Man pages for dlill/conveniencefunctions
Convenience Functions
| add_stepcolumn | Add step column and fitrank |
| alignAssign | Align a highlighted region's assignment operators. |
| alignAssignArrow | Align a highlighted region's assignment operators. |
| alignAssignEqual | Align a highlighted region's assignment operators. |
| allCommitted | Check if everythiing is commmitted |
| are_names_of | Pipe-friendly assigning of vectors when their names are known... |
| as.condition.grid | Set rownames so that the covtable is in condition.grid format |
| as.datalist.datalist | Identity function for datalists |
| as.datalist.NULL | As.datalist method for NULL |
| as.parvec.tbl_df | #' Try getting conditions #' #' first from obj, then from... |
| assign_folders | Create output folders and assign names to variables |
| assignFormals | Title |
| asSnippet | Title |
| ast | From lobstr package, but rlang independent |
| ast_tree | Title |
| catDfToExcel | Title |
| cf_applyPaginate | Get list of paginated plots |
| cf_as.parframe | Better as_parframe |
| cfcolors | Colors copied and adapted from dMod |
| cfcolors2 | Colors copied and adapted from dMod |
| cfcolorsFULL | Colors Copied from dMod |
| cf_copy_script | Rename a script, change filename occurences within script,... |
| cf_copy_scripts_multiple | cf_copy_script for multiple scripts at once |
| cfgg_getAllAesthetics | Get comprehensive list of all aesthetics accepted by each... |
| cfggplot | cfggplot |
| cfgrab | Grab a base plot into grid object |
| cf_install_rstudio | Quick setup of RStudio on a new machine |
| cfn | *.fn in functional form for safe evaluation and allowing for... |
| cf_normL2 | normL2 with NULL allowed for data or x |
| cf_outputFigure | Output figures |
| cfoutput_MdTable | Output table as markdown |
| cf_parf_getMeta | Title |
| cf_parf_getPars | Select parameter columns of parframe |
| cf_parf_getStepRepresentatives | Title |
| cf_parf_metaNames | Title |
| cf_parf_parNames | get Parameter names of a parframe |
| cf_parframe | Improved version of parframe |
| cf_parf_rbindlist | Rbind some parframes |
| cf_plotData.datalist | Copied from dMod with additional title showing covariates |
| cf_predict | predict.prdfn with options bowser and verbose |
| cf_profile | Better wrapper around dMod::profile |
| cf_profile_getOpenProfiles | Title |
| cf_profile_getOptimum | Title |
| cf_profile_getProfilesOptimumBelowFit | getProfiles with optimum below the fit$argument |
| cf_profile_getStartPar | Title |
| cf_profile_plotPathsAffected | Title |
| cf_profile_prepareAffectedPaths | Prepare parameters affected by a profile |
| cf_script_extractIdentifier | Extract the numeric identifier of a script |
| cf_script_identifyStale | Title |
| cf_script_makeFilenames | Generate filenames |
| cf_script_remove | Remove scripts AND their output folders |
| cf_script_templateVersions | Display template versions |
| cf_slides | Title |
| cf_slide_section | Title |
| cf_slide_titlecontent | Title |
| cf_slide_twocontent | Title |
| check | Run expression and print OK/FAILED if expression returns... |
| check_clusterTimeStamp | Check for the time stamp |
| checkSensitivities | Check function to check sensitivities |
| compare | Compare function |
| compare_objlist | compare two objlists |
| construct_parframe | Helper function to reproducibly construct parframes |
| cor2cov | Turn correlation matrix and standard deviations back to... |
| d2d2dMod_data | Bring wide d2d format of data into long dMod format |
| datatimes | create vector of times from min to max |
| dMod_files | Consistent dMod filenames |
| dMod_readL1 | Title |
| dMod_readMstrust | Title |
| dMod_readProfiles | Title |
| dMod_saveL1 | Title |
| dMod_saveMstrust | Title |
| dMod_saveProfiles | Consistently save profiles |
