Manual Errata

Following errata apply to Canoco 5 manual printing that contains, on its second page, a copyright date range "1998-2012".

pg. 23, 2nd line of 3rd paragraph: should now read "and check below the list that the chosen worksheets will define 2 project tables. After"...

pg. 24, 3rd paragraph: replace first sentence with the following three sentences: "Both data-tables are imported into a new Canoco 5 project and Canoco informs you that the Environment data table contains factors. This is not a problem report, rather additional information that you might even suppress for the next import event. After you close this box with OK, a dialog titled Introductory Analysis is shown."

pg. 25: figure at top has changed, so that the full page looks as follows.

pg. 32: figure in the middle part has changed, so that the full page looks as follows.

pg. 102: both figures have changed, so that the full page looks as follows.

pgs. 104-106: content of Tables 4.2 and 4.3 has changed, so the three pages look as follows.

pg. 115: figure has changed and the description below it was extended, so that the full page looks as follows.

pg. 116: first figure has changed and a new paragraph was inserted below the second figure, so that the full page looks as follows.

pg. 134: figure has changed and the full page looks as follows.

pg. 137: figure has changed and the full page looks as follows.

pg. 150: figure has changed as well as the text of next-to-last paragraph, so that the full page looks as follows.

pg. 163: second figure has changed, as well as the text of the paragraph that follows it, so that the full page looks as follows.

pg. 179: insert following paragraph before the one starting with "In linear methods":
"With more than 100 explanatory variables, the above correlation matrix is not inserted into the log view, unless this default behaviour is overridden (see section"

pg. 288, 6th and 7th line of the last paragraph: change value 12 to 14 and value 43 to 22.

pg. 294: the figure has changed, so that the full page looks as follows.

pg. 297: the figure has changed, so that the full page looks as follows.

pg. 328: the figure has changed, so that the full page looks as follows.

pg. 349: the figure has changed, so that the full page looks as follows.

pg. 380: second figure has changed, so that the full page looks as follows.

pg. 382: after the 1st paragraph append following two:  
"AIC with finite sample correction - when chosen, Canoco calculates (and uses during model selection) the AIC with finite sample correction, proposed by Hurvich & Tsai (1989).
Do not output correlation matrix - when checked, the matrix of correlations among explanatory or supplementary variables is not placed into log when there are >100 predictors."

pg. 394: replace second half of 2nd paragraph (i.e. the text starting with "Canoco 5 computes") with the following text:
"When the AIC with finite sample correction option is checked (see section, Canoco computes and uses AICc version of the AIC statistic, as proposed by Hurvich & Tsai (1989)."

pg. 413: the second figure and the first part of the paragraph below it has changed, so that the full page now looks as follows. Note that a part of the text now overflows into page 414, but there is no change in that text.

pg. 453: before the section 7.7 (Graph submenu) insert following text:
"7.6.11 Clone unlocked
This command is enabled only when the active analysis was created by the New Analysis Wizard, and creates a customizable copy that can be more freely modified."

pg. 460: Append following text at the end of first paragraph:
"Additionally, when you choose axis flipping in analysis options (see section 7.6.9), it is applied in XY(Z) diagram whenever an axis represents ordination scores."

pg. 487: after Hope, A.C.A. citation, insert following one:
"Hurvich, C.M. & Tsai, C.L. (1989) Regression and time series model selection in small samples. Biometrika, 76, 297-307."

pg. 493-496: several new entries were added to Index, so that it now looks as follows.


Canoco 5 Frequently Asked Questions


  1. Is there an upgrade available for users of older versions?
  2. Does Canoco 5 run on Windows 8/10 and other Windows platforms?
  3. Does Canoco 5 run on Linux or MacOS?
  4. Is Canoco 5 a 64-bit program?
  5. How does Canoco deal with the stability issues reported by Oksanen & Minchin (1997)?
  6. Does Canoco 5 provide NMDS?
  7. Is Canoco 5 able to analyse my data set with 20,000 samples and 600 species?
  8. How does Canoco 5 compare to PC-ORD version 6?
  9. How does Canoco 5 compare to the Vegan package in R?
  10. I bought Canoco 4.x at Scientia Software, which is no longer distributing Canoco. Whom should I ask for technical support or upgrade?
  11. How do I omit cases or response variables from an analysis?
  12. How can I display ordination score values?
  13. Why is the transformation of response data disabled in the Analysis Setup Wizard?


