Man pages for functClust
Functional Clustering of Redundant Components of a System
| add_ass_names | Add assemblage names on a plot |
| affect_motifs | Label assemblages by assembly motif |
| agglomerative_ftree | Hierarchical agglomerative clustering of components |
| AIC_ | AIC of two numeric vectors |
| AICc | AICc of two numeric vectors |
| amean | Arithmetic mean |
| amean_byelt | Arithmetic mean by components occurring within an assembly... |
| amean_byelt_jack | Arithmetic mean by elements occurring within assembly motif... |
| amean_byelt_LOO | Predicting the performances by elements occurring within... |
| amean_bymot_jack | Arithmetic mean of performances by assembly motif using... |
| amean_bymot_LOO | Arithmetic mean by assembly motif using leave-one-out method |
| argchr | Index of different instances of a given char in a string |
| argmax | Index of the maximum values of a vector |
| argmin | Index of the minimum values of a vector |
| asd | Arithmetic standard deviation |
| binary_to_logical | Convert a binary into logical matrix |
| build_random_matrix | Build a matrix of missing indices |
| calibrate_amean_byelt | Modelling of performances by components occurring within an... |
| calibrate_amean_byelt_xpr | Modelling of performances by components occurring within an... |
| calibrate_amean_bymot | Modelling of performances by assembly motif |
| calibrate_amean_bymot_xpr | Modelling of performances by assembly motif over several... |
| calibrate_byminrss | Modelling of performances of assemblages |
| calibrate_gmean_byelt | Modelling the performances by components occurring within an... |
| calibrate_gmean_byelt_xpr | Modelling the performances by components occurring within an... |
| calibrate_gmean_bymot | Modelling of performances by assembly motif |
| calibrate_gmean_bymot_xpr | Modelling of performances by assembly motif over several... |
| CedarCreek.2004.2006.boot.assemblages | Evaluate by bootstrapping the robustness of species... |
| CedarCreek.2004.2006.boot.performances | Evaluate by bootstrapping the robustness of species... |
| CedarCreek.2004.2006.dat | Data of Cedar Creek experiment for the years 2004, 2005 and... |
| CedarCreek.2004.2006.res | Functional clustering of species used in Cedar Creek... |
| CedarCreek.2004.2006.test.assemblages | Test of significance of species assemblages (plots) used in... |
| CedarCreek.2004.2006.test.components | Test of significance of components (species) used in Cedar... |
| CedarCreek.2004.2006.test.performances | Test of significance of different performances (yearly... |
| CedarCreek.2004.res | Functional clustering of species used in Cedar Creek... |
| char_to_int | Convert a character into integer vector |
| check_foption | Check an option |
| check_ftree | Check a matrix of component affectation to functional groups |
| check_plot_options | Check options |
| check_repeat | Check for identical assemblages |
| compact_index | Compact a vector of indices |
| complete_ftree | Hierarchical clustering of components from an _a priori_... |
| compute_fit_stats | Statistics of model goodness-of-fit |
| compute_ftree_stats | Valid hierarchical tree and Statistics of model... |
| compute_motif_stats | Statistics of assembly motifs |
| concat_by_line | Concat a list of strings segmented by line |
| cut_ftree | Cut a tree at a given level |
| delstr_begin | Delete the beginning of a string |
| delstr_end | Delete the end of a string |
| divisive_ftree | Hierarchical divisive clustering of components |
| extend_letters | Extends a vector of letters |
| extend_vector | Extends a vector |
| fboot | Evaluate the robustness of a functional clustering by... |
| fboot_assemblages | Evaluate the robustness of a functional clustering to... |
| fboot_one_point | Evaluate the robustness of a functional clustering to... |
| fboot_performances | Evaluate the robustness of a functional clustering to... |
| fboot_plot | Plot the robustness of a functional clustering evaluated by... |
| fboot_read | Read the robustness of a functional clustering evaluated by... |
| fboot_read_one_point | Read a test of significance of functional clustering |
| fboot_write | Record the robustness of a functional clustering evaluated by... |
