version 0.1.2

DESCRIPTION

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+Package: arsenal
+Title: An Arsenal of 'R' Functions for Large-Scale Statistical
+        Summaries
+Version: 0.1.2
+Date: 2016-12-29
+Authors@R: c(
+    person("Ethan", "Heinzen", email = "heinzen.ethan@mayo.edu", role = c("aut", "cre")),
+    person("Jason", "Sinnwell", role="aut"),
+    person("Elizabeth", "Atkinson", role="aut"),
+    person("Tina", "Gunderson", role="aut"),
+    person("Gregory", "Dougherty", role="aut"),
+    person("Patrick", "Votruba", role="ctb"),
+    person("Emily", "Lundt", role="ctb")
+  )
+Description: An Arsenal of 'R' functions for large-scale statistical summaries,
+  which are streamlined to work within the latest reporting tools in 'R' and
+  'RStudio' and which use formulas and versatile summary statistics for summary
+  tables and models. The primary functions include tableby(), a Table-1-like
+  summary of multiple variable types 'by' the levels of a categorical
+  variable; modelsum(), which performs simple model fits on the same endpoint
+  for many variables (univariate or adjusted for standard covariates);
+  and freqlist(), a powerful frequency table across many categorical variables.
+Suggests: knitr, rmarkdown, xtable, survival, testthat, coin, pROC,
+        MASS, gam, rpart
+Depends: R (>= 3.2.0), stats (>= 3.2.0)
+Imports: broom, stringr
+VignetteBuilder: knitr
+License: GPL (>= 2)
+RoxygenNote: 5.0.1
+NeedsCompilation: no
+Packaged: 2016-12-29 15:03:54 UTC; m144326
+Author: Ethan Heinzen [aut, cre],
+  Jason Sinnwell [aut],
+  Elizabeth Atkinson [aut],
+  Tina Gunderson [aut],
+  Gregory Dougherty [aut],
+  Patrick Votruba [ctb],
+  Emily Lundt [ctb]
+Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
+Repository: CRAN
+Date/Publication: 2016-12-30 01:18:42