1. Is there an upgrade available for users of older versions?

Yes, you can upgrade from older versions of Canoco. Please, contact the distributor from whom you bought your original Canoco version to get more precise information on availability and pricing (Scientia customers, please see the question 10).

2. Does Canoco 5 run on Windows 8/10 and other Windows platforms?

Canoco works fine on standard desktop and laptop computers with Windows 8, 8.1 or 10 for both the 32-bit and 64-bit versions, available at the time Canoco 5 was released. Window 8.x and 10 also support other platforms, such as small mobile devices managed by touching the screen with your fingers, but, as any program analyzing and visualizing scientific data, Canoco 5 will not excel on them.

Canoco 5 works on other Microsoft operating systems as well, starting from Microsoft Windows XP with SP (service pack) 2 or SP3 installed. This includes also Windows Vista and Windows 7.

3. Does Canoco 5 run on Linux or MacOS?

There is no native implementation of Canoco 5 for those operating systems, but Canoco 5 was tested to run under the Wine environment on Linux and likewise in a similar environment of CrossOver package. The following snapshot illustrates working with a biplot diagram in Ubuntu Linux workspace.


4. Is Canoco 5 a 64-bit program?

There is now just one application within Canoco 5 package and the installer installs its 64-bit version on 64-bit Windows and the 32-bit version on 32-bit Windows. The files read and stored are compatible between 32-bit and 64-bit versions of Canoco 5.

5. How does Canoco deal with the stability issues reported by Oksanen & Minchin (1997)?

The bug in the original DECORANA (Hill, 1979) code for Detrended Correspondence Analysis has been studied and was repaired before Canoco 4 version, 15 years ago. It turned out that the change suggested by Oksanen and Minchin (1997) did not make the smoothing routine order-invariant. Another change was required as well, as agreed upon by Oksanen & Minchin in subsequent correspondence (see

6. Does Canoco 5 provide NMDS?

Yes, the non-metric multidimensional scaling (NMDS or NMS) method is now fully integrated into Canoco 5, replacing the add-on program WinKyst from the previous version. The WinKyst program remains available as a free alternative solution for performing NMDS analyses.

In addition, Canoco 5 provides a wide array of ordination methods that operate directly on the data, instead of on derived similarity or dissimilarity (distance) measures, as NMDS does. The advantage of these methods over NMDS are that:

  • The resulting ordination readily provides information on the level of individual variables in the data table
  • The ordination can be focused on the effect of particular explanatory variable(s) – in the form of constrained ordination – so that it shows e.g. the community response to explanatory variables
  • Background variation can be removed from the ordination by using covariate data, so that the ordination can display new information rather than trivial or uninteresting variation, or variation that is already well understood.

7. Is Canoco 5 able to analyse my data set with 20,000 samples and 600 species?

Yes, most certainly it is, and much larger data as well! There are always limits to the size of data one can analyze on a personal computer, but in version 5, Canoco itself enforces only the limit of 16.7 millions table rows and 16.7 millions table column, which is not very limiting. The operating systems, however, impose much harsher limits, namely in the case of 32-bit Windows. Standard applications cannot allocate in 32-bit Windows more than 2 GB of memory in total, but Canoco 5 uses a special provision to extend its data space to 3 GB (after proper Windows re-configuration). A single, contiguous memory block cannot be allocated with a size greater than ca 1 GB, so Canoco 5 data tables are limited to roughly 134 million entries. Yet another limitation usually comes from the processor speed, making analyses of really big data unbearably slow (but you can leave the computer working overnight, then).

8. How does Canoco 5 compare to PC-ORD version 6?

Canoco 5 is software primarily focused on ordination methods, while PC-ORD offers a wider range of methods, including cluster analysis, TWINSPAN, species-area curves, Mantel test and similar distance-based permutation tests.

We believe, however, that due to its focus on ordination, Canoco does a better job in this field both in terms of offered statistical methods and user friendliness of the software and produced graphical output. PC-ORD version 6 (as of October 2012) does not support partial constrained and unconstrained analyses, needed to address many of the non-trivial research questions of today. Consequently, PC-ORD has neither support for selecting a subset of explanatory variables reasonably describing the community variation, nor the ability to easily evaluate simple as well as conditional effects of individual predictors collected in the project. Additionally, PC-ORD does not support correct permutation tests for datasets coming from several frequently encountered design types, including repeatedly measured permanent plots or data coming from linear transects or rectangular sampling grids.

