forked from pik-piam/mip
-
Notifications
You must be signed in to change notification settings - Fork 0
/
validationpdf.R
449 lines (413 loc) · 17.7 KB
/
validationpdf.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
#' Create a validation PDF file
#'
#' @param x Data to be validated. All formats allowed which can be converted to quitte (including characters containing the path to a mif or rds file)
#' @param hist Validation data.All formats allowed which can be converted to quitte (including characters containing the path to a mif or rds file)
#' @param file file name of the output PDF or a Sweave object. If a sweave object is provided the function will return the updated object, otherwise
#' it will write its content to the file
#' @param style data style for the returned data. Currently available: "trafficlight", "detailed", "comparison"
#' @param only_historical boolean deciding whether only historical data should be used for validation or also projections from other sources
#' @param digits integer indicating the number of digits to be shown.
#' @param filter Additional filter to be applied on the data to only plot a subset of the provided data
#' @param prefix Prefix which will be put in front of each part title (useful if validation is integrated into a bigger document)
#' @param hideEmptySection removes sections in output file which would be empty for the reason that variables in input 'x' has have correspondance in the hist file
#' @param show_stats boolean specifying whether additional statistic section should show up or not
#' @param debug Switch to activate or deactivate debug mode.
#' @param pdfStyle list of style-options for the pdf
#' @author Jan Philipp Dietrich
#' @importFrom magclass as.magpie ndata dimSums nyears getRegions getNames nregions
#' @importFrom quitte as.quitte getRegs read.quitte
#' @importFrom lusweave swopen swclose swfigure swR swtable swlatex
#' @importFrom trafficlight trafficlight
#' @importFrom reshape2 melt
#' @export
#'
validationpdf <- function(x,hist,file="validation.pdf",style="comparison", only_historical=FALSE, digits=3, filter=NULL, prefix=NULL, hideEmptySection=FALSE, show_stats=TRUE, debug=getOption("debug"), pdfStyle=NULL) {
if(is.null(debug)) debug <- FALSE
styles <- c("trafficlight","comparison","detailed")
if(!(style %in% styles)) stop("Unknown style \"",style,"\", please use one of the following: ",paste(styles,collapse=", "))
# convert x into a quitte object
if(is.character(x)) {
filetype <- sub("^.*\\.","",x)
if(filetype=="rds") {
x <- readRDS(x)
} else {
x <- read.quitte(x, check.duplicates = FALSE)
}
} else {
x <- as.quitte(x)
}
# select only the time horizon specified in pdfStyle
if("years" %in% names(pdfStyle) ) {
y <- pdfStyle$years
x <- x[x$period %in% y,]
x <- as.quitte(x)
}
if(!is.null(hist)) {
if(is.character(hist)) {
filetype <- sub("^.*\\.","",hist)
if(filetype=="rds") {
hist <- readRDS(hist)
} else {
hist <- read.quitte(hist, check.duplicates = FALSE)
}
} else {
hist <- as.quitte(hist)
}
# strip down NAs
hist <- hist[!is.na(hist$value),]
}
colcheck <- names(hist) %in% c("model","scenario","region","variable","unit","period","value")
if(any(!colcheck)) {
hist <- hist[colcheck]
warning("Unknown column in validation data removed!")
}
#rename "World" in GLO
.tmp <- function(x) {
if(is.factor(x)) {
if("World" %in% levels(x)) levels(x)[levels(x)=="World"] <- "GLO"
} else {
w <- which(x=="World")
if(length(w)>0) x[w] <- "GLO"
}
return(x)
}
x$region <- .tmp(x$region)
hist$region <- .tmp(hist$region)
if(all(is.na(x$scenario))) x$scenario <- "default"
tmp <- function(filter,x) {
if(is.null(filter)) return(TRUE)
else return(grepl(filter,x))
}
#filter data
x <- droplevels(x[!is.na(x$value) & tmp(filter,x$variable),])
hist <- droplevels(hist[!is.na(hist$value) & tmp(filter,hist$variable),])
if(only_historical) hist <- droplevels(hist[hist$scenario=="historical",])
if(dim(x)[1]==0) stop("No data remaining to be validated after all filter have been applied!")
