Package CUFF. May 28, 2018

Transcription

1 Note -*- Encoding: utf-8 -*- Type Package Title Charles's Utility Function using Formula Version 1.5 Date Author Package CUFF May 28, 2018 Maintainer Depends R (>= 3.2.2) Imports openls, table Utility functions that provides wrapper to descriptive base functions like cor, mean and table. It makes use of the formula interface to pass variables to functions. It also provides operators to concatenate (%+%), to repeat (%n%) and manage character vectors for nice display. License GPL (>= 2) Encoding UTF-8 LazyLoad TRUE LazyData YES URL NeedsCompilation no Repository CRAN Date/Publication :36:06 UTC R topics documented: correlation cross freq ftab printcross strutils

2 2 correlation sum.n f tab Inde 11 correlation Bivariate correlations This is a function that creates correlation matri objects that can be printed with the corresponding N and p-values. It is a wrapper for cor and cor.test. correlation(, y = NULL, method = "pearson", alternative = "two.sided", eact = NULL, use = "pairwise.complete.obs", continuity = FALSE, data = NULL) ## S3 method for class 'corr' print(,..., tolate = FALSE, cutstr = NULL, tomarkdown = FALSE) y method alternative eact use continuity is a matri/data.frame or a formula defining which variable to use in the correlation matri (see details). y is a matri/data.frame to correlate against. If is a formula y is passed to data argument Method used to compute correlations. Unilateral (one.sided) test or bilateral (two.sided) test. See help(cor) for more details. Logical value to know if a p.value is eact or asymptotic. See help(cor) for more details. Methods to deal with missing values. Logical value to know if continuity correction must be used. See help(cor) for more details.... Unused in this function data tolate cutstr tomarkdown data.frame to use in conjuction with formula Logical value to know if output displayed as a late tabular environment. Optional digits that cut the length of variable names Logical value to know if output should be displayed as a markdown table for report

3 cross 3 Returns a list with correlations, N for each pair of correlations and p.value for each correlations. X=rnorm(10) Y=rnorm(10) correlation(cbind(x,y)) cross Crosstabs Functions to display (2 2) contingency table cross(,...) Object of type table or formula, vector to tabulate... passed to table of tabs Details The tab functions corrects the inability to deal with missing values in the original tabs that comes with R base. The cross methods returns an object of type cross with the original table and the marginal percentages by row and by column. A print methods is associated with a cross object. tab returns an object of type table (see details). Total returns a sum with na.rm=true by default and replaces NA with 0.

4 4 freq ### eample of crosstabs cr1 <- cross( ~ N + P, npk) print(cr1, test = c("chisq.test", "fisher.test")) freq Frequencies Functions to display frequency freq(, y = NULL,..., labels = NULL, data = NULL) ## S3 method for class 'frequencies' print(,..., tolate = FALSE) y Object of type formula, matri or data.frame If is a formula,y or data contains the data from or are set to NULL if the variables are in the main environment... used for compatibility labels data tolate Optional vector of labels the same length as the dimension of or the number of variables in formula. see y for details Logical value that indicates if the print methods should return a tabular late environment to use with Sweave or knitr. Details The freq methods returns an object of type frequencies object with a print methods associated. An object of type "frequencies" that is a list of matri containing the frequencies the % and the % with missing value.

5 ftab 5 ### eample of crosstabs fr1 <- freq( ~ N + P, npk, c("nitrogen", "Phosphate")) fr1 ### To use with sweave or knitr. print(fr1, tolate = TRUE) ftab Fonctions pour ajouter les pourcentages dans les tables La fonction retourne une table avec le contenu en caractères de la fréquence et du pourcentage ftab(t, margin = seq_along(dim(t)), fmt = "%d (%5.1f %%)", quiet = FALSE) t margin fmt quiet Une table de contingence généré avec table ou tabs Si 22, est que le pourcentage est en ligne (1) ou en colonne(2) ou total (1:2). Par défaut, pourcentage total. Ne sert à rien lorsque le tableau est à une dimension. format d affichage Valeur logique qui indique si le tableau est imprimé Retourne une table avec le contenu en caractères de la frequence et du pourcentage e <- as.table(cbind(3:4,5:6)) ftab(e,2)

