Merge pull request #1082 from dbetebenner/master

Updating names for SGP_SIMEX_RANKED

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SGP
 Type: Package
 Title: Student Growth Percentiles & Percentile Growth Trajectories
-Version: 1.6-9.2
-Date: 2017-4-19
+Version: 1.7-0.0
+Date: 2017-4-21
 Authors@R: c(person(given=c("Damian", "W."), family="Betebenner", email="dbetebenner@nciea.org", role=c("aut", "cre")),
 		person(given=c("Adam", "R."), family="Van Iwaarden", email="avaniwaarden@gmail.com", role="aut"),
 		person(given="Ben", family="Domingue", email="ben.domingue@gmail.com", role="aut"),

R/courseProgressionSGP.R

@@ -39,7 +39,7 @@ function(
 		if (any(levels(sgp_object_subset[["GRADE_CHAR"]])=="CT")) {
 			levels(sgp_object_subset[["GRADE_CHAR"]])[which(levels(sgp_object_subset[["GRADE_CHAR"]])=="CT")] <- "EOCT"
 		}
-		suppressWarnings(invisible(sgp_object_subset[, CONTENT_AREA_by_GRADE:=paste(CONTENT_AREA, GRADE_CHAR, sep=".")]))
+		invisible(sgp_object_subset[, CONTENT_AREA_by_GRADE:=paste(CONTENT_AREA, GRADE_CHAR, sep=".")])
 		invisible(sgp_object_subset[,YEAR_INTEGER:=as.integer(as.factor(YEAR))])
 		invisible(sgp_object_subset[,CONTENT_AREA:=NULL])
 		invisible(sgp_object_subset[,GRADE_CHAR:=NULL])

R/studentGrowthPercentiles.R

@@ -684,20 +684,18 @@ function(panel.data,         ## REQUIRED
 		if (is.null(save.matrices)) simex.coef.matrices <- NULL
 		if (calculate.simex.sgps) {
 			quantile.data.simex <- data.table(rbindlist(tmp.quantiles.simex), key=c("ID", "SIMEX_ORDER"))
-      invisible(quantile.data.simex[, RANK_SIMEX := as.integer(round(100*(rank(SGP_SIMEX, ties.method = "average")/length(SGP_SIMEX)), 0)), by = "SIMEX_ORDER"])
+      invisible(quantile.data.simex[, SGP_SIMEX_RANKED := as.integer(round(100*(rank(SGP_SIMEX, ties.method = "average")/length(SGP_SIMEX)), 0)), by = "SIMEX_ORDER"])
       if (convert.0and100) {
-        invisible(quantile.data.simex[RANK_SIMEX==0L, RANK_SIMEX := 1L])
-        invisible(quantile.data.simex[RANK_SIMEX==100L, RANK_SIMEX := 99L])
+        invisible(quantile.data.simex[SGP_SIMEX_RANKED==0L, SGP_SIMEX_RANKED := 1L])
+        invisible(quantile.data.simex[SGP_SIMEX_RANKED==100L, SGP_SIMEX_RANKED := 99L])
       }
 			setkey(quantile.data.simex, ID) # first key on ID and SIMEX_ORDER, then re-key on ID only to insure sorted order. Don't rely on rbindlist/k ordering...
-		} else quantile.data.simex <- data.table("ID"=NA, "SIMEX_ORDER"=NA, "SGP_SIMEX"=NA, "RANK_SIMEX"=NA) # set up empty data.table for ddcast and subsets below.
+		} else quantile.data.simex <- data.table("ID"=NA, "SIMEX_ORDER"=NA, "SGP_SIMEX"=NA, "SGP_SIMEX_RANKED"=NA) # set up empty data.table for ddcast and subsets below.
 		if (print.other.gp) {
 			tmp.quantile.data.simex <- ddcast(quantile.data.simex, ID ~ SIMEX_ORDER, value.var=setdiff(names(quantile.data.simex), c("ID", "SIMEX_ORDER")), sep="_ORDER_")
-			# setnames(tmp.quantile.data.simex, setdiff(names(tmp.quantile.data.simex), c("ID", "SGP_SIMEX", "SIMEX_ORDER")), paste("SGP_SIMEX_ORDER",
-				# setdiff(names(tmp.quantile.data.simex), c("ID", "SGP_SIMEX", "SIMEX_ORDER")), sep="_")) # Not needed once RANK_SIMEX included.
 			quantile.data.simex <- data.table(tmp.quantile.data.simex,
         SGP_SIMEX=quantile.data.simex[c(which(!duplicated(quantile.data.simex, by=key(quantile.data.simex)))[-1L]-1L, dim(quantile.data.simex)[1L])][["SGP_SIMEX"]],
-        RANK_SIMEX=quantile.data.simex[c(which(!duplicated(quantile.data.simex, by=key(quantile.data.simex)))[-1L]-1L, dim(quantile.data.simex)[1L])][["RANK_SIMEX"]])
+        SGP_SIMEX_RANKED=quantile.data.simex[c(which(!duplicated(quantile.data.simex, by=key(quantile.data.simex)))[-1L]-1L, dim(quantile.data.simex)[1L])][["SGP_SIMEX_RANKED"]])
 			return(list(
 				DT=quantile.data.simex,
 				MATRICES = simex.coef.matrices))
@@ -708,7 +706,7 @@ function(panel.data,         ## REQUIRED
 					MATRICES=simex.coef.matrices))
 			} else {
 				return(list(
-					DT=quantile.data.simex[c(which(!duplicated(quantile.data.simex, by=key(quantile.data.simex)))[-1L]-1L, dim(quantile.data.simex)[1L]), c("ID", "SGP_SIMEX", "RANK_SIMEX"), with=FALSE],
+					DT=quantile.data.simex[c(which(!duplicated(quantile.data.simex, by=key(quantile.data.simex)))[-1L]-1L, dim(quantile.data.simex)[1L]), c("ID", "SGP_SIMEX", "SGP_SIMEX_RANKED"), with=FALSE],
 					MATRICES=simex.coef.matrices))
 			}
 		}
@@ -1028,7 +1026,7 @@ function(panel.data,         ## REQUIRED
 