if(dim(hist)[1]==0) stop("No validation data remaining after all filter have been applied!")
x$fullname <- paste0(x$variable, " (",x$unit,")")
hist$fullname <- paste0(hist$variable, " (",hist$unit,")")
vars <- x$fullname
remove_symbols <- function(x) return(gsub("(\\++|\\-+)\\|","", x))
extract_symbols <- function(x) return(gsub("(\\+|\\-)\\|","\\1",gsub("[^\\|^\\+^\\-]*","",x)))
x$fullname <- as.factor(remove_symbols(x$fullname))
hist$fullname <- as.factor(remove_symbols(hist$fullname))
xtrax <- setdiff(x$fullname,hist$fullname)
xtrahist <- setdiff(hist$fullname,x$fullname)
x$variable <- remove_symbols(x$variable)
hist$variable <- remove_symbols(hist$variable)
splitvars <- function(vars, nlevel=4) {
properties <- extract_symbols(vars)
fullname <- remove_symbols(vars)
unit <- sub("^.* \\(([^\\)]*)\\)$","\\1",fullname)
vars <- sub("^(.*) \\(([^\\)]*)\\)$","\\1",fullname)
.split <- function(vars, ignore_rest=FALSE) {
out <- vars
tmp <- vars
for(i in 1:(nlevel-1)) {
out <- cbind(out,sub("\\|.*$","",tmp))
tmp <- sub("^[^\\|]*(\\||$)","",tmp)
}
if(ignore_rest) tmp <- sub("\\|.*$","",tmp)
return(cbind(out,tmp))
}
out <- cbind(fullname, unit, .split(vars), .split(properties,TRUE))
out <- as.data.frame(out, stringsAsFactors = TRUE)
names(out) <- c("fullname","unit","name",paste0("level",1:nlevel),"props",paste0("prop",1:nlevel))
return(out)
}
vars <- splitvars(vars, nlevel=4)
calc_digits <- function(tmpx,digits) {
d <- max(0,-1*ceiling(log10(max(tmpx)))+digits)
if(is.finite(d) & is.numeric(d)) return(d)
return(0)
}
prepmagpie <- function(x,hist) {
tmpsort <- function(x){
reg <- sort(getRegions(x))
if("GLO" %in% reg) reg <- c("GLO",reg[reg!="GLO"])
return(x[reg,,])
}
tmpx <- tmpsort(as.magpie(as.quitte(x)))
tmphist <- tmpsort(as.magpie(as.quitte(hist)))
regs <- intersect(getRegions(tmpx),getRegions(tmphist))
return(list(x=tmpx[regs,,],hist=tmphist[regs,,]))
}
preptitle <- function(x) {
# put unit in brackets
x <- sub("\\.([^\\.]*)$"," (\\1)",x)
# combine model and scenario
x <- sub(".", " ", x, fixed=TRUE)
# remove scenario name if it is "historical"
x <- sub(" historical", "", x, fixed=TRUE)
# replace remaining .-separators
x <- gsub(".", " | ", x, fixed=TRUE)
# replace "%" with "percent" to avoid error in tex
x <- gsub("%", "\\%", x, fixed = TRUE)
return(x)
}
histtables <- function(sw, m, digits) {
dimnames(m$x)[[2]] <- sub("y","",dimnames(m$x)[[2]])
for(s in 1:ndata(m$x)) {
swlatex(sw,"\\hspace{10 mm}")
swtable(sw,m$x[,,s],preptitle(getNames(m$x)[s]), digits=calc_digits(m$x,digits), vert.lines = 0, align="r", table.placement="H", colsplit=11)
}
if(any(grepl(".historical.",getNames(m$hist),fixed=TRUE))) {
m$hist <- m$hist[,,"historical"]
for(i in 1:ndata(m$hist)) {
mhist2 <- m$hist[,,i]
#remove NAs
mhist2 <- mhist2[,dimSums(!is.na(mhist2),dim=c(1,3))!=0,]
if(nyears(mhist2)>0) {
swlatex(sw,"\\hspace{10 mm}")
dimnames(mhist2)[[2]] <- sub("y","",dimnames(mhist2)[[2]])
