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Merge pull request #1451 from dbetebenner/master
Multiple updates including studentGrowthProjections changes to align scale score targets with exact time frame of projection. See individual commits for changes
2 parents 7445489 + 34f439a commit 35a08bf

27 files changed

Lines changed: 389 additions & 327 deletions

CITATION.cff

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,8 @@ authors:
1111
- family-names: "Yi"
1212
given-names: "Shang"
1313
title: "SGP: Student Growth Percentiles & Percentile Growth Trajectories"
14-
version: 2.1-0.22
14+
<<<<<<< HEAD
15+
version: 2.2-0.0
1516
doi: 10.5281/zenodo.3634024
16-
date-released: 2024-8-12
17+
date-released: 2024-10-6
1718
url: "https://sgp.io"

DESCRIPTION

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
Package: SGP
22
Type: Package
33
Title: Student Growth Percentiles & Percentile Growth Trajectories
4-
Version: 2.1-0.23
5-
Date: 2024-8-23
4+
Version: 2.2-0.0
5+
Date: 2024-10-6
66
Authors@R: c(person(given=c("Damian", "W."), family="Betebenner", email="[email protected]", role=c("aut", "cre")),
77
person(given=c("Adam", "R."), family="Van Iwaarden", email="[email protected]", role="aut"),
88
person(given="Ben", family="Domingue", email="[email protected]", role="aut"),
@@ -70,6 +70,8 @@ Authors@R: c(person(given=c("Damian", "W."), family="Betebenner", email="dbetebe
7070
person(given="Brendan", family="Houng", role="ctb", comment="University of Melbourne, Australia, NAPLAN"),
7171
person(given="Leslie", family="Rosale", role="ctb", comment="Ministry of Education, Guatemala"),
7272
person(given="Nathan", family="Wall", role="ctb", comment="eMetric working with Nevada Department of Education and South Dakota Department of Education"),
73+
person(given="Julia", family="English", role="ctb", comment="Massachusetts DESE"),
74+
person(given="Sarah Jo", family="Torgrimson", role="ctb", comment="Massachusetts DESE"),
7375
person(given="Narek", family="Sahakyan", role="ctb", comment="World Class Instruction and Design (WIDA)"))
7476
Maintainer: Damian W. Betebenner <[email protected]>
7577
Depends: R (>= 4.1.0)

R/abcSGP.R

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@ function(sgp_object,
77
grades=NULL,
88
prepareSGP.var.names=NULL,
99
prepareSGP.create.additional.variables=FALSE,
10+
prepareSGP.create.achievement.level=TRUE,
1011
sgp.percentiles=TRUE,
1112
sgp.projections=TRUE,
1213
sgp.projections.lagged=TRUE,
@@ -75,6 +76,7 @@ function(sgp_object,
7576
state=state,
7677
var.names=prepareSGP.var.names,
7778
create.additional.variables=prepareSGP.create.additional.variables,
79+
create.achievement.level=prepareSGP.create.achievement.level,
7880
fix.duplicates=fix.duplicates)
7981
if (save.intermediate.results) save(sgp_object, file="sgp_object.Rdata")
8082
}

R/analyzeSGP.R

Lines changed: 8 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -363,6 +363,13 @@ function(sgp_object,
363363
goodness.of.fit.print <- FALSE
364364
}
365365

