Function reference • ktools

All functions
`AR2_Q()`	Autoregressive order 2 - AR(2) precision matrix generator
`AUC()`	AUC calculation
`AddAlpha()`	AddAlpha
`KLD()`	Kullback Liebler
`Kaxis()`	Kaxis
`Kgrid()`	Kgrid function
`Kolygon()`	Kolygon
`MakeADFunSafe()`	MakeADFun safely terminated if there is a bound error
`PlotData()`	PlotData function
`R_binary()`	Find R binary depending on systems
`STATA_date_to_date()`	STATA long date format to R date
`S_glogisI()`	Generalized logistic type I survival
`add()` `subtract()` `multiply()` `divide()` `xtract()` `xxtract()` `dollar()`	Convinient for R4 pipe
`adj_to_precision()`	Generate precision matrix for spatial model from matrix of adjacency
`allot()`	Right assign to using with pipe
`as_field()`	Convert a R list of variable to mongo fields
`as_or()`	Convert an R named list to mongo `OR`
`as_query()`	Convert a R named list of variable and condition to mongo query
`bang()`	table that take pipe input
`barplott()`	Plot bar chart in terminal
`bg()`	Plot text
`bracket()`	Brackets
`browse()`	Show data frame in browser
`cd()`	replicate some features of bash cd
`char()`	Convenient create vector of character without the need to quote
`compute()`	Do calculation, automatically converting type
`corfrankCopula()`	Frank copulas parameter to kendall tau or spearman rho
`crash_test()`	Crash testing an expression
`cutat0()`	Cut at zero
`d2r()`	Date to Rate
`date_to_cmc()`	CMC from R date
`dfrankCopula()`	Frank copulas density
`dgumbelCopula()`	gumbel copulas density
`double_logistic()`	Double logistic function
`double_logistic2()`	Double logistic with three bounds
`download()`	Download with httr
`dskewlogis()` `qskewlogis()` `pskewlogis()` `rskewlogis()` `sskewlogis()` `var_skewlogis()` `mu_skewlogis()`	Skew-log-logistic distribution
`dttb()`	Display HTML with common options
`efunc()`	To use in in tryCatch
`eval_text()`	Evaluate a text as expression
`f_glogisI()` `F_glogisI()`	Generalized logistic type I density
`facet_unwrap()`	Unwrap a facet_wrap plot
`file_name()`	clean file name
`fill_polygon_h3()`	Fill `sf` with `h3` indexes
`findInterval2()`	findInterval and return factor with label
`find_consecutive()`	Find consecutive (by one unit only)
`find_in_zip()`	find filename matching regex in a zipped file
`format_pvalue()`	format p-value for publishing
`fracpoly()`	Fractional polynomial
`fractional_poly()`	Find best fit fractional polynomial using GLM
`fwrite_bz2()`	Write bzipped data file
`genR()`	Generate random walk precision structure matrix
`genSmooth()`	genSmooth
`gen_brewer()`	genCols
`gen_colors()`	genCols
`gen_rw()`	Simulated random walk
`gen_widths()`	Generate widths for geom_tile with unevenly space x-axis
`get_report()`	Get values of summary(`sd_report`) by name
`getcoding_readstata13()`	Read variable coding of a variable from stata file
`getmeta_readstata13()`	Read meta data from stata file
`gg_group()`	Prepare ggplot by groups
`gg_img()`	Plot a 2D matrix as image
`gg_mat()`	Plot a 2D matrix as lines
`ggcol()`	Default column plot for ktools
`gghist()`	Default histogram plot for ktools
`ggpie()`	Default pie plot for ktools
`%notin%`	Not in
`%out%`	Not in = out
`grept()`	Find text match regex with grep with some tailored options
`hex_fill()`	Find most frequent occurrences in the neighbors and fill in the missing hexagon
`histt()`	Plot density in terminal
`hlegend()`	hlegend
`hline()`	hline
`image2()`	Auto sort the columns to plotable matrix
`invert()`	Invert
`is_negative()`	Is negative
`is_sorted()`	is sorted?
`is_windows()`	Check if system is Windows
`iso2name()`	shorthand ISO to country name from countrycode package with some custom match
`join_list()`	Join elements of list a from list b
`kill()`	Kill R session
`kompile()`	Compile TMB with ktools header
`kring_smooth()`	K-ring smoothing
`kut()`	Cut but automatically include min and max data's value
`labelOutlier()`	labelOutlier
`label_table()`	Generate lookup table for haven read spss/stata
`list_name_to_column()`	Add nested list name to nested data column
`list_zip()`	List zip file contents with unzip or unar (default)
`load_pkg()`	Wrapper of suppress message library loadings
`log_prec_prior()`	Log penalized complexity precision prior like INLA's internal
`logistic()`	Logistic shape generator
`logplot()`	logplot