| do_checkSensitivities | Do Check sensitivities over a list of prds |
| doPlots1 | do Plots |
| dplyrdt | Title |
| dtParseAssignment | Title |
| dtParseDtCall | Title |
| duplicateArguments | Title |
| duplicated_includeFirst | ALL indices of a vector with duplicates |
| duplicated_values | Values which are duplicated |
| expand.grid2 | Expand.grid which takes in data.frames as well |
| exposeAsArgument | Like extract variable, but this writes it into the function... |
| extract_derivs | Augmentation of getDerivs to subset wrt to... |
| extract_importFrom | Title |
| extract_loopargs | Get the arguments of a for loop or of lapply |
| fileEditHistory | Edit the current history |
| findConnectedCode | Find rows which, taken together, are parseable code |
| findFunctionCode | Find rows which, taken together, are a function |
| findFunctionStartRow | Title |
| fit2obj | Turn a fit into a 2nd order taylor approximation |
| fitErrorModel_plot | Get the nice plot of fitErrormodel |
| fixCommas | Fix commas in rearranged lists |
| flexZirkel | Flexzirkel Stoppuhr |
| funnames_in_package | Write a regex to search for all function names in a package |
| gall | gitall from R command line |
| get_compartments | Read COMPARTMENTS |
| get_conditions | Read CONDITIONS |
| get_derived | Read DERIVED |
| get_description | Read DESCTRIPTION |
| get_doseresponse | Read DOSERESPONSE |
| get_errors | Read ERRORS |
| getFacets | Title |
| get_fitted_pars_from_readme | Get fitted pars from Readme.txt |
| getFormalValues | Title |
| get_inputs | Read INPUTS |
| get_observables | Read OBSERVABLES |
| getPaginateInfo | get the pagination info from a plot |
| get_parcolindices | Get indices of parmaeter columns in a parframe |
| get_predictor | Read PREDICTOR |
| get_random | Read RANDOM |
| get_reactions_or_odes | Read REACTIONS |
| getSnippetPath | get file path of snippet file |
| get_states | Read STATES |
| get_substitutions | Read SUBSTITUTIONS |
| gitam | gitcom -amend from R command line |
| gitcom | gitcom from R command line |
| guess_function | Guess function name of interest |
| id_test | Clemens Kreutz Quick identifiability test |
| insert_debugonce | Insert debugonce(function) |
| insertDput | Title |
| insertFormals | Title |
| insertHistory | Insert parts of the history |
| insert_loopdebugger | Insert the arguments of a loop into the script |
| insert_values_by_name | Insert values from another vector with some shared names |
| inspire | Get some inspiration |
| install_cfBashAliases | Title |
| install_cfkeybindings | Install keybindings |
| install_cfreservedWords | Copy a standard setup_options_IQRtools.R for custom settings |
| install_cfsnippets | Title |
| install_thunarshortcuts | Install thunar shortcuts |
| install_vscode | Title |
| installVSCodeAddinsBindings | get file path of snippet file |
| jODE_funJ | Generate Julia source code of prediction function |
| jODE_indify_est_grid | Create an index-based version of an est_grid |
| jODE_normL2 | normL2 for julia interface |
| jODE_prepare_matrices | Turn fixed_grid and est_grid in numerical matrices |
| jODE_setup | Setup Julia for the session and load some jODE functions... |
| jODE_write_sourcefile | Conveniencefunction to output source file without having to... |
| jODE_writeTestScript | Output a little test script to play around with current... |
| mat_simplify | Simplify with Mathematica |
| meld_dfs | Meld two dfs |
| meld_files | Meld two files/dirs |
| msNarrow | Construct a parframe with tightly sampled parameters around... |
| mypublish_eqnvec2wordtable | Print the odes of an eqnvec in a tex and a docx table |
| mypublish_matlist2wordmath | Print a list of matrices as matrices in word math environemt |
| mypublish_matlist2wordtable | Print a list of matrices to a single word file with a table... |