366+
if (!is.null(SGPstateData[[state]][["SGP_Configuration"]][["max.forward.projection.sequence"]]) &&
367+
!is.null(SGPstateData[[state]][["SGP_Configuration"]][["max.sgp.target.years.forward"]]) &&
368+
max(SGPstateData[[state]][["SGP_Configuration"]][["max.sgp.target.years.forward"]]) > min(unlist(SGPstateData[[state]][["SGP_Configuration"]][["max.forward.projection.sequence"]]))
369+
) {
370+
stop(paste("SGPstateData configuration value for 'max.forward.projection.sequence' is less than the largest specified value for 'max.sgp.target.years.forward'. Reconcile these values in", state, "meta-data."))
371+
}
372+
366373
###########################################################################################################
367374
### Utility functions
368375
###########################################################################################################
@@ -2415,7 +2422,7 @@ function(sgp_object,
24152422
use.my.knots.boundaries=list(my.year=tail(sgp.iter[["sgp.panel.years"]], 1), my.subject=tail(sgp.iter[["sgp.content.areas"]], 1)),
24162423
performance.level.cutscores=state,
24172424
max.order.for.progression=getMaxOrderForProgression(tail(sgp.iter[["sgp.panel.years"]], 1),
2418-
tail(sgp.iter[["sgp.content.areas"]], 1), state, sgp.projections.equated),
2425+
tail(sgp.iter[["sgp.content.areas"]], 1), state, sgp.projections.equated),
24192426
percentile.trajectory.values=lagged.percentile.trajectory.values,
24202427
max.forward.progression.grade=sgp.projections.max.forward.progression.grade,
24212428
panel.data.vnames=getPanelDataVnames("sgp.projections.lagged", sgp.iter, sgp.data.names, equate.variable),

R/combineSGP.R

Lines changed: 23 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -120,25 +120,13 @@ function(
120120
sgp.target.scale.scores.merge <- SGP::SGPstateData[[state]][["SGP_Configuration"]][["sgp.target.scale.scores.merge"]]
121121
}
122122

123-
### Check return.target.num.years
123+
### Check return.sgp.target.num.years
124124

125125
if (!is.null(SGP::SGPstateData[[state]][["SGP_Configuration"]][["return.sgp.target.num.years"]])) {
126126
return.sgp.target.num.years <- SGP::SGPstateData[[state]][["SGP_Configuration"]][["return.sgp.target.num.years"]]
127-
} else return.sgp.target.num.years <- FALSE
128-
129-
### Check whether to calculate current year lagged targets
130-
if (1 %in% max.sgp.target.years.forward || identical(SGP::SGPstateData[[state]][["SGP_Configuration"]][['current.year.lagged.target']], TRUE)) {
131-
current.year.lagged.target <- TRUE
132-
} else current.year.lagged.target <- FALSE
133-
134-
## Odd things happened (e.g. in WIDA_CO) when max.sgp.targe.years.forward = 1 (length 1 only)
135-
if (identical(SGP::SGPstateData[[state]][["SGP_Configuration"]][['current.year.lagged.target']], FALSE)) {
136-
current.year.lagged.target <- FALSE
137-
}
138-
127+
} else return.sgp.target.num.years <- FALSE
139128

140129
### Utility functions
141-
142130
get.target.arguments <- function(system.type, target.type=NULL, projection.unit.label, year.for.equate) {
143131
tmp.list <- list()
144132
if (is.null(system.type)) {
@@ -216,6 +204,14 @@ function(
216204
return(tmp.list)
217205
} ### END get.target.arguments
218206

207+
getInitialStatusNames <- function(target.type.iter) {
208+
if (target.type.iter=="sgp.projections") tmp.names <- c("CATCH_UP_KEEP_UP_STATUS_INITIAL_CURRENT", "MOVE_UP_STAY_UP_STATUS_INITIAL_CURRENT")
209+
if (target.type.iter=="sgp.projections.baseline") tmp.names <- c("CATCH_UP_KEEP_UP_STATUS_INITIAL_CURRENT_BASELINE", "MOVE_UP_STAY_UP_STATUS_INITIAL_CURRENT_BASELINE")
210+
if (target.type.iter=="sgp.projections.lagged") tmp.names <- c("CATCH_UP_KEEP_UP_STATUS_INITIAL", "MOVE_UP_STAY_UP_STATUS_INITIAL")
211+
if (target.type.iter=="sgp.projections.lagged.baseline") tmp.names <- c("CATCH_UP_KEEP_UP_STATUS_INITIAL_BASELINE", "MOVE_UP_STAY_UP_STATUS_INITIAL_BASELINE")
212+
return(tmp.names)
213+
}
214+
219215
catch_keep_move_functions <- c(min, max)
220216

221217
getTargetData <- function(tmp.target.data, projection_group.iter, tmp.target.level.names) {
@@ -226,7 +222,6 @@ function(
226222
na.omit(tmp.data, cols=grep("MOVE_UP_STAY_UP", tmp.target.level.names, invert=TRUE, value=TRUE))
227223
}
228224

