Merge branch 'new_summary_tables'

.Rbuildignore

@@ -6,4 +6,5 @@ tests/.*\.Rout\.save$
 ^\.travis\.yml$
 ^appveyor\.yml$
 .*\.tar\.gz
-.Rproj
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -0,0 +1,3 @@
+.Rproj.user
+.Rhistory
+.RData

DESCRIPTION

@@ -1,17 +1,19 @@
 Package: papeR
 Title: A Toolbox for Writing 'knitr', 'Sweave' or Other 'LaTeX'-Based Papers and Reports
 Version: 1.0-0
-Date: 2015-08-25
+Date: 2015-10-22
 Author: Benjamin Hofner, with contributions by many others (see inst/CONTRIBUTIONS)
 Maintainer: Benjamin Hofner <[email protected]>
 Description: A toolbox for writing 'knitr', 'Sweave' or other 'LaTeX'-based
 	     reports and to prettify the output of various estimated models.
 Depends:
-    car
+    car,
+    xtable
 Enhances:
     nlme,
     lme4,
-    survival
+    survival,
+    knitr
 Imports:
     utils,
     gmodels,
@@ -23,7 +25,7 @@ Copyright: See inst/COPYRIGHTS.
 Collate:
     'helpers.R'
     'labels.R'
-    'latex_table.R'
+    'summarize.R'
     'plot.R'
     'prettify.R'
-    'toLatex.R'
+    'toLatex.R'

NAMESPACE

@@ -4,13 +4,14 @@ importFrom("gmodels", "ci")
 importFrom("graphics", "abline", "barplot", "boxplot")
 importFrom("stats", "as.formula", "coef", "coefficients", "complete.cases",
            "fivenum", "lm", "qnorm", "qt", "sd", "symnum", "vcov")
+import(xtable)
 
 export(as.labeled.data.frame,
        is.labeled.data.frame,
        as.labelled.data.frame,
        is.labelled.data.frame,
        convert.labels,
-       get_options,
+       get_option,
        labels,
        labels.data.frame,
        latex.table.cont,
@@ -20,10 +21,11 @@ export(as.labeled.data.frame,
        print.table.fac,
        prettify,
        prettifyPValue,
+       summarize, summarise,
+       summarize_numeric, summarize_factor,
        toLatex,
        toLatex.character,
-       "labels<-",
-       get_options)
+       "labels<-")
 
 S3method(Anova, lme)
 S3method(confint, lme)
@@ -42,8 +44,8 @@ S3method(prettify, anova)
 S3method(prettify, data.frame)
 S3method(mySapply, default)
 S3method(mySapply, data.frame)
-S3method(print, table.cont)
-S3method(print, table.fac)
+S3method(xtable, summary)
+S3method(print, xtable.summary)
 S3method(toLatex, default)
 S3method(toLatex, character)
 S3method(toLatex, sessionInfo)

R/helpers.R

@@ -22,14 +22,14 @@ Anova.lme <- function(mod, type = c("marginal", "sequential"), ...) {
 
 ################################################################################
 # add and get options from tables
-add_options <- function(object, ..., class) {
-    attr(object, "latex.table.options") <- list(...)
+set_options <- function(object, ..., class) {
+    attr(object, "table.options") <- list(...)
     class(object) <- c(class, class(object))
     object
 }
 
-get_options <- function(object, name) {
-    attr(object, "latex.table.options")[[name]]
+get_option <- function(object, name) {
+    attr(object, "table.options")[[name]]
 }
 
 

R/plot.R

@@ -68,7 +68,8 @@ plot.ldf <- function(x, variables = names(x),
             boxplot(x[, i], main = variables[i], ylab = labels[i], ...)
         }
         for (i in which.fac) {
-            barplot(table(x[, i]), main = variables[i], ylab = labels[i], ...)
+            barplot(table(x[, i]),
+                    main = variables[i], ylab = labels[i], ...)
         }
     } else {
         grp_label <- ifelse(!is.null(grp_label), grp_label, by)