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
|
.tag_in <- function(x, tags){
a <- attr(x,"Rd_tag")
is.character(a) && length(a) == 1 && a %in% tags
}
.tag_eq <- function(x, tag){
a <- attr(x,"Rd_tag")
is.character(a) && length(a) == 1 && a == tag
}
.ocompare <- function(x,y){ # outer compare
f <- function(z) sapply(x, function(w) identical(z,w))
sapply(y,f)
}
.asym_compare <- function(x,y){
cmp <- .ocompare(x,y)
if(length(x) == 1){ # 2012-10-03 added this if
cmp <- matrix(cmp, nrow=1)
}
if(length(x) == 0){
inew <- seq_along(y)
irem <- icom <- integer(0)
}else if(length(y) == 0){
irem <- seq_along(x)
inew <- icom <- integer(0)
}else{
inew <- which( ! apply(cmp, 2, any) ) # in y but not in x
irem <- which( ! apply(cmp, 1, any) ) # in x but not in y
icom <- which( !(seq_along(x) %in% c(inew, irem)) ) # in both, x and y
}
list( i_new = inew,
i_removed = irem,
i_common = icom )
}
rattr <- function(x,y){ # restore attributes, see Rdapply below
if(is.list(x)){
if(!identical(attributes(x), attributes(y)))
attributes(x) <- attributes(y)
for(i in seq_along(x))
x[[i]] <- Recall(x[[i]], y[[i]])
}
x
}
Rdapply <- function(x, ...){ # needed since rapply loses attributes of x
wrk <- rapply(x, ...)
rattr(wrk, x)
}
.pos_in_eqnpos <- function(verb, eqn){ # not a complete solution
f <- function(x,y) length(x) > length(y) && all( x[seq_along(y)] == y )
flag <- FALSE
res <- vector(mode="logical", length = length(verb))
for(i in seq_along(verb)){
for(j in seq_along(eqn)){
flag <- f(verb[[i]], eqn[[j]])
if(flag)
break
}
res[i] <- flag
}
res
}
# 2012-09-08 new
Rdtagapply <- function(object, FUN, rdtag, classes = "character", how = "replace", ...){
if(rdtag %in% c("mathVERB", "nonmathVERB", "nonmath")){ # special care for \eqn and \deqn
feqnpos <- function(x) .tag_in(x, c("\\eqn", "\\deqn"))
eqnpos <- Rdo_locate(object, feqnpos, lists = TRUE)
eqnpos <- lapply(eqnpos, function(x) c(x,1)) # 1st arg. of \eqn or \deqn
if(rdtag == "nonmath"){
anypos <- Rdo_locate_leaves(object)
pos <- anypos[ !.pos_in_eqnpos(anypos, eqnpos) ]
}else{ # is it better to use Rdo_locate_leaves here?
fverbpos <- function(x) .tag_eq(x, "VERB")
verbpos <- Rdo_locate(object, fverbpos, lists = FALSE)
pos <- if(rdtag == "mathVERB") # verbpos[ verbpos %in% eqnpos ]
verbpos[ .pos_in_eqnpos(verbpos, eqnpos) ]
else # (rdtag == "nonmathVERB") # verbpos[ !( verbpos %in% eqnpos) ]
verbpos[ !.pos_in_eqnpos(verbpos, eqnpos) ]
}
for(ind in pos)
object[[ind]] <- FUN(object[[ind]], ...)
object
}else{
locfun <- function(x,...) if(.tag_eq(x, rdtag)) FUN(x,...) else x
Rdapply(object,locfun, classes = classes, how = how, ...)