MD5

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+966d309a0df5d55be152e36454793ba7 *DESCRIPTION
+3f62d030021234740076da4d1ba8f002 *NAMESPACE
+a5124b7fb1a608cf22414d0d439c5893 *NEWS.md
+babe9da5c34ab0be1462ebb582b67f01 *R/arsenal.R
+79e2033244f329fa85d87cbc4013f678 *R/formulize.R
+cfa9ea4571efbb3e9de3bc79dcc56041 *R/freqlist.R
+e42ce669505128b0f0b20ac6c621e91d *R/freqlist.internal.R
+02a7e6a76fe38503ed55d6d0da6e12dd *R/internal.functions.R
+2f474534e9fc946996d331ad8103b5ea *R/magic8.R
+e54a23c0326058d798de6b3c912a8003 *R/mdy.Date.R
+1de6a042544ab82b1d3e5d5264e3ffe9 *R/mockstudy.R
+8a60fb9fd3e6b75451fd52a671343fdf *R/modelsum.R
+8972abaedd55f0c7f1418ad70f233302 *R/modelsum.control.R
+8c879e7ce937bdbedb5fd3fb31a11d3f *R/modelsum.internal.R
+0e56f25775a178e261295319e70889bd *R/not.in.R
+50cd5149107450c83f3e3f855aeb57ad *R/release_questions.R
+915d58ab60615cd9c66bfc92131cfba1 *R/summary.freqlist.R
+1dff52d601070cac366b7123de8f8680 *R/summary.modelsum.R
+318e7c0c95e3737f5c209a9ba9ebea7b *R/summary.tableby.R
+918558ed28af0fd4f0338c9d9787b926 *R/tableby.R
+6cd26e41a5b57be0697d1e98594fb16d *R/tableby.control.R
+4b5df64d48a8f090b29f7eb55008b5db *R/tableby.internal.R
+9bb29fd9186f2e7c11351693f70aa2e8 *R/tableby.stat.tests.R
+d795cb92f9d3e5ec846b31c0579badd3 *R/tableby.stats.R
+872993fdbe93e6707fae16f6e0a0c99f *R/write2.R
+018618b1d1fb15a1945e7892e2868204 *README.md
+4aafc7bc18223c036874a46def9050bc *build/vignette.rds
+30cd2d9369ee4d94dd76dcbf5a215559 *data/mockstudy.RData
+79433ae6628afba73b4751b5e6bbb32e *inst/doc/freqlist.R
+b90b634df89f2a4dc597b834d4a0457d *inst/doc/freqlist.Rmd
+197db4ba70c32f0a3579ba56e71b8c7b *inst/doc/freqlist.pdf
+2be512c16c57f0c19d46a03559fa66ed *inst/doc/modelsum.R
+cfe0b0bd54ea0d5dd64b179d025a5621 *inst/doc/modelsum.Rmd
+85570c3c621adb383c345f2e09bd5a1e *inst/doc/modelsum.html
+48ac3590253a78deafa97b9c8a30ba4f *inst/doc/tableby.R
+0f686caa3862dd071b6538bd17b5d0c8 *inst/doc/tableby.Rmd
+78a397ba49bf53164ac6bf6eb5278c0b *inst/doc/tableby.html
+fb7f3dd8cf45309fc533d5cb863271b8 *man/arsenal.Rd
+a08790dee110e6f91216f1c9f7b9888e *man/as.data.frame.freqlist.Rd
+fb7c429f3c12092d0fad2dc88754fd8f *man/as.data.frame.modelsum.Rd
+1326c71d7954bf79cd26895f0aedd30f *man/as.data.frame.tableby.Rd
+2133b459a58b59f77b1e835fafc009e6 *man/formulize.Rd
+c15c3a5f78637e5ac782800687fd2289 *man/freqlist.Rd
+b149f67287b2605109b516fbd9ef8f20 *man/freqlist.internal.Rd
+5148640645d5b9f0de27a83ba4ed6788 *man/grapes-nin-grapes.Rd
+2e1f8c2d941134f65a82f84346247458 *man/mdy.Date.Rd
+4cd57758131c3d1dffce65879eb34e76 *man/mockstudy.Rd
+fb624ea9b801473dae9d30eefe8a1047 *man/modelsum.Rd
+ee7241120bee38b7c92d9160f86699e0 *man/modelsum.control.Rd
+56b926cfc2d81c0539e70ca8a4d68794 *man/modelsum.internal.Rd
+562faf3ed641a245644af5887f5704aa *man/summary.freqlist.Rd
+1a749d94bb67684290e8d11927700f0d *man/summary.modelsum.Rd
+b03d9fe7d9940a052a7b539b58a4f2c5 *man/summary.tableby.Rd
+d8894b3a8db813af90570d664d3009dd *man/tableby.Rd
+e60ebe8ed16f9112a141ec2b24574b10 *man/tableby.control.Rd
+c00a698159af17705b7306ce44e2070b *man/tableby.internal.Rd
+a7d8a4fca049fadfeb6be460b35a209f *man/tableby.stats.Rd
+6d0a923e8398c923744d26bcbb44ddc3 *man/write2.Rd
+b86d96d2b720f7aeeb3b9412b87d67ef *tests/testthat.R
+ba8ab9b99798b694a5f5b06b9a28f2d8 *tests/testthat/test_formulize.R
+6811553415304e4626ae831d29c1d680 *tests/testthat/test_freqlist.R
+d4732617af6ee210bbdc165014b5a4b2 *tests/testthat/test_modelsum.R
+357806abad78c1b6ca0c358d6d4d9b4a *tests/testthat/test_tableby.R
+b90b634df89f2a4dc597b834d4a0457d *vignettes/freqlist.Rmd
+cfe0b0bd54ea0d5dd64b179d025a5621 *vignettes/modelsum.Rmd
+0f686caa3862dd071b6538bd17b5d0c8 *vignettes/tableby.Rmd

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+S3method("[",modelsum)
+S3method("[",tableby)
+S3method("labels<-",freqlist)
+S3method("labels<-",modelsum)
+S3method("labels<-",tableby)
+S3method(as.data.frame,freqlist)
+S3method(as.data.frame,modelsum)
+S3method(as.data.frame,tableby)
+S3method(labels,freqlist)
+S3method(labels,modelsum)
+S3method(labels,tableby)
+S3method(merge,modelsum)
+S3method(merge,tableby)
+S3method(print,freqlist)
+S3method(print,modelsum)
+S3method(print,modelsumList)
+S3method(print,tableby)
+S3method(summary,freqlist)
+S3method(summary,modelsum)
+S3method(summary,tableby)
+S3method(tests,tableby)
+export("%nin%")
+export("labels<-")
+export(Date.mdy)
+export(N)
+export(Nevents)
+export(Nmiss)
+export(countpct)
+export(formulize)
+export(freqlist)
+export(mdy.Date)
+export(meansd)
+export(medSurv)
+export(medianq1q3)
+export(medianrange)
+export(modelsum)
+export(modelsum.control)
+export(modpval.tableby)
+export(na.modelsum)
+export(na.tableby)
+export(q1q3)
+export(tableby)
+export(tableby.control)
+export(tests)
+export(write2html)
+export(write2pdf)
+export(write2word)
+import(broom)
+import(stringr)