229-
230225
############################################################################
231226
### Check update.all.years
232227
############################################################################
@@ -486,7 +481,7 @@ function(
486481
invisible(slot.data[, paste0("SCALE_SCORE_PRIOR_", tmp.prior-1L) := as.numeric(sapply(tmp.split, function(x) rev(x)[tmp.prior]))])
487482
}}}
488483

489-
tmp.data <- getTargetSGP(sgp_object, slot.data, content_areas, state, years, target.type.iter, target.level.iter, current.year.lagged.target, max.sgp.target.years.forward, fix.duplicates=fix.duplicates, return.sgp.target.num.years=return.sgp.target.num.years)
484+
tmp.data <- getTargetSGP(sgp_object, slot.data, content_areas, state, years, target.type.iter, target.level.iter, max.sgp.target.years.forward, fix.duplicates=fix.duplicates, return.sgp.target.num.years=TRUE)
490485

491486
if (dim(tmp.data)[1] > 0) {
492487
if (!is.null(fix.duplicates)) dup.by <- c(key(tmp.data), grep("SCALE_SCORE$|SCALE_SCORE_PRIOR", names(tmp.data), value=TRUE)) else dup.by <- key(tmp.data)
@@ -542,7 +537,8 @@ function(
542537
}
543538

544539
### SGP_TARGET_CONTENT_AREA calculation
545-
terminal.content_areas <- unique(slot.data[!slot.data[,all(is.na(.SD)), .SDcols=grep("SGP_TARGET", grep(paste(max(max.sgp.target.years.forward), "YEAR", sep="_"), names(slot.data), value=TRUE), value=TRUE), by=seq_len(nrow(slot.data))][['V1']]][['CONTENT_AREA']])
540+
tmp.cols.to.test <- grep("SGP_TARGET", grep(paste(max(max.sgp.target.years.forward), "YEAR", sep="_"), names(slot.data), value=TRUE), value=TRUE)
541+
terminal.content_areas <- unique(slot.data[slot.data[, rowSums(!is.na(.SD)) > 0, .SDcols = tmp.cols.to.test]][['CONTENT_AREA']])
546542
if (!is.null(SGP::SGPstateData[[state]][["SGP_Configuration"]][["content_area.projection.sequence"]])) {
547543
terminal.content_areas <- intersect(terminal.content_areas, sapply(SGP::SGPstateData[[state]][["SGP_Configuration"]][["content_area.projection.sequence"]], tail, 1))
548544
}
@@ -605,7 +601,6 @@ function(
605601
}
606602
}
607603

608-
609604
### MOVE_UP_STAY_UP_STATUS Calculation
610605

611606
if ("MOVE_UP_STAY_UP" %in% target.args[['target.level']] & (sgp.projections.lagged | sgp.projections.lagged.baseline) & "MOVE_UP_STAY_UP_STATUS_INITIAL" %in% names(slot.data)) {
@@ -674,7 +669,7 @@ function(
674669
for (target.type.iter in target.args[['sgp.target.scale.scores.types']]) {
675670
for (target.level.iter in target.args[['target.level']]) {
676671
tmp.target.list[[paste(target.type.iter, target.level.iter)]] <-
677-
data.table(getTargetSGP(sgp_object, slot.data, content_areas, state, years, target.type.iter, target.level.iter, current.year.lagged.target, max.sgp.target.years.forward, return.lagged.status=FALSE, fix.duplicates=fix.duplicates, return.sgp.target.num.years=TRUE),
672+
data.table(getTargetSGP(sgp_object, slot.data, content_areas, state, years, target.type.iter, target.level.iter, max.sgp.target.years.forward, return.lagged.status=FALSE, fix.duplicates=fix.duplicates, return.sgp.target.num.years=TRUE, return.sgp.target.num.years.note=FALSE),
678673
key=c(getKey(sgp_object), "SGP_PROJECTION_GROUP"))
679674
}
680675
}
@@ -690,19 +685,15 @@ function(
690685