 	tmp.objects <- c("Coefficient_Matrices", "Cutscores", "Goodness_of_Fit", "Knots_Boundaries", "Panel_Data", "SGPercentiles", "SGProjections", "Simulated_SGPs")
 	Coefficient_Matrices <- Cutscores <- Goodness_of_Fit <- Knots_Boundaries <- Panel_Data <- SGPercentiles <- SGProjections <- Simulated_SGPs <- SGP_STANDARD_ERROR <- Verbose_Messages <- NULL
-	SGP_SIMEX <- RANK_SIMEX <- SGP_NORM_GROUP_SCALE_SCORES <- SGP_NORM_GROUP_DATES <- SGP_NORM_GROUP <- NULL
+	SGP_SIMEX <- SGP_SIMEX_RANKED <- SGP_NORM_GROUP_SCALE_SCORES <- SGP_NORM_GROUP_DATES <- SGP_NORM_GROUP <- NULL
 
 	if (identical(class(panel.data), "list")) {
 		for (i in tmp.objects) {
@@ -1597,7 +1595,7 @@ function(panel.data,         ## REQUIRED
 				quantile.data <- quantile.data[quantile.data.simex[["DT"]]]
 			} else {
         quantile.data[, SGP_SIMEX:=quantile.data.simex[['DT']][["SGP_SIMEX"]]]
-        quantile.data[, RANK_SIMEX:=quantile.data.simex[['DT']][["RANK_SIMEX"]]]
+        quantile.data[, SGP_SIMEX_RANKED:=quantile.data.simex[['DT']][["SGP_SIMEX_RANKED"]]]
       }
 		}
 
@@ -1648,8 +1646,8 @@ function(panel.data,         ## REQUIRED
 
 		if (is.character(goodness.of.fit) || goodness.of.fit==TRUE) {
 			if (simex.tf) {
-				sgps.for.gof <- c("SGP", "SGP_SIMEX", "RANK_SIMEX")
-				sgps.for.gof.path <- c(tmp.path, paste(tmp.path, "SIMEX", sep="."), paste(tmp.path, "RANK_SIMEX", sep="."))
+				sgps.for.gof <- c("SGP", "SGP_SIMEX", "SGP_SIMEX_RANKED")
+				sgps.for.gof.path <- c(tmp.path, paste(tmp.path, "SIMEX", sep="."), paste(tmp.path, "SGP_SIMEX_RANKED", sep="."))
 			} else {
 				sgps.for.gof <- "SGP"
 				sgps.for.gof.path <- tmp.path
@@ -1741,7 +1739,7 @@ function(panel.data,         ## REQUIRED
 		if (identical(sgp.labels[['my.extra.label']], "BASELINE") && "SGP_STANDARD_ERROR" %in% names(quantile.data)) setnames(quantile.data, gsub("SGP_STANDARD_ERROR", "SGP_BASELINE_STANDARD_ERROR", names(quantile.data)))
 		if (identical(sgp.labels[['my.extra.label']], "BASELINE") && "SGP_ORDER" %in% names(quantile.data)) setnames(quantile.data, gsub("SGP_ORDER", "SGP_BASELINE_ORDER", names(quantile.data)))
 		if (identical(sgp.labels[['my.extra.label']], "BASELINE") && "SGP_NORM_GROUP" %in% names(quantile.data)) setnames(quantile.data, gsub("SGP_NORM_GROUP", "SGP_NORM_GROUP_BASELINE", names(quantile.data)))
-		if (identical(sgp.labels[['my.extra.label']], "BASELINE") && simex.tf) setnames(quantile.data, gsub("_SIMEX", "_SIMEX_BASELINE", names(quantile.data))) # SGP_SIMEX and RANK_SIMEX
+		if (identical(sgp.labels[['my.extra.label']], "BASELINE") && simex.tf) setnames(quantile.data, gsub("_SIMEX", "_SIMEX_BASELINE", names(quantile.data))) # SGP_SIMEX and SGP_SIMEX_RANKED
 		if (identical(sgp.labels[['my.extra.label']], "EQUATED")) setnames(quantile.data, "SGP", "SGP_EQUATED")
 		if (identical(sgp.labels[['my.extra.label']], "EQUATED") && tf.growth.levels) setnames(quantile.data, "SGP_LEVEL", "SGP_LEVEL_EQUATED")
 		if (identical(sgp.labels[['my.extra.label']], "EQUATED") && "SGP_NORM_GROUP" %in% names(quantile.data)) setnames(quantile.data, gsub("SGP_NORM_GROUP", "SGP_NORM_GROUP_EQUATED", names(quantile.data)))