swtable(sw,mhist2, preptitle(getNames(m$hist)[i]), digits=calc_digits(mhist2,digits), vert.lines = 0, align="r", table.placement="H", colsplit=11)
}
}
}
}
styleTrafficlight <- function(sw, x, hist, stats) {
m <- prepmagpie(x,hist)
p <- trafficlight(m$x,m$hist, detailed=FALSE)
stats$trafficlight <- rbind(stats$trafficlight,melt(attr(p,"data")))
swfigure(sw,print,p, sw_option="width=10,height=2")
return(stats)
}
styleDetailed <- function(sw, x, hist, varname, stats) {
m <- prepmagpie(x,hist)
name <- paste0(sub("^.*\\|","",varname["name"]), " (",x$unit[[1]],")")
if("GLO" %in% intersect(getRegs(x),getRegs(hist))) {
if("plot.priority" %in% names(pdfStyle) ) {
prio <- pdfStyle$plot.priority
swfigure(sw,mipLineHistorical,x[x$region=="GLO",],hist[hist$region=="GLO",], ylab=name, plot.priority = prio)
} else {
swfigure(sw,mipLineHistorical,x[x$region=="GLO",],hist[hist$region=="GLO",], ylab=name)
}
}
regs <- setdiff(intersect(getRegs(x),getRegs(hist)),"GLO")
if(length(regs)>0) {
if("plot.priority" %in% names(pdfStyle) ) {
prio <- pdfStyle$plot.priority
swfigure(sw,mipLineHistorical,x[x$region %in% regs,],hist[hist$region %in% regs,], ylab=name, facet.dim = "region", size=12, plot.priority = prio)
} else {
swfigure(sw,mipLineHistorical,x[x$region %in% regs,],hist[hist$region %in% regs,], ylab=name, facet.dim = "region", size=12)
}
}
p <- trafficlight(m$x,m$hist)
stats$trafficlight <- rbind(stats$trafficlight,melt(attr(p,"data")))
swfigure(sw,print,p, sw_option="width=8,height=11")
histtables(sw,m,digits)
return(stats)
}
styleComparison <- function(sw, x, hist, varname, stats, debug) {
m <- prepmagpie(x,hist)
name <- paste0(sub("^.*\\|","",varname["name"]), " (",x$unit[[1]],")")
if(debug) save(x,hist,file = paste0("mipLineHistorical_",make.names(varname["name"]),".Rda"))
if("plot.priority" %in% names(pdfStyle)) {
plot.priority <- pdfStyle$plot.priority
} else {
plot.priority <- c("x", "x_hist", "x_proj")
}
if("GLO" %in% intersect(getRegs(x),getRegs(hist))) {
mLH <- swfigure(sw,mipLineHistorical,x[x$region=="GLO",],hist[hist$region=="GLO",], ylab=name, plot.priority = plot.priority)
swfigure(sw, print, mLH)
}
regs <- setdiff(intersect(getRegs(x),getRegs(hist)),"GLO")
if(length(regs) > 0) {
mLH <- mipLineHistorical(x[x$region %in% regs,],hist[hist$region %in% regs,], ylab=name, facet.dim = "region", size=12, plot.priority = plot.priority)
swfigure(sw, print, mLH)
}
for(s in 1:ndata(m$x)) {
x <- m$x[,,s]
xc <- m$hist
if(debug) save(x,xc,file = paste0("trafficlight_",make.names(varname["name"]),s,".Rda"))
p <- trafficlight(m$x[,,s],m$hist, detailed=(nregions(m$x)<2))
stats$trafficlight <- rbind(stats$trafficlight,melt(attr(p,"data")))
swfigure(sw,print,p, tex_caption=preptitle(getNames(m$x)[s]), sw_option="width=10,height=2")
}
histtables(sw,m,digits)
return(stats)
}
hascontent <- function(stats, ...) {
test <- list(...)