691686
for (projection_group.iter in unique(tmp.target.data[['SGP_PROJECTION_GROUP']])) {
692687
for (target.type.iter in target.args[['sgp.target.scale.scores.types']]) {
693-
if (target.type.iter %in% c("sgp.projections.lagged", "sgp.projections.lagged.baseline")) {
694-
max.sgp.target.years.forward.tmp <- max.sgp.target.years.forward + 1L
695-
if (current.year.lagged.target) max.sgp.target.years.forward.tmp <- c(1, max.sgp.target.years.forward.tmp)
696-
max.sgp.target.years.forward.tmp <- max.sgp.target.years.forward.tmp - 1L
697-
} else max.sgp.target.years.forward.tmp <- max.sgp.target.years.forward
698-
for (target.years.iter in max.sgp.target.years.forward.tmp) {
688+
for (target.years.iter in max.sgp.target.years.forward) {
699689
tmp.target.level.names <- as.character(sapply(target.args[['target.level']], function(x) getTargetName(state, target.type.iter, x, target.years.iter, "SGP_TARGET", projection.unit.label, projection_group.iter)))
700690
if (any(!tmp.target.level.names %in% names(tmp.target.data))) {
701691
tmp.target.data[,tmp.target.level.names[!tmp.target.level.names %in% names(tmp.target.data)]:=as.integer(NA)]
702692
}
703-
tmp.target.level.names.years.to.target <- paste(tmp.target.level.names, "NUM_YEARS_TO_TARGET", sep="_")
704693

705-
targetData <- getTargetData(tmp.target.data, projection_group.iter, c(tmp.target.level.names, tmp.target.level.names.years.to.target))
694+
tmp.target.level.names.years.to.target <- paste(tmp.target.level.names, "NUM_YEARS_TO_TARGET", sep="_")
695+
tmp.initial.status.names <- getInitialStatusNames(target.type.iter)
696+
targetData <- getTargetData(tmp.target.data, projection_group.iter, c(tmp.target.level.names, tmp.target.level.names.years.to.target, tmp.initial.status.names))
706697

707698
if (dim(targetData)[1] > 0) {
708699
sgp_object <- getTargetScaleScore(
@@ -722,10 +713,12 @@ function(
722713
}
723714
}
724715
}
725-
}
716+
} ## END projection.group.iter
717+
726718
if (length(max.sgp.target.years.forward) > 1) {
727-
for (names.iter in grep("TARGET_SCALE_SCORES", names(sgp_object@SGP$SGProjections), value=TRUE)) {
728-
sgp_object@SGP$SGProjections[[names.iter]] <- sgp_object@SGP$SGProjections[[names.iter]][,lapply(.SD, mean_nan), by=c("ID", "GRADE", "SGP_PROJECTION_GROUP", "SGP_PROJECTION_GROUP_SCALE_SCORES")]
719+
for (names.iter in getTargetScaleScoreTableNames(names(sgp_object@SGP[['SGProjections']]), years)) {
720+
sgp_object@SGP[['SGProjections']][[names.iter]] <- sgp_object@SGP[['SGProjections']][[names.iter]][,lapply(.SD, mean, na.rm=TRUE), by=c("ID", "GRADE", "SGP_PROJECTION_GROUP", "SGP_PROJECTION_GROUP_SCALE_SCORES")] # nolint
721+
sgp_object@SGP[['SGProjections']][[names.iter]] <- sgp_object@SGP[['SGProjections']][[names.iter]][,lapply(.SD, function(x) ifelse(is.nan(x), NA, x))]
729722
}
730723
}
731724
if (!identical(sgp.target.scale.scores.merge, FALSE)) {
@@ -745,8 +738,3 @@ function(
745738

746739
return(sgp_object)
747740
} ## END combineSGP Function
748-
749-
`mean_nan` <-
750-
function(x) {
751-
if (all(is.na(x))) return(as.numeric(NA)) else return(mean(x, na.rm=TRUE))
752-
} ### END mean_nan function

R/csemScoreSimulator.R

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -54,7 +54,7 @@ function(
5454
} else {
5555
tmp.scores <- data.table(SIM=round(rnorm(length(scale_scores), scale_scores, tmp.omega), digits=round.digits))
5656
}
57-
tmp.scores[SIM < min.max[1L], SIM:=min.max[1L]]
58-
tmp.scores[SIM > min.max[2L], SIM:=min.max[2L]]
57+
58+
tmp.scores[SIM < min.max[1L] | SIM > min.max[2L], SIM:=fifelse(SIM < min.max[1L], min.max[1L], min.max[2L])]
5959
return(tmp.scores[['SIM']])
6060
} ### END csemScoreSimulator