R/zzz.R

@@ -7,6 +7,6 @@ function(libname, pkgname) {
 `.onAttach` <-
 function(libname, pkgname) {
 	if (interactive()) {
-		packageStartupMessage(magenta$bold('SGP',paste(paste0(unlist(strsplit(as.character(packageVersion("SGP")), "[.]")), c(".", "-", ".", "")), collapse=""),' (4-19-2017). For help: >help("SGP") or visit https://github.com/CenterForAssessment/SGP/wiki'))
+		packageStartupMessage(magenta$bold('SGP',paste(paste0(unlist(strsplit(as.character(packageVersion("SGP")), "[.]")), c(".", "-", ".", "")), collapse=""),' (4-21-2017). For help: >help("SGP") or visit https://github.com/CenterForAssessment/SGP/wiki'))
 	}
 }

README.md

@@ -4,7 +4,7 @@ The **SGP** Package is open source software built for the [**R** software enviro
 
 [![Build Status](https://travis-ci.org/CenterForAssessment/SGP.svg?branch=master)](https://travis-ci.org/CenterForAssessment/SGP)
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/SGP)](http://cran.r-project.org/package=SGP)
-[![Development Version](https://img.shields.io/badge/devel-1.6--9.2-brightgreen.svg)](https://github.com/CenterForAssessment/SGP)
+[![Development Version](https://img.shields.io/badge/devel-1.7--0.0-brightgreen.svg)](https://github.com/CenterForAssessment/SGP)
 [![Rstudio mirror downloads](http://cranlogs.r-pkg.org/badges/grand-total/SGP)](https://github.com/metacran/cranlogs.app)
 [![License](http://img.shields.io/badge/license-GPL%203-brightgreen.svg?style=flat)](https://github.com/CenterForAssessment/SGP/blob/master/LICENSE.md)
 [![Join the chat at https://gitter.im/CenterForAssessment/SGP](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/CenterForAssessment/SGP?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

inst/CITATION

@@ -4,10 +4,10 @@ citEntry(entry = "Manual",
          title        = "{SGP}: Student Growth Percentiles \\& Percentile Growth Trajectories.",
          author       = "Damian W. Betebenner and Adam {VanIwaarden}, Ben Domingue and Yi Shang",
          year         = "2017",
-         note         = "R package version 1.6-9.2",
+         note         = "R package version 1.7-0.0",
          url          = "sgp.io",
 
          textVersion  = paste("Damian W. Betebenner, Adam VanIwaarden, Ben Domingue and Yi Shang (2017).",
                         "SGP: Student Growth Percentiles & Percentile Growth Trajectories.",
-                        "(R package version 1.6-9.2)",
+                        "(R package version 1.7-0.0)",
                         "URL: sgp.io"))

inst/NEWS

@@ -2,6 +2,7 @@ Changes in version: SGP_1.7-0.0
 
   USER VISIBLE CHANGES:
 	  o Adding in dual mode for RLI analyses to be performed using RASCH scores (default) or STAR scores
+	  o Better accomodation of duplicates in data. Nonetheless, MUCH better to get rid of duplicates
 
 Changes in version: SGP_1.6-0.0
 

man/SGP-package.Rd

@@ -19,8 +19,8 @@ growth projections to be calculated across assessment transitions by equating th
 \tabular{ll}{
 Package: \tab SGP\cr
 Type: \tab Package\cr
-Version: \tab 1.6-9.2\cr
-Date: \tab 2017-4-19\cr
+Version: \tab 1.7-0.0\cr
+Date: \tab 2017-4-21\cr
 License: \tab GPL-3\cr
 LazyLoad: \tab yes\cr
 }