| fboot_write_one_point | Record a test of significance of functional clustering |
| fclust | Build a functional clustering for one or more performances |
| fclust_plot | Plot various graphs of a functional clustering for one or... |
| fclust_predict | nnnn |
| fclust_read | Read a functional clustering for one or several performances |
| fclust_write | Record a functional clustering for one or several... |
| fcolours | Series of colours used in 'functClust' |
| fepsilon | Value of epsilon used in 'functClust' |
| first_argchr | Index of a first instance of char in a string |
| first_argmax | Index of the first maximum value of a vector |
| first_argmin | Index of the first minimum value of a vector |
| fit_ftree | Clustering of components for the performances of assemblages |
| fletters | Series of letters used in 'functClust' |
| fnbdigits | Number of digits kept when writing in a file |
| format_fclust | Format a raw dataset for a functional clustering |
| fpvalue | Standard p-value used in the package functClust |
| fstd_colour | Standard colour used in the package functClust |
| fsymbols | Series of symbols used in 'functClust' |
| ftest | Test the significance of different variables of a functional... |
| ftest_assemblages | Evaluate the weight of each assemblage on functional... |
| ftest_components | Evaluate the weight of each component on functional... |
| ftest_performances | Evaluate the weight of each performance on functional... |
| ftest_plot | Plot the significance of different variables of a functional... |
| ftest_plot_assemblages | Plot the evaluation of weight of each assemblage on... |
| ftest_plot_components | Plot test of the weight of each component on functional... |
| ftest_plot_performances | Plot the evaluation of weight of each performance on... |
| ftest_read | Read the significance of different variables of a functional... |
| ftest_write | Record the significance of different variables of a... |
| functClust-package | Functional Clustering of Redundant Components of a System |
| fwindow | Standard number of components to plot in the package... |
| gmean | Geometric mean |
| gmean_byelt | Geometric mean by components occurring within an assembly... |
| gmean_byelt_jack | Geometric mean by elements occurring within assembly motif... |
| gmean_byelt_LOO | Geometric mean by elements occurring within assembly motif... |
| gmean_bymot_jack | Geometric mean by assembly motif using jackknife method |
| gmean_bymot_LOO | Geometric mean by assembly motif using leave-one-out method |
| gsd | Geometric standard deviation |
| index_inturn | Reverse an indexation |
| is_binary | Test if a vector is binary |
| list_in_quote | Concat a list of strings |
| logical_to_binary | Convert a logical into binary matrix |
| maffect_motifs | Labelling of a whole tree of component clustering by assembly... |
| make_fclust | Make the formatted result from a functional clustering |
| mark_string | Mathematical mark of an ordered string vector |
| mean_fct | Switch mean function. |
| mse | Mean Square Error (MSE). |
| name_clusters | Labelling (by lowercase letters) of components by cluster |
| name_motifs | Labelling (by lowercase letters) of assemblages by assembly... |
| nb_tests | Maximal number of clustering models to test |
| notify_fclust | Message for following functional clustering computation |
| plot_by_page | Plot a list of strings on several pages |
| plot_clusters_content | Write the components belonging to each functional group |
| plot_components_box | Plot mean performances of assemblages that contain a given... |
| plot_components_content | Write the components belonging to each functional group |
| plot_fass | Plot performances of some given assemblages |
| plot_fcomp | Plot mean performances of assemblages containing a given... |
| plot_fmotif | Plot as boxplot mean performances of assemblages sorted by... |
| plot_fperf | Plot modelled and predicted performances resulting from... |
| plot_ftree | Plot a hierarchical tree |
| plot_ftrees | Plot trees resulting from functional clustering |
| plot_motifs_box | Plot performances of assembly motifs |
| plot_motifs_content | Write the assemblages belonging to each assembly motif |