R/getPanelData.R

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -225,7 +225,7 @@ function(sgp.data,
225225
tmp.data <- ddcast(rbindlist(tmp.lookup.list),
226226
ID ~ tmp.timevar, value.var=c("GRADE", "SCALE_SCORE", "YEAR_WITHIN", state, sgp.scale.score.equated, SGPt), sep=".")[
227227
sgp.targets[CONTENT_AREA==tail(sgp.iter[[sgp.projection.content.areas.label]], 1L) & YEAR==tail(sgp.iter[["sgp.panel.years"]], 1L) & GRADE==tail(sgp.iter[[sgp.projection.grade.sequences.label]], 1L)], nomatch=0][,
228-
!c("CONTENT_AREA", "YEAR"), with=FALSE]
228+
!c("CONTENT_AREA", "YEAR", "GRADE"), with=FALSE]
229229
if (dim(tmp.data)[1] > 0) {
230230
setnames(tmp.data, tail(sort(grep("YEAR_WITHIN", names(tmp.data), value=TRUE)), 1L), "YEAR_WITHIN")
231231
if (length(setdiff(grep("YEAR_WITHIN", names(tmp.data), value=TRUE), "YEAR_WITHIN")) > 0L) {
@@ -311,15 +311,15 @@ function(sgp.data,
311311
tmp.data <- ddcast(tmp.data,
312312
ID ~ tmp.timevar, value.var=c("GRADE", "SCALE_SCORE", state, sgp.scale.score.equated, SGPt), sep=".")[
313313
sgp.targets[CONTENT_AREA==tail(sgp.iter[[sgp.projection.content.areas.label]], 1L) & YEAR==tail(sgp.iter[[sgp.projection.panel.years.label]], 1L) &
314-
GRADE==tail(sgp.iter[[sgp.projection.grade.sequences.label]], 1L)], nomatch=0][,!c("CONTENT_AREA", "YEAR"), with=FALSE]
314+
GRADE==tail(sgp.iter[[sgp.projection.grade.sequences.label]], 1L)], nomatch=0][,!c("CONTENT_AREA", "YEAR", "GRADE"), with=FALSE]
315315
} else { ### END if (is.character(fix.duplicates)
316316
tmp.data <- ddcast(
317317
data.table(dbGetQuery(con, paste0("select * from sgp_data where CONTENT_AREA in ('", paste(tmp.lookup$V2, collapse="', '"), "')",
318318
" AND GRADE in ('", paste(tmp.lookup$V4, collapse="', '"), "')", " AND YEAR in ('", paste(tmp.lookup$V3, collapse="', '"), "')"))
319319
, key=c("VALID_CASE", "CONTENT_AREA", "YEAR", "GRADE"))[tmp.lookup, nomatch=0][,'tmp.timevar':=paste(YEAR, CONTENT_AREA, sep=".")],
320320
ID ~ tmp.timevar, value.var=c("GRADE", "SCALE_SCORE", state, sgp.scale.score.equated, SGPt), sep=".")[
321321
sgp.targets[CONTENT_AREA==tail(sgp.iter[[sgp.projection.content.areas.label]], 1L) & YEAR==tail(sgp.iter[[sgp.projection.panel.years.label]], 1L) &
322-
GRADE==tail(sgp.iter[[sgp.projection.grade.sequences.label]], 1L)], nomatch=0][,!c("CONTENT_AREA", "YEAR"), with=FALSE]
322+
GRADE==tail(sgp.iter[[sgp.projection.grade.sequences.label]], 1L)], nomatch=0][,!c("CONTENT_AREA", "YEAR", "GRADE"), with=FALSE]
323323
}
324324
dbDisconnect(con)
325325
} else {
@@ -364,7 +364,7 @@ function(sgp.data,
364364
ID ~ tmp.timevar, value.var=c("GRADE", "SCALE_SCORE", state, sgp.scale.score.equated, SGPt), sep=".")[
365365
sgp.targets[CONTENT_AREA==tail(sgp.iter[[sgp.projection.content.areas.label]], 1L) &
366366
YEAR==tail(sgp.iter[[sgp.projection.panel.years.label]], 1L) & GRADE==tail(sgp.iter[[sgp.projection.grade.sequences.label]], 1L)],
367-
on="ID", nomatch=0][,!c("CONTENT_AREA", "YEAR"), with=FALSE]
367+
on="ID", nomatch=0][,!c("CONTENT_AREA", "YEAR", "GRADE"), with=FALSE]
368368
}
369369
}
370370