NEWS.md

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+# arsenal 0.1.2
+
+* `broom` and `stringr` have been moved to `imports` instead of `depends`.
+
+* Several minor tweaks to `freqlist` for better readability and performance.
+
+# arsenal 0.1.1
+
+* The description and the title are more descriptive now, per request.
+
+# arsenal 0.1.0
+
+* First release contains major functions `tableby()`, `modelsum()`, `freqlist()`, `formulize()`, and `write2...`.
+
+* Vignettes are included for `tableby()`, `modelsum()`, and `freqlist()`.
+

R/arsenal.R

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+## Created: 12/13/2016
+## Author: Ethan Heinzen
+
+#' An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
+#'
+#' An Arsenal of 'R' functions for large-scale statistical summaries,
+#'   which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and
+#'   which use formulas and versatile summary statistics for summary tables and models.
+#'
+#' @section Functions:
+#' 
+#' Below are listed some of the most widely used functions available in \code{arsenal}:
+#'
+#' \code{\link{tableby}}: Summary statistics Of a set of independent variables by a categorical variable.
+#' 
+#' \code{\link{modelsum}}: Fit models over each of a set of independent variables with a response variable.
+#' 
+#' \code{\link{freqlist}}: Approximate the output from SAS's \code{PROC FREQ} procedure when using the \code{/list} option of the \code{TABLE} statement.
+#' 
+#' \code{\link{write2word}}, \code{\link{write2html}}, \code{\link{write2pdf}}: Functions to generate a word, html, or pdf document containing a single table.
+#' 
+#' \code{\link{formulize}}: A shortcut to generate one-, two-, or many-sided formulas.
+#' 
+#' \code{\link{mdy.Date}} and \code{\link{Date.mdy}}: Convert numeric dates for month, day, and year to Date object, and vice versa.
+#' 
+#' @section Data:
+#' 
+#' \code{\link{mockstudy}}: Mock study data for examples.
+#' 
+#' @examples
+#' library(arsenal)
+#'
+#' @docType package
+#' @name arsenal
+#'
+NULL
+
+#### commands to build the package using devtools
+# devtools::document()
+# devtools::check_man()
+# devtools::test()
+# devtools::check()
+# withr::with_libpaths(c("/data5/bsi/adhoc/s200555.R-infrastructure/devel/eph/testinstalls/", .libPaths()),
+#                      devtools::install("../arsenal-eph/", build_vignettes = TRUE, dependencies = FALSE))
+# devtools::build("../arsenal-eph/")
+## < restart R >
+## library(arsenal, lib.loc = "/data5/bsi/adhoc/s200555.R-infrastructure/devel/eph/testinstalls/")
+
+#### to upload to CRAN
+## Update DESCRIPTION, README.md, NEWS.md, and cran-comments.md
+# devtools::revdep_check()
+# devtools::release()

R/formulize.R

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+#' formulize
+#' 
+#' A shortcut to generate one-, two-, or many-sided formulas from vectors of variable names.
+#' 
+#' @param y,x,... Character vectors to be collapsed (by \code{"+"}) and put left-to-right in the formula.
+#'   If \code{data} is supplied, these can also be numeric, denoting which column name to use. See examples.
+#' @param data An R object with non-null column names.
+#' @author Ethan Heinzen
+#' @examples
+#' ## two-sided formula
+#' formulize("y", c("x1", "x2", "x3"))
+#' 
+#' ## one-sided formula
+#' formulize(x = c("x1", "x2", "x3"))
+#' 
+#' ## multi-sided formula
+#' formulize("y", c("x1", "x2", "x3"), c("z1", "z2"), "w1")
+#' 
+#' ## can use numerics for column names
+#' data(mockstudy)
+#' formulize(y = 1, x = 2:4, data = mockstudy)
+#' 
+#' ## mix and match
+#' formulize(1, c("x1", "x2", "x3"), data = mockstudy)
+#' 
+#' ## get an interaction
+#' formulize("y", c("x1*x2", "x3"))
+#' 
+#' ## use in an lm
+#' form <- formulize(2, 3:4, data = mockstudy)
+#' summary(lm(form, data = mockstudy))
+#' 
+#' @export
+
+formulize <- function(y = "", x = "", ..., data = NULL)
+{
+  dots <- list(y = y, x = x, ...)
+  if(!is.null(data))
+  {
+    if(is.null(colnames(data))) stop("colnames(data) is NULL")
+    dots <- lapply(dots, function(elt, cn) if(is.numeric(elt)) cn[elt] else elt, cn = colnames(data))
+  }
+  trash <- lapply(dots, function(elt) if(!is.character(elt)) stop("One or more argument isn't a character vector"))
+  elts <- vapply(dots, paste0, character(1), collapse = " + ")
+  stats::as.formula(paste0(elts, collapse = " ~ "))
+}