Naturally, both programs continue to develop. Version 6 of PC-ORD added linear constrained ordination (redundancy analysis - RDA) that was missing in previous versions, while Canoco 5 adds the non-metric multidimensional scaling (NMDS) that was previously available only as a (free) add-on package. Canoco 5 features the symmetric  form of co-correspondence analysis to relate two biotic communities together. Both Canoco 5 and PC-ORD are valuable analytical tools which can be used to corroborate one another where they offer overlapping functionality. Each complements the other with analyses not available in the other package.

We would like to mention here some of the gross mistakes in the PC-ORD – Canoco comparison table published on PC-ORD web site ( as of October 2012). This comparison concerns the previous version of Canoco (4.5), so newly added features of Canoco 5 are naturally not covered (no strict size limits either in analyses or in graphing, import from CSV files, presence of NMDS, storage of distance matrix), but some of the claims were not correct even for version 4.5 and may be perpetuated into any new comparisons.

Most important is the comparison of prices, where MjM company boasts about a substantially cheaper product, but the comparison for a single user license compares a personal license of PC-ORD with a Canoco price for private companies. A fairer comparison would be among educational licenses purchased by an academic department for its employee. As the PC-ORD pages tell you, if the license should stay at the institution which bought it for you, the price is – for a single user – 299 + 100 USD, which does not compare so well with a single educational  license of 368 USD for Canoco 5 (same as for Canoco 4.5). Similarly, the student licenses are offered for Canoco as additional educational licenses for 238 USD, which does not compare so badly with the 199 USD for PC-ORD. It is only fair to add that shipping costs are smaller for PC-ORD.

As a rather minor point, we shall note that Canoco 4.5 had (and continues to have in version 5) the "successional vectors" called series collections in PC-ORD, that monotonic transformations (namely log and sqrt) are available, as are the diversity indices computed for individual cases, and the detection of outliers with leverage statistics for individual predictors as well as for their whole set.

9. How does Canoco 5 compare to Vegan package in R?

The vegan package in the R program implements most of the methods available in Canoco 5 as well as a few more. But as R is an open system, those Canoco methods missing in vegan can be found in other packages, related or unrelated to vegan. However, the R environment is primarily command-oriented and to import data, perform analysis or create simple ordination diagrams, commands calling functions are needed, often with a complex set of function parameters to correctly choose from. We see the R environment as excellent for a statistically-oriented ecologist, but for researchers focused on their research subjects, using vegan in the R environment has a steep learning curve, which must be climbed repeatedly for someone evaluating their data after longer periods of work in field or lab. There is a relatively user-friendly interface in the Rcmdr package, offering in combination with the DiversityR package some of the multivariate methods of vegan, but only for a small subset, excluding all the advanced methods and advanced options.

10. I bought Canoco 4.x at Scientia Software, which is no longer distributing Canoco. Whom should I ask for technical support or upgrade?

Please ask your support or upgrade questions at this address:  This email address is being protected from spambots. You need JavaScript enabled to view it.


11. How do I omit cases or response variables from an analysis?

When you start to use Canoco 5 on a particular user account, the Analysis Setup Wizard is shown in so-called QuickWizard mode. This is reflected in the QuickWizard button (emphasized by a red rectangle in the following snapshot) being shown in depressed state.

Whenever you want to omit (or weight) cases or response variables, you must switch the QuickWizard mode off by clicking once this button (its look then becomes flat), before creating the new analysis (e.g. clicking the New button below the list of analyses) or before changing options for an existing analysis (e.g. by clicking the Modify button and then selecting Replace in existing analysis).

With QuickWizard mode switched off, the Analysis Setup Wizard shows more pages, including the Response and Explanatory Data page:

If you check (as in the above snapshot) one or both boxes labelled "Select"..., the setup wizard will later show corresponding pages where a subset of cases and/or response variables can be selected for the analysis.

To switch the QuickWizard mode on again, you click the same button in the toolbar (it is a toggle button).

You can define groups of cases and of variables using the Project | Groups | of ... menu commands and then select or omit cases or variables belonging to a particular group by using the From group button on the respective item selection page of the setup wizard.