@@ -378,7 +378,7 @@ function(sgp.data,
378378

379379

380380
###
381-
### sgp.projections.lagged
381+
### sgp.projections.lagged & sgp.projections.lagged.baseline
382382
###
383383

384384
if (sgp.type %in% c("sgp.projections.lagged", "sgp.projections.lagged.baseline")) {
@@ -458,7 +458,7 @@ function(sgp.data,
458458
tmp.data <- ddcast(rbindlist(tmp.lookup.list),
459459
ID ~ tmp.timevar, value.var=c("GRADE", "SCALE_SCORE", "ACHIEVEMENT_LEVEL", "YEAR_WITHIN", state, sgp.scale.score.equated, SGPt), sep=".")[
460460
sgp.targets[CONTENT_AREA==tail(sgp.iter[["sgp.content.areas"]], 1L) &
461-
YEAR==tail(sgp.iter[["sgp.panel.years"]], 1L) & GRADE==tail(sgp.iter[["sgp.grade.sequences"]], 1L)], nomatch=0][,!c("CONTENT_AREA", "YEAR"), with=FALSE]
461+
YEAR==tail(sgp.iter[["sgp.panel.years"]], 1L) & GRADE==tail(sgp.iter[["sgp.grade.sequences"]], 1L)], nomatch=0][,!c("CONTENT_AREA", "YEAR", "GRADE"), with=FALSE]
462462

463463
setnames(tmp.data, names(tmp.data)[grep(achievement.level.prior.vname, names(tmp.data))], achievement.level.prior.vname)
464464
setnames(tmp.data, tail(sort(grep("YEAR_WITHIN", names(tmp.data), value=TRUE)), 1L), "YEAR_WITHIN")
@@ -563,7 +563,7 @@ function(sgp.data,
563563
tmp.data <- ddcast(tmp.data,
564564
ID ~ tmp.timevar, value.var=c("GRADE", "SCALE_SCORE", state, sgp.scale.score.equated, SGPt), sep=".")[
565565
sgp.targets[CONTENT_AREA==tail(sgp.iter[["sgp.content.areas"]], 1L) &
566-
YEAR==tail(sgp.iter[["sgp.panel.years"]], 1L) & GRADE==tail(sgp.iter[[sgp.projection.grade.sequences.label]], 1L)], nomatch=0][, !c("CONTENT_AREA", "YEAR"), with=FALSE]
566+
YEAR==tail(sgp.iter[["sgp.panel.years"]], 1L) & GRADE==tail(sgp.iter[[sgp.projection.grade.sequences.label]], 1L)], nomatch=0][, !c("CONTENT_AREA", "YEAR", "GRADE"), with=FALSE]
567567
dbDisconnect(con)
568568
} else {
569569
tmp.lookup1 <- SJ("VALID_CASE",
@@ -619,7 +619,7 @@ function(sgp.data,
619619
'tmp.timevar':=paste(YEAR, CONTENT_AREA, sep=".")],
620620
ID ~ tmp.timevar, value.var=c("GRADE", "SCALE_SCORE", state, sgp.scale.score.equated, SGPt), sep=".")[
621621
sgp.targets[CONTENT_AREA == tmp.lookup1[["CONTENT_AREA"]] & YEAR == tmp.lookup1[["YEAR"]] & GRADE == tmp.lookup1[["GRADE"]]], nomatch=0][,
622-
!c("CONTENT_AREA", "YEAR"), with=FALSE]
622+
!c("CONTENT_AREA", "YEAR", "GRADE"), with=FALSE]
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}
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}
625625

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