hascontent <- TRUE
for(n in names(test)) {
if(all(test[[n]]$value==0, na.rm=TRUE)) {
if(is.null(stats$ignored_all0)) stats$ignored_all0 <- list()
stats$ignored_all0[[n]] <- c(stats$ignored_all0[[n]],levels(droplevels(test[[n]]$fullname)))
hascontent <- FALSE
}
}
stats$hascontent <- hascontent
return(stats)
}
fillcontent <- function(sw, x, hist, varname, style, stats) {
stats <- hascontent(stats,x=x,hist=hist)
if(!stats$hascontent) return(stats)
x$fullname <- NULL
hist$fullname <- NULL
if(varname["level4"]!="") {
cat(" ...",varname["level4"],"\n")
swlatex(sw,paste0("\\subsubsection{",varname["level4"],"}"))
}
if(style=="trafficlight") {
stats <- styleTrafficlight(sw, x, hist, stats)
} else if(style=="comparison") {
stats <- styleComparison(sw, x, hist, varname, stats, debug)
} else if(style=="detailed") {
stats <- styleDetailed(sw, x, hist, varname, stats)
} else {
stop("Unknown style ",style)
}
return(stats)
}
template <- c("\\documentclass[a4paper, portrait ]{article}",
"\\setlength{\\parindent}{0in}",
"\\usepackage{float}",
"\\usepackage[bookmarksopenlevel=section]{hyperref}",
"\\hypersetup{bookmarks=true,pdfauthor={PIK Landuse group}}",
"\\usepackage{graphicx}",
"\\usepackage{rotating}",
"\\usepackage[strings]{underscore}",
"\\usepackage[margin=2cm]{geometry}",
"\\usepackage{fancyhdr}",
"\\pagestyle{fancy}",
"\\begin{document}",
"<<echo=false>>=",
"options(width=110)",
"@")
cat("Start preparing data...\n")
if(is.environment(file)) {
sw <- file
} else {
sw <- swopen(outfile = file, template = template)
swlatex(sw,c("\\title{Model Validation}","\\author{HAL 9000}","\\maketitle","\\tableofcontents"))
on.exit(swclose(sw, clean_output=!debug, engine="knitr"))
}
stats <- list()
if (hideEmptySection)
{
vars <- vars[vars$fullname %in% levels(hist$fullname),]
vars <- droplevels(vars)
}
for(l1 in levels(vars$level1)) {
cat("...",l1,"\n")
swlatex(sw,"\\clearpage")
swlatex(sw,paste0("\\part{",prefix,l1,"}"))
vars1 <- droplevels(vars[vars$level1==l1,])
stackedbar(sw, vars1, x, level=2, debug=debug)
for(l2 in levels(vars1$level2)) {
if(l2!="") {
cat(" ...",l2,"\n")
swlatex(sw,paste0("\\section{",l2,"}"))
}
vars2 <- droplevels(vars1[vars1$level2==l2,])
stackedbar(sw, vars2, x, level=3, debug=debug)
for(l3 in levels(vars2$level3)) {
vars3 <- droplevels(vars2[vars2$level3==l3,])
stackedbar(sw, vars3, x, level=4, debug=debug)
stats <- hascontent(stats,x=x[x$fullname %in% levels(vars3$fullname),],hist=hist[hist$fullname %in% levels(vars3$fullname),])
if(!stats$hascontent) next
if(l3!="") {
cat(" ...",l3,"\n")
swlatex(sw,paste0("\\subsection{",l3,"}"))
}
for(l4 in levels(vars3$level4)) {
varname <- as.matrix(vars3[vars3$level4==l4,])
if(dim(varname)[1]>1) warnings("There seems to be a problem with the variable names. Use only first option!")