| plot_motifs_histo | Plot histogram of assemblage performances by assembly motif |
| plot_motifs_infos | Plot reference graphs for checking that plot of sorted data... |
| plot_prediction_LOO | Plot Simulated and Predicted _vs_ Observed performances |
| plot_prediction_simple | Plot Simulated or Predicted _vs_ Observed performances |
| plot_stats | Plot statistics of combinatorial analysis |
| pmse | Probability associated with the Coefficient of determination... |
| points_sd | Plot a point with x- and y-error bars |
| predict_amean_byelt | Prediction of supplementary assemblages computed |
| predict_amean_bymot | Prediction of supplementary assemblages by motif |
| predict_gmean_byelt | Prediction of supplementary assemblages computed gmean = by... |
| predict_gmean_bymot | Prediction of supplementary assemblages |
| predict_performance | Predicting performances of assemblages by only knowing their... |
| pvalue_dependent_R2mse | Test for the dependence of two R2 |
| R2 | Pearson' R2. |
| R2mse | Coefficient of Determination ('R2') |
| read_finputs | Read the file containing initial data of occurrence and... |
| read_fmatrices | Read the file containing the Matrices resulting from a... |
| read_foptions | Read the file containing options for a functional clustering |
| read_fstats | Read the file containing the statistics of a functional... |
| read_ftrees | Read the file containing the trees resulting from a... |
| remove_components | Remove components from dataset |
| reverse_table | Reverse a table along its first dimension |
| rmse | Root Mean Square Error ('RMSE') |
| rss | Residual Sum of Squares ('RSS'). |
| rss_clustering | Residual Sum of Squares of a given clustering model |
| rss_total | Total Residual Sum of Squares of observed performances |
| shift_affectElt | Renumber a vector of component affectation |
| simplify_ftree | Simplify a tree by keeping only significant components |
| sort_components | Sort assembly centroids by decreasing or increasing mean... |
| sort_ftree | Sort the resulting file of tree |
| sort_matrix | sort a matrix |
| sort_motifs | Sort assembly motifs |
| stirling | Number of Stirling of second kind |
| test_dependent_R2 | Test for the dependence of two Pearson' R2 |
| test_dependent_R2mse | Test for the dependence of two Coefficients of Determination... |
| test_posthoc | Test posthoc of variance analysis |
| validate_amean_byelt_jack | Predicting the performances by elements occurring within... |
| validate_amean_byelt_jack_xpr | Predicting the performances by elements occurring within... |
| validate_amean_byelt_LOO | Predicting the performances by elements occurring within... |
| validate_amean_byelt_LOO_xpr | Predicting the performances by elements occurring within... |
| validate_amean_bymot_jack | Predicting the performances by assembly motif using jackknife... |
| validate_amean_bymot_jack_xpr | Predicting the performances by assembly motif using jackknife... |
| validate_amean_bymot_LOO | Predicting the performances by assembly motif using... |
| validate_amean_bymot_LOO_xpr | Predicting the performances by assembly motif using... |
| validate_ftree | Predictions of assembly performances using a species... |
| validate_gmean_byelt_jack | Predicting the performances by elements occurring within... |
| validate_gmean_byelt_jack_xpr | Predicting the performances by elements occurring within... |
| validate_gmean_byelt_LOO | Geometric mean by elements occurring within assembly motif... |
| validate_gmean_byelt_LOO_xpr | Geometric mean by elements occurring within assembly motif... |
| validate_gmean_bymot_jack | Predicting the performances by assembly motif using jackknife... |
| validate_gmean_bymot_jack_xpr | Predicting the performances by assembly motif using jackknife... |
| validate_gmean_bymot_LOO | Predicting the performances by assembly motif using... |
| validate_gmean_bymot_LOO_xpr | Predicting the performances by assembly motif using... |
| validate_using_cross_validation | Predicting by cross-validation of assembly performances |
| wamean | Weighted arithmetical mean |
| wasd | Weighted arithmetic standard deviation |
| wgmean | Weighted geometric mean |
| wgsd | Weighted geometric standard deviation |