12. How can I display ordination score values?

The ordination scores and additional ordination statistics that could be obtained in CANOCO 4.x versions from a solution (.SOL) file are still available in Canoco 5 analyses, but normally they are not shown. When you start using Canoco 5 on a particular user account, the analysis notebooks are shown in a brief mode with only the summarizing pages and created graphs available, the other information (ordination scores and analysis log) being hidden. To display analysis notebook in a non-brief mode, you must select the Edit | Settings | Canoco5 options command from the main menu and in the General page of the Canoco Options dialog box uncheck the "Show brief version of notebooks with analysis results" box:

 - closing then the dialog with OK button.

Please note that already displayed notebooks do not change its contents after this change in options. You must close the notebook (e.g. using the Hide button below the list of analyses) and then reopen it again (e.g. using the Show button that replaces the Hide button for an analysis with closed notebook). When hiding and re-displaying analysis notebook, you should note that if there are multiple analyses defined and an analysis notebook is hidden, the focus often switches to another analysis. So to re-open the analysis notebook for the original analysis, you must re-select it in the list of analyses.

The scores shown in the score pages can be copied to Clipboard and further reused within or outside of the Canoco 5 program. There are two context menu commands for copying selected score columns:Copy scores copies the table contents as seen in the score page, whileCopy expanded aligns the set of rows with the corresponding set of data items (cases, response variables, etc.) present in the project: this is important when you want to copy computed scores into the project as a new data table (some data items might be absent in the analysis output, factor variables on the other hand generate more than one set of scores).


13. Why is the transformation of response data disabled in the Analysis Setup Wizard?

You might need to execute principal components analysis (PCA) on your data, for example, and you want to log-transform the values of the variables used in this PCA. But when you arrive to the appropriate setup wizard page, the log transformation is not available:


Why is it so? There are essentially two possibilites:

(a) Your data table is incorrectly specified as a general type, while it is in fact compositional one. Data table type was specified at the time of data import and you have perhaps made a mistake. The most important property of a compositional data table is that all its variables (columns) are measured in the same units and it makes a good sense to sum them up within each case (table row). For example, each column can be a biotic species and the values are abundances or biomass estimates for each species within each case. Or the columns can be different types of phospholipid fatty acids (PLFA) and the values are their concentrations in different samples. If this is your case, you can change the table type by selecting the table in the upper left area of Canoco 5 (as Table 2 in the following snapshot) and then choosing the Data | Change table kind to ‘compositional’ menu command.


(b) Your data table is correctly specified as a general type. Different columns of such data table are measured in different units or – if the units are identical for all of them – it still does not make sense to sum them up. This is the case with many data sets characterising the environment in which a community was sampled (e.g. water analysis results, soil chemistry analysis results etc.). In such a case, you can still specify transformations of the variables, but you must do it for each of them separately (because, likely, the chosen transformations will differ across the variables). These transformations can be specified by selecting the concerned data table in the upper left area of the Canoco workspace and then the Data | Default transformation and standardization menu command from the Canoco 5 menu. This command displays following dialog box where you can select individual variables (except the factor variables) and then choose an appropriate transformation. In fact, Canoco Adviser tries to suggest transformation type, but its scope is limited to the choice between “No transformation” and log-transformation (suggesting appropriate constants in the latter case).


With the default transformations set, they are used always when the concerned variable is used in an analysis, whether you use it as a response variable or as a predictor variable (explanatory, supplementary or covariate). To make sure this happens, you can either check back at the Variable Transformations dialog box or you can inspect the Log tab of the analysis notebook (see the previous FAQ 12, How can I display ordination score values, for the description of how to display analysis notebook in a non-brief mode).

Canoco 5 Resources

Presentations and Tutorials

Here are handouts for a presentation (pdf) given by Cajo ter Braak when introducing Canoco 5 at Wageningen University on 5th February 2013. The presentation focuses on existing users of the older (4.0 and 4.5) CANOCO versions.

Cajo ter Braak also offered a 45-minute hands-on tutorial after the presentation, using these materials. This tutorial refers to data available after installing Canoco 5 on your computer.

Video Tutorials

These brief videos will demonstrate the software use, using recorded screen actions with Petr Šmilauer' commentary.