varname <- varname[1,]
stats <- fillcontent(sw,x[x$fullname==varname["fullname"],],hist[hist$fullname==varname["fullname"],],varname, style, stats)
}
}
}
}
if(show_stats & (!is.null(stats$trafficlight) | length(xtrax)>0 | length(xtrahist)>0 | !is.null(stats$ignored_all0)) ) {
swlatex(sw,"\\clearpage")
swlatex(sw,paste0("\\part{",prefix,"Statistics}"))
if(!is.null(stats$trafficlight)) {
swlatex(sw,"\\section{Traffic Lights}")
tl <- stats$trafficlight
tlsummary <- function(tl) {
tl[is.na(tl)] <- -1
summary <- data.frame(green = sum(tl$value==2),
yellow = sum(tl$value==1),
red = sum(tl$value==0),
"NA" = sum(tl$value==-1))
summary <- rbind(summary,round(summary/sum(summary),2))
rownames(summary) <- c("total","relative")
return(summary)
}
stats$summary <- list()
for(i in grep(".",levels(tl$Var2),fixed=TRUE,invert=TRUE,value=TRUE)) {
stats$summary[[i]] <- list(GLO=tlsummary(tl[tl$Var2==i & tl$Var1=="GLO",]),
REG=tlsummary(tl[tl$Var2==i & tl$Var1!="GLO",]))
swlatex(sw,paste0("\\subsection{",i,"}"))
tmp <- stats$summary[[i]][["GLO"]]
if(any(tmp[1,]>0, na.rm = TRUE)) {
tmp[2,] <- paste0(tmp[2,]*100,"%")
swtable(sw,tmp, caption="Global",table.placement="H")
}
tmp <- stats$summary[[i]][["REG"]]
if(any(tmp[1,]>0, na.rm = TRUE)) {
tmp[2,] <- paste0(tmp[2,]*100,"%")
swtable(sw,tmp, caption="Regional",table.placement="H")
}
}
}
if(!is.null(stats$ignored_all0)) {
swlatex(sw,"\\section{Ignored data}")
if(!is.null(stats$ignored_all0$x) && !is.null(stats$ignored_all0$hist)) {
swlatex(sw, "Variables of data and validation data that only contain a mix of 0 and NA values and are ignored.")
swR(sw, cat, intersect(stats$ignored_all0$x, stats$ignored_all0$hist), sep="\n")
}
if(!is.null(stats$ignored_all0$x)){
swlatex(sw, "Data contains only a mix of 0 and NA values and is ignored, but validation data contains other values.")
swR(sw, cat,setdiff(stats$ignored_all0$x, stats$ignored_all0$hist) ,sep="\n")
}
if(!is.null(stats$ignored_all0$hist)){
swlatex(sw, "Validation data contains only a mix of 0 and NA values and is ignored, but data contains other values.")
swR(sw, cat,setdiff(stats$ignored_all0$hist, stats$ignored_all0$x) ,sep="\n")
}
# if(!is.null(stats$ignored_all0$x)) {
# swlatex(sw,"Data contains only a mix of 0 and NA values and is ignored.")
# swR(sw,cat,stats$ignored_all0$x,sep="\n")
# }
# if(!is.null(stats$ignored_all0$hist)) {
# swlatex(sw,"Validation data contains only a mix of 0 and NA values and is ignored.")
# swR(sw,cat,stats$ignored_all0$hist,sep="\n")
# }
}
if(length(xtrax)>0 | length(xtrahist)>0) {
swlatex(sw,"\\section{Non-Matching Data}")
if(length(xtrax)>0) {
swlatex(sw,"\\subsection{Model outputs}")
swR(sw,cat,xtrax,sep="\n")
}
if(length(xtrahist)>0) {
swlatex(sw,"\\subsection{Validation data}")
swR(sw,cat,xtrahist,sep="\n")
}
}
}
cat("Finished preparing data!\n")
return(stats)
}
stackedbar <- function(sw, vars, x, level, debug=FALSE) {
# analyze wether a stacked bar plot should be plotted and prepare data
tmp <- function(sw, vars, x, level, symbol, debug=FALSE) {
vars <- droplevels(vars[vars[[paste0("prop",level)]]==symbol,])
if(dim(vars)[1]==0) return(FALSE)
x <- as.quitte(droplevels(x[x$fullname %in% levels(vars$fullname),]))
if(all(x==0,na.rm = TRUE)) return(FALSE)
if(debug) {
name <- attr(shorten_legend(x$variable, identical_only = TRUE), "front")
save(x,file = paste0("mipArea_",make.names(name),".Rda"))
}
if("GLO" %in% levels(x$region)) swfigure(sw,mipArea,x[x$region=="GLO",])
if(length(setdiff(levels(x$region),"GLO"))>0) swfigure(sw,mipArea,x[x$region!="GLO",])
return(TRUE)
}
symbol <- "+"
while(tmp(sw,vars,x,level,symbol,debug)) {
symbol <- paste0(symbol,"+")
}
}