`long_matrix()`	Matrix with names to long table with rowname as column
`lsSize()`	lsSize
`make_re_matrix()`	Generate model matrix for random effect, such as AR model
`map()`	Leaflet map wrapper
`meanstat()`	format cross table for publushing
`month_year_to_cmc()`	Month year to cmc
`more()`	Pager view similar to more
`most_frequent()`	Find most frequent occurrences with rle
`mustats_3plus()`	format cross-IQR by groups (>2) for publishing
`n_unique()`	Number of unique elements in a vector
`name2iso()`	shorthand country name to ISO from countrycode package with some custom match
`name2list()`	Convert named vector to a named list
`otherwise` `is_missing()`	Collection of naming, renaming functions, values
`named_list()`	Constructing list with named from object name
`nan_rm()`	Remove NA/Inf from objects
`napply()`	n(amed)apply: lapply but automatic add names to output
`nullspace_penalty()`	Null-space penalty of the precision matrix
`open_file()`	Open file with system's program (on MAC)
`orderBy()`	Order data frame
`p_adj()`	Adjusted prevalence using sensitivity and specificity
`pfrankCopula()`	Frank copulas prob
`pfu2TCID50()`	PFU 2 2 TCID50
`pgumbelCopula()`	gumbel copulas prob
`pick()`	Pick element in vector base on regex
`plot_segment()`	Plot segments
`plot_smooth()`	lo
`plotb()`	blankplot
`ploth()`	hplot
`plotlnp()`	bothplot
`plotm()`	Plot text
`plotp()`	pointplot
`plott()`	Plot text
`plottc()`	plot in terminal with color
`prec2sd()`	precision to sd
`put()`	put
`py2r()`	Convert ipynb to Rmarkdown or R script
`quantile95()`	quantile 95% with name
`quartz_off()`	Print ggplot off-screen
`query_label()`	Query variable and labels from data read with haven
`query_name()`	Query variable and labels from data read with haven
`query_readstata13()`	Query data frame read with readstata13
`rBind()`	Binding rows, auto set colnames
`range2seq()`	Range to sequence
`range_label()`	Range label like 2019-20
`read_in_zip()`	Read a file match a pattern inside a zip file
`readnbind()`	Read and bind
`rebase()`	Rebase for indexing/modellin
`recode_if()`	recode keeping original data when conditions have NA
`refactor()`	Help to refactor the factor easier
`remove_consecutive()`	Remove consecutive (by one unit only)
`remove_text()`	Remove text from strings with gsub
`rename_col()`	Rename a column
`resize()`	dev.new with named width and height
`rmvnorm_sparseprec()`	Sample multivariates with precision matrix
`row2id()`	rownames to id
`s2n()` `s2n()`	s2n - String to numeric
`sample_tmb()`	Sample TMB fit
`savePDF()`	savePDF function
`savePNG()`	savePNG function
`savePs()`	savePs function
`save_jpg_for_submission()`	ggplot to 300 dpi JPG for article submission
`save_to()`	create dir, change to, and return the name
`sbatch()`	Submit SLURM job
`scale_inverse()`	Get original value before scale
`scale_to_n()`	scale_to_length
`scale_to_range()`	scale to defined range
`screen_to_file()`	Open output of a function in a new text file (in default application)
`sd2prec()`	sd to precision
`sizing()`	Sizing the figure in Python notebook IRKernel
`skim()`	Simpler data overview
`slurm()`	Prepare the R script and sh file to submit to HPC managed with SLURM
`snaking()`	Convert to snake case from package snakecase
`square()`	Square
`squeue()`	Monitor SLURM queue
`strip_U()`	Strip unicode characters
`surv_split()`	Split time to interval for survival model - improved
`table()`	tabulate a variable with pipe
`table_as_html()`	View table as html
`tabstat()`	format cross-table for publishing
`take_note()`	Write a note to file
`tbl_AB()`	Tabulate 2 variables with count and percentage
`tmb_ICs()`	Calculate Information criteria for TMB model
`tmb_compile_and_load()`	TMB compile and load
`tmb_fixit()`	TMB fix parameters
`tmb_load()`	Basic loading of TMB model with basic name handling, unloading
`tmb_unload()`	Unload loaded TMB dynamics
`today()`	Today date
`unar()`	Unzip file with unar instead of unzip
`unkount()`	Uncounting data frame using a weights
`unroll_zip()`	Unroll zipped files
`var_ll()`	Variance of adjusted prevalence using sensitivity and specificity
`vline()`	vline
`wait()`	wait function
`which_empty()`	Find empty element in a nested list
`which_in()`	Find element in a vector and extract name not indice
`which_not()`	Find element not in a vector and extract name not indice
`xyline()`	xyline

Reference

All functions