Canoco 5 tour for novices

1 - Importing data  WMV format MP4 format
2 - First analysis WMV format MP4 format
3 - Analysis notebook WMV format MP4 format
4 - Constrained ordination WMV format MP4 format


These articles will clarify or describe in more detail selected topics about statistical or visualization methods available in Canoco 5.

In the pdf sub-folder of Canoco 5 installation folder, you can find two articles:

  • article in terBraak_et_Smilauer_2015_Topics_constr_unconstr.pdf deals with constrained ordination, but also with a defense of the detrending in unimodal unconstrained methods
  • article in terBraak_et_al_2017_dc-CA_preprint.pdf provides basic information about the dc-CA method, introduced in Canoco 5.10.

Bugs and features

For an overview of issues that we found in the latest released Canoco 5 version, as well as those fixed in the preceding minor versions, click here: Canoco 5 Issues. If you want to report any issues missing in the overview, please This email address is being protected from spambots. You need JavaScript enabled to view it..

Manual Errata

You can find the present errata here.

Recommended Reading

Canoco 5 manual that comes with your software licence is the place for you to start. We suggest you begin with section 1.1, read and exercise the contents of Chapter 2 (experienced Canoco 4.x users might start at section 2.9), and then read all or selected parts of Chapter 3. Chapters 4, 5, and 7 are of referential nature, although they also contain introductions to working with various parts of user interface. You may find useful to read selected (or all) parts of Chapter 6, where available example projects, build around real-world datasets and research problems are described. Each section is supported by a project where the described analyses and graphs are already present, so that you can examine the required analysis setup, but also do your own experiments with the same data. To open example projects, use the File | Open project menu command and locate the Canoco 5 Application | Samples shortcut at the left side of the opening dialog box (not present under Windows XP and takes various forms in later Windows versions).

Unimodal Models booklet contains many of the seminal papers that introduced the ideas and methods, on which the Canoco software is based. Starting as a doctoral thesis of Cajo Ter Braak, his later papers were added. As from version 5.10, this booklet comes as pdf Unimodal_Models.pdf in the Canoco/pdf  folder. The numbering of pages in the pdf agrees with those mentioned in the Canoco 5 manual. You find in the pdf folder also the paper Topics in constrained ordination(terBraak_et_Smilauer_2015_Topics_constr_unconstr.pdf) and a preprint of a paper
on double constrained ordination (terBraak_et_al_2017_dc-CA_preprint.pdf).

From the multitude of books published on the subject of multivariate analysis and covering also the methods available with Canoco 5, we would recommend particularly two:

For those in need of lighter reading, the P. Šmilauer & J. Lepš (2014) Multivariate Analysis of Ecological Data using Canoco 5, published by Cambridge University Press is recommended. This book describes the methods with examples refering to Canoco 5, unlike the first edition (published in 2003).

Another introductory booklet for ordination (but also classification, regression, spatial analysis) is R.H.G. Jongman, C.J.F. Ter Braak & O.F.R. Van Tongeren (1995), Data Analysis in Community and Landscape Ecology, also available from the Cambridge University Press.

More heavy reading (literally) is the P. Legendre & L. Legendre (2012) Numerical Ecology, published at Elsevier Press. Please note the publication year, using the third edition is essential for some of the newer development (e.g. the analysis including spatial information, such as the PCNM method also implemented in Canoco 5).

If you have support questions

If you have problems with installing the Canoco 5 software or it does not behave as expected from its documentation, you are entitled to a free support. Please contact the software distributor (Microcomputer Power) for this. If they are unable to handle your issue properly, they will pass it on to software authors.

For Canoco 5 related technical and statistical questions, the licensed owners of Canoco 5 are invited to join a subscription-based web discussion board, moderated by Petr Šmilauer, co-author of the Canoco 5 (and earlier 4.x versions).

To join this group, go to the following web page:

and click the [Register] link in the upper left corner of the page, then confirm the registration statement by clicking the I agree button, and then fill the required details on the following page, confirming them subsequently with the Submit button at the page bottom. Please make sure that you correctly specify the license number provided by the software distributor (as given on your install disc envelope or on your manual' cover). Without this number, your membership will not be approved.