6 6 printcross printcross Crosstabs print methods Functions to display (2 2) contingency table ## S3 method for class 'cross' print(,..., test = "chisq.test", eport = NULL) Object of type cross to print... Unused arguments test eport list of statistical tests (as character vector) passed to the 22 table. By default, test is set to "chisq.test" which performs a khi-square test with Yates continuity correction. Either "pdf" or "ls" or NUll. Crosstab is flushed into either a pdf using late or an Ecel spreadsheet using package openls Details Eport to "pdf", "ls" open the crosstabs in the corresponding formats. Print methods associated with the cross object. ### eample of crosstabs cr1 <- cross( ~ N + P, npk) print(cr1, test = c("chisq.test", "fisher.test"))

7 strutils 7 strutils Utility functions to treat characters Function %+% paste characters with other characters pairwise. Function %n% is used to repeat a character n time. Function numtostr converts numeric to a string in a nice format. %+% y %n% y numtostr(,nch,digits=4) y nch digits Character vector or a numeric vector for numtostr functions Character vector (Optionnal) length of the resulting character vector Number of digits in the resulting strings Function %+% is an operator that shortens paste(, y, sep="") see help(paste) for more options. Function %n% returns the character vector repeated y times. If both and y are vector each element of are applied to each element of y. Function numtostr converts numerical vector to a character vector using a nice format. "Hello " %+% "world." cat(" " %n% c(rep(1,9),2) %+% 1:10,fill=TRUE) ### Returns a * because specified length of character is unsufficient. numtostr( ,nch=8)

8 8 sum.n sum.n sum weighted on the number of non-missing values Methods that estimates a sum weighted by the number of non-missing values ## S3 method for class 'n' sum(,n = 1,...) A vector of values possibly containing missing values. n Minimum number of valid values... etra parameters to sum Details sum(,n) = mean() * length() / n.valid() sum.n returns the values of the weighted sum. sum.n(c(1, 2, NA, NA), n = 2) ### [1] 6 sum.n(c(1, NA, NA, NA), n = 2) ### [1] NA

9 f 9 f Methods that apply a function across a levels of one or more factors Methods that apply a function across a levels of one or more factors. It works like aggregate but returns a table instead. It also has a usena options that adds NA as a level before applying the function. f(formula,data,fun,...,subset,na.action=na.omit,usena = FALSE) formula data FUN Formula defining the variables. On the left is the variable we are applying the function to, on the right, variables defining levels of the tables Data.frame containing the variables The function to apply to each subset of data... etra parameters to FUN subset na.action usena Vectors defining a subset of data.frame (see help(aggregate)). Action functions to deal with NA in data file Make NA a level of the factors (if any) f returns an object "f" that behaves like a table with all associated methods. res <- f(sepal.length~species,iris,mean) barplot(res)

10 10 tab tab Crosstabulations using formula Functions to create contingency table using formula tab(formula, data, usena = FALSE, eclude = c(na,nan), miss.char = "-", na.action = na.eclude, subset = NULL, sparse = FALSE, drop.unused.levels = FALSE) Total() formula Object of class cross to be printed data data frame to use with formula usena logical values to add NA to the levels in the table eclude levels to eclude from table miss.char Character to replace NA na.action methods to deal with NA subset subset to use in data sparse see help(tabs) for details drop.unused.levels logical values indicating whether we drop empty levels numerical vector Details The tab functions corrects the inability to deal with missing values in the original tabs that comes with R base. Total is a utility function to use in conjunction with addmargins instead of sum. tab returns an object of type table (see details). Total returns a sum with na.rm=true by default and replaces NA with 0. ### eample of crosstabs tab( ~ N + P, npk)

11 Inde Topic character strutils, 7 Topic char strutils, 7 Topic correlation correlation, 2 Topic corr correlation, 2 Topic cor correlation, 2 Topic cross cross, 3 printcross, 6 tab, 10 Topic frequencies freq, 4 Topic freq freq, 4 Topic ftab, table, tabs, tab ftab, 5 Topic missing sum.n, 8 Topic paste strutils, 7 Topic sum sum.n, 8 Topic table cross, 3 printcross, 6 f, 9 tab, 10 Topic f f, 9 %+% (strutils), 7 %+%-methods (strutils), 7 %n% (strutils), 7 freq, 4 ftab, 5 numtostr (strutils), 7 paste (strutils), 7 print.corr (correlation), 2 print.cross (printcross), 6 print.frequencies (freq), 4 printcross, 6 strutils, 7 sum.n, 8 Total (tab), 10 f, 9 tab, 10 correlation, 2 cross, 3 11