trying to get kable working again

Author: tbates

DESCRIPTION

@@ -18,18 +18,16 @@ URL: https://github.com/tbates/umx
 Description: Quickly create, run, and report structural equation and twin models.
     See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
     Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R.
-    Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
+    Twin Research and Human Genetics, 22, 27-41. DOI: \doi{10.1017/thg.2019.2}.
 Depends:
     R (>= 3.5.0),
     OpenMx (>= 2.11.5)
 Imports:
+	ggplot2,
     cowplot,
     DiagrammeR,
 	DiagrammeRsvg,
 	rsvg,
-	ggplot2,
-    kableExtra,
-	knitr,
     lavaan,
     MASS,
     Matrix,
@@ -42,7 +40,9 @@ Imports:
     RCurl,
     scales,
     utils,
-    xtable
+    xtable,
+	knitr,
+    kableExtra
 Suggests:
     cocor,
     devtools,

INSTALL

@@ -2,8 +2,3 @@ See the umx and OpenMx home pages for more.
 
  - (\url{https://github.com/tbates/umx})
   - (\url{https://openmx.ssri.psu.edu})
-
-Note: In addition to the version of OpenMx on CRAN, a version with
-NPSOL-enabled is available. To install it, once you have umx installed run
-
-install.OpenMx("NPSOL")

NAMESPACE

@@ -358,6 +358,7 @@ importFrom(graphics,plot)
 importFrom(kableExtra,add_footnote)
 importFrom(kableExtra,column_spec)
 importFrom(kableExtra,footnote)
+importFrom(kableExtra,kable)
 importFrom(kableExtra,kable_classic)
 importFrom(kableExtra,kable_classic_2)
 importFrom(kableExtra,kable_material)

NEWS.md

@@ -1,5 +1,10 @@
 ## dev umx 4.9.0
-* NEW: 
+* NEW: `umxACEv` works with nSib = 3
+* NEW: `umxACE` works with nSib = 3
+* IMPROVED: `umxAPA` more use of cat to print (easier to read and copy)
+* IMPROVED: `fin_interest` compute effective interest
+* FIXED: `tmx_show` works for M matrix
+* IMPROVED: `xmuTwinSuper_NoBinary` update for nSib>2
 
 # Releases
 ## umx 4.8.0

R/build_run_modify.R

@@ -74,39 +74,30 @@
 #' @importFrom utils combn data flush.console read.table txtProgressBar
 #' @importFrom utils globalVariables write.table packageVersion
 #' @importFrom utils browseURL install.packages str read.csv
-
 #' @importFrom cowplot draw_label plot_grid ggdraw 
 #' @importFrom ggplot2 ggplot qplot ggtitle ylab xlab labs
 #' @importFrom ggplot2 scale_x_continuous scale_x_continuous theme 
 #' @importFrom ggplot2 geom_point geom_segment geom_line geom_ribbon
 #' @importFrom ggplot2 element_text element_blank expand_limits aes
-#' @importFrom kableExtra kbl add_footnote column_spec footnote
-#' @importFrom kableExtra kable_classic kable_classic_2 kable_minimal kable_material kable_material_dark kable_paper
-
-# # ' @importFrom knitr
 
+# knitr and kableExtra used in printing tables
+# #' @importFrom knitr kable knit_print
+#' @importFrom kableExtra kable kbl add_footnote column_spec footnote
+#' @importFrom kableExtra kable_classic kable_classic_2 kable_minimal kable_material kable_material_dark kable_paper
 # Used in plot
 #' @importFrom DiagrammeR DiagrammeR
-
 # Used in umx_make_TwinData
 #' @importFrom MASS mvrnorm
-
 # Used in umxAPA
 #' @importFrom nlme intervals
-
 # Used in umxHetCor
 #' @importFrom polycor hetcor
-
 # Used in umxCompare
 #' @importFrom xtable xtable
-
 # Used in umxWeightedAIC
 #' @importFrom MuMIn Weights
 
 
-# Not used?
-NULL
-
 utils::globalVariables(c(
 	'x',
 	'xtable',
@@ -5054,7 +5045,9 @@ umxPath <- function(from = NULL, to = NULL, with = NULL, var = NULL, cov = NULL,
 #' # umxSummary generates journal-ready fit information.
 #' # We can choose std=T for standardized parameters and can also
 #' # filter out some types of parameter (e.g. means or residuals)
-#' 
+#'
+#' knitr::kable(mtcars[1,1:2])
+#'
 #' umxSummary(m1, std = TRUE, residuals=FALSE)
 #' 
 #' # parameters() flexibly retrieves model coefficients. 

R/fit_and_reporting.R

@@ -1009,8 +1009,7 @@ umxSummary.MxModel <- function(model, refModels = NULL, std = FALSE, digits = 2,
 			toShow = parameterTable[, namesToShow]
 		}
 		toShow = xmu_summary_RAM_group_parameters(model, toShow,  means= means, residuals = residuals)
-
-		umx_print(toShow, digits = digits, report = report, caption = "Model Parameter loadings", na.print = "", zero.print = "0", justify = "none")
+		umx_print(toShow, digits = digits, report = report, caption = paste0("Parameter loadings for model ", omxQuotes(model$name)), na.print = "", zero.print = "0", justify = "none")
 	}
 	with(modelSummary, {
 		if(!is.finite(TLI)){
@@ -4049,7 +4048,7 @@ umx_aggregate <- function(formula = DV ~ condition, data = df, what = c("mean_sd
 	if(report == "html"){
 		umx_print(tmp, digits = digits, file = "tmp.html")
 	} else if(report == "markdown"){
-		return(knitr::kable(tmp))
+		return(kable(tmp))
 	}else{
 		# umx_print(tmp, digits = digits)
 		return(tmp)

R/misc_and_utility.R

@@ -3966,7 +3966,7 @@ umx_print <- function (x, digits = getOption("digits"), caption = NULL, report =
 	        print(x, quote = quote, right = TRUE, ...)
 		} else if(report == "html"){
 			# From report = "html"
-			if(both){ print(knitr::kable(x, caption= caption)) }
+			if(both){ print(kable(x, caption= caption)) }
 			if(kableExtra){
 				# default html output
 				x = kbl(x,  caption = caption)
@@ -3982,8 +3982,11 @@ umx_print <- function (x, digits = getOption("digits"), caption = NULL, report =
 				system(paste0("open ", file))
 			}
 	    }else{
-			print(knitr::kable(x, caption = caption))
-			# print(kbl(x, caption = caption, format = umx_set_table_format(silent=TRUE)))
+			# markdown/latex
+			# knit_print(kbl(x, caption = caption, format = umx_set_table_format(silent=TRUE)))
+			# print(kbl(x, caption = caption))
+			# return(kbl(x, caption = caption, format = umx_set_table_format(silent=TRUE) ))
+			print(kable(x, caption = caption))
 	    }
 	    invisible(x)
 	}