On the other hand, the specification of your birthday comes from the platform itself and we could not avoid the form asking for it. We recommend that you immediately set its use to "Completely hide birthday from public viewing" (at the following line of the form), so that even the administrator will not see it (we do not care about your age and do not send birthday presents either :-).

Once you submit the page, your subscription request will wait for the administrator (Petr Smilauer) approval and he will inform you by a personal welcome e-mail once it is confirmed, so that you know you can log into the group, read existing support questions and their answers and eventually ask your own questions.

A general list about ordination methods and other methods of multivariate statistical analysis is the ORDNEWS mailing list. Please see the page for all the fine details about how to subscribe, how to post and what (not) to do in the list correspondence.

Support Utilities

 To remove user-account specific settings of Canoco 5 and reset program behaviour to the state immediately after its installation, you can download and execute following small utility named C5CleanReg.

This is an executable file and you do not need to install it in any special way, simply store it in any folder and execute from there. Please note that to remove Canoco 5 custom settings, Canoco 5 cannot be running at the time you execute this utility. If it does, C5CleanReg warns you and does not proceed until you close Canoco 5 application.


Canoco 5 Overview

The main features of the Canoco 5 program are summarized in the following points.

Click on an image icon to see a more detailed snapshot illustrating the described Canoco 5 feature.

Analytical and graphing capabilities are integrated with an easy-to-use spreadsheet data editor in a single program. All analyses done on a set of data tables are now collected within a Canoco 5 project, sharing the analytical and graphing settings.

All statistical methods offered by Canoco for Windows 4.5 are available, such as DCA, CA, CCA, DCCA, PCA, and RDA methods - including their partial variants, with Monte Carlo permutation tests for constrained ordination methods, offering appropriate permutation setup for data coming from non-trivial sampling designs.

For newly available methods see below.

All visualization tools offered by CanoDraw 4.x are available (including loess, GLM and GAM models for the visualization of data attributes in ordination space) and many of them are improved.

Data can be entered within the program itself or easily imported from Excel (.XLS or .XLSX formats) or from Canoco 4.x data files. Labels no longer need to be shortened to 8 characters, but these brief forms are still available for display in the ordination diagrams and can even be automatically generated from the long ones. Standard coding of factors (categorical predictors) is now used, dummy (0/1) variables are generated internally. The editor allows transformation from dummy variables to factors and, if needed, the reverse.

Principal coordinate analysis (PCoA) and distance based RDA (db-RDA) are now easily accessible, with new distance measures added (11 distance types in total, including Bray-Curtis, Gower distance, or Jaccard coefficients). Similarly, non-metric multidimensional scaling (nMDS) is also supported.

Variation partitioning is easily accessible for two or three groups of predictors including calculations of individual fractions of explained variation, based either on partial or non-partial analyses and using either raw or adjusted variation estimates.

Principal coordinates of neighbour matrices (PCNM) method is available within the variation partitioning framework. Present implementation matches the suggestions described in Legendre & Legendre (2012) under an alternative method name (dbMEM).

Computing, testing and graphing of the Principal Response Curves (PRC) is now an easy task.
Co-correspondence analysis (CoCA, symmetric form) is available, including Monte Carlo permutation testing of the covariation among the two compared community types.

Stepwise selection of predictors was visually enhanced and provides now the support for protection against Type I error inflation (preliminary test with all predictors and the adjustment of p values by one of three methods: false discovery rate (FDR) estimates, Holm correction, and Bonferroni correction.

Straightforward testing of all constrained axes as well as comparing results of two ordinations with Procrustes analysis is available.

You can easily work with species functional traits or import the data on phylogenetic relatedness of species, as well as calculate and use functional diversity.

Visualization capabilities were enhanced with features such as the semi-transparent fill colours, displaying calibration axes for variable' arrows in ordination diagrams, or plotting enclosing ellipses as an alternative to enclosing polygons. Additional types of export in JPEG, TIFF, and PDF file formats were added to existing ones (PNG, BMP, EMF, Adobe Illustrator).

Every step of your work is supported by an context-sensitive help system and by the Canoco Adviser – an expert system that helps you to select a proper analytical method for your research question, correct type of ordination model (linear vs. unimodal), data transformation, or appropriate visualization of the results. It even advises you how to interpret ordination diagrams you create with the help of Graph Wizard.

Advanced users can combine multiple methods in a single analysis, including generalized linear models to correlate scores etc.


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