}
}
.aux_Rdo_locate_leaves <- function(x, i){
if(is.logical(x)){
if(isTRUE(x))
i
else
FALSE
}else{ # here x is a list of integer vectors
lapply(x, function(x){ c(i,x)})
}
}
# inn1 <- parse_Rd("inner-methods.Rd")
# Rdo_locate_leaves(inn1, function(x) grepl("^signature\\(", x))
Rdo_locate_leaves <- function(object, f = function(x) TRUE){
fxx <- function(x){
if(is.character(x)){
return(f(x)) # evaluate `f' for this leaf
}else if(is.list(x)){
if(length(x)==0) # list()
return(x)
wrk <- lapply(x, fxx)
for(i in seq_along(wrk))
wrk[[i]] <- .aux_Rdo_locate_leaves(wrk[[i]], i)
indx <- sapply(wrk, function(y) !identical(y,FALSE) )
wrk <- wrk[indx]
wrk <- do.call("c",wrk)
return(wrk)
}else{
return(FALSE) # todo: replace this with a function and additional argument
}
}
fxx(object)
}
.merge_pos0 <- function(a, b){ # 2012-09-25 new
if(is.numeric(b))
c(a,b)
else if(is.list(b)){
res <- vector(mode="list", length=length(b))
for(i in seq_along(b)){
res[[i]] <- Recall(a, b[[i]])
}
res
}else if(is.logical(b)){
if(isTRUE(b))
a
else
as.numeric(NA) # numeric(0)
}else{
attr(a, "merge_tag") <- b # obache tozi tag se gubi po-kasno
a
}
}
.merge_pos <- function(a, b, ...){ # 2012-09-25 new
if(is.numeric(a) && length(a)==1){
a <- as.list(1:a) # todo: process the case a=0
}
wrk <- list()
for(i in a){
wrk <- c(wrk, .merge_pos0(a[[i]], b[[i]]) )
}
res <- wrk
len <- sapply(res, length)
res <- res[len>0] # drop zero length values
drop <- sapply(res, function(x) any(is.na(x)))
res[ !drop]
}
.notFALSE <- function(x) !identical(x, FALSE)
.notTRUE <- function(x) !isTRUE(x) # !identical(x, TRUE)
# 2012-10-20 dobavyam argument nested
# 2012-10-07 dobavyam argument fpos
Rdo_locate <- function(object, f = function(x) TRUE, pos_only = TRUE, lists = FALSE,
fpos = NULL, nested = TRUE){
fxx <- function(x){
if(is.character(x)){ # a leaf, evaluate `f' for it
f(x)
}else if(is.list(x)){
fli <- if(lists) f(x)
else FALSE
if(!nested && fli)
return(TRUE)
wrk <- if(fli) list(fli)
else list()
if(length(x)>0)
wrk <- c(wrk, .merge_pos(length(x), lapply(x, fxx)) ) # recurse
wrk
}else{ # this should not happen for Rd objects
FALSE # todo: replace this with a function and additional argument?
}
}
pos <- fxx(object)
f <- if(is.function(fpos))
function(x) list(pos = x, value = fpos(object, x))
else if(isTRUE(pos_only))
NULL
else if(is.function(pos_only))
function(x) list(pos = x, value = pos_only(object[[x]]))
else
function(x) list(pos = x, value = object[[x]])
if(!is.null(f))
lapply(pos, f)
else
pos
}
# insert sep between successive elements of x
.Rdinter <- function(x, sep = Rdo_newline(), before_first = FALSE, after_last = FALSE){
indx <- c(rbind(seq_along(x), length(x) + 1))
if(before_first)
indx <- c( length(x) + 1, indx)
if(!after_last)
indx <- head(indx,-1)
c(x, list(sep))[indx]
}
.Rd_tidy <- function(rdo){ # todo: optionally remove empty sections?
tags <- Rdo_tags(rdo) # todo: remove multiple empty lines?
secpos <- which(tags != "TEXT") # remove empty lines at top level?
secpos <- secpos[secpos > 1]
if(length(secpos)==0)
return(rdo)
nl <- Rdo_newline()
nlpos <- integer(0)
for(i in secpos){ # 2012-09-20 smenyam (!identical(rdo[[i-1]], nl)) s dolnoto.
if(!Rdo_is_newline(rdo[[i-1]])) # inache tryabva da se grizha za "srcref" attribute
nlpos <- c(nlpos, i)
}
if(length(nlpos)==0)
return(rdo)
# todo: this is lazy
for(i in sort(nlpos, TRUE)){ # sort in decreasing order, otherwise indices change
rdo <- Rdo_insert_element(rdo, nl, i)
}
rdo
}
Rdo_remove_srcref <- function(rdo){
f <- function(x){
a <- attributes(x)
if(is.list(x)){
x <- lapply(x,f)
if(!is.null(a)) # 2012-10-07 check for NULL
attributes(x) <- a
}
if(!is.null(attr(x,"srcref")))
attr(x,"srcref") <- NULL
x
}
f(rdo)
}
Rd_combo <- function(rd, f, ..., .MORE){ # todo: allow a directory?
dots <- list(...)
flag <- missing(.MORE)
locfun <- function(x){
locwrk <- permissive_parse_Rd(x)
locargs <- c(list(locwrk), dots)
locres <- try( do.call(f, locargs), silent=TRUE)
if(flag || inherits(locres,"try-error"))
locres
else{
try( do.call(.MORE, list(locres)), silent=TRUE)
}
}
lapply(rd, locfun)
}
|