| mypublish_matrix2wordmath | Print single matrices as matrices in word math environemt |
| mypublish_namedvec2wordtable | Print the odes of an eqnvec in a tex and a docx table |
| open_in_calc | Write an excel file and cat a name to open it. |
| open_in_file | Write a characeter vector to a file and open it. |
| openUnitTestFile | Title |
| optimal_cuts | Choose the best out of several cut lenghts |
| parframes_summary | Quickly print the number of converged fits |
| pars2parframe | Turn a pars vector into a single-row parframe |
| parseDt | Title |
| plotAsDatalist | Quickly plot data |
| plotCombined | bla |
| plotMulti | PlotMulti |
| plotPars | Plot parameter values for a fitlist |
| prepare_argpath | Look at the argpath of a fit |
| printCFShortcuts | Title |
| printJobInfo | Title |
| print_mathematica.character | Print a character in mathematica format |
| print_mathematica.eqnlist | Print ode vector in mathematica format |
| print_mathematica.eqnvec | Print ode vector in mathematica format |
| print_mathematica.matrix | Print mathematica |
| print_mathematica.name_equals_value | Print the values such that they are assignments in... |
| print_r.df2tribble | Print data.frame as tribble-call |
| print_r.eqnlist2addReaction_pipe | Print an eqnlist as a pipe of addReaction()-calls and insert... |
| print_r.named_vector | nicely formatted dput for named vectors |
| proj_create_folders | Create the basic project folder structure |
| projSnippetsAndAliases | Title |
| protect_so | Zip .so files in a file with unique name |
| pullJobs | Git pull all projects in the PROJTOOLS fodler |
| read_def_content | Read the *.def file an prepare it for later use |
| readDMod.frame | Load a saved dMod.frame |
| readSnippets | Title |
| reexports | Reexports |
| refactor_functionCall | Title |
| remove_geom | Remove a geom layer |
| report_dMod.frame | Print plots and shit |
| scale_centerY | Center y axes of different facets around 0 or 1 |
| scale_color_cf | scalecolorcf Copied from dMod |
| showUndocumentedParams | For development only |
| signif_stars | Significance Stars |
| simulate_data | Simluate data with a dMod.frame |
| sort_by_name | Sort a vector by names in ascending order |
| str0 | str with max.level = 0 |
| str_align | Align some lines of code along a pattern |
| str_detect_any | Is (any element) of pattern in any of the elements of vec? |
| str_escape | Escape all special characters in a string |
| str_replace_in_file | Title |
| str_subset_keep_names | str_subset that preserves names |
| str_subset_name | subset a vector by matching names against a pattern |
| str_subset_not | The "opposite" of str_subset. |
| subtract_by_name | Subtract elements with matching names |
| suggestFunctions | Suggest some functions/Snippets |
| tblprint | "tibble-print" a matrix |
| test_dMod.frame | Test some basic functionalities of a dMod.frame |
| theme_cf | Nice ggplot theme |
| theme_msb | Title |
| todolist | Todolist |
| toggle | Toggle sections |
| toggle_attach.input | Toggle attach.input in a dMod.frame |
| toggle_blabla | Toggle BLABLA so the documentwalker can extract functions |
| toggle_mclapply | Insert the arguments of a loop into the script |
| toggle_mclapply_off | Title |
| toggle_mclapply_on | Title |
| toggle_roxyComments | Switch between # and #' comments |
| transformSnippets | Title |
| trustAna_getArg | Get the i'th row of an argpath or argtry as a named vector |
| trustAna_obj_along_path | evaluate objfun along an argpath of a fit |
| trustBlatherResults | Get blather results in nice data.table |
| uniteFits | Title |
| unlink_dMod | Unlink standard dMod-generated files |
| unnest_listcol_dt | Unnest list column |
| update_cf | Update package via devtools |
| update_thunarshortcuts_in_cf | Title |
| write_clusterTimeStamp | Write the time stamp when you logged into the cluster |
