cute_little_R_functions.R 700 KB
Newer Older
Gael  MILLOT's avatar
Gael MILLOT committed
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
identical.content <- NULL
if(identical(data1, data2) & any(class(data1) %in% c("matrix", "data.frame", "table"))){
same.class <- TRUE
class <- class(data1)
same.dim <- TRUE
dim <- dim(data1)
same.row.nb <- TRUE
row.nb <- nrow(data1)
same.col.nb <- TRUE
col.nb <- ncol(data1)
same.row.name <- TRUE
row.name <- dimnames(data1)[[1]]
any.id.row.name <- TRUE
same.row.name.pos1 <- 1:row.nb
same.row.name.pos2 <- 1:row.nb
common.row.names <- dimnames(data1)[[1]]
same.col.name <- TRUE
col.name <- dimnames(data1)[[2]]
any.id.col.name <- TRUE
same.col.name.pos1 <- 1:col.nb
same.col.name.pos2 <- 1:col.nb
common.col.names <- dimnames(data1)[[2]]
any.id.row <- TRUE
same.row.pos1 <- 1:row.nb
same.row.pos2 <- 1:row.nb
any.id.col <- TRUE
same.col.pos1 <- 1:col.nb
same.col.pos2 <- 1:col.nb
identical.object <- TRUE
identical.content <- TRUE
Gael  MILLOT's avatar
Gael MILLOT committed
1031
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
identical.object <- FALSE
if(all(class(data1) == "table") & length(dim(data1)) == 1){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE data1 ARGUMENT IS A 1D TABLE. USE THE fun_comp_1d FUNCTION\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(all(class(data2) == "table") & length(dim(data2)) == 1){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE data2 ARGUMENT IS A 1D TABLE. USE THE fun_comp_1d FUNCTION\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if( ! identical(class(data1), class(data2))){
same.class <- FALSE
}else if( ! any(class(data1) %in% c("matrix", "data.frame", "table"))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE data1 AND data2 ARGUMENTS MUST BE EITHER MATRIX, DATA FRAME OR TABLE\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else{
same.class <- TRUE
class <- class(data1)
Gael  MILLOT's avatar
Gael MILLOT committed
1049
}
Gael  MILLOT's avatar
Gael MILLOT committed
1050
1051
if( ! identical(dim(data1), dim(data2))){
same.dim <- FALSE
Gael  MILLOT's avatar
Gael MILLOT committed
1052
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
same.dim <- TRUE
dim <- dim(data1)
}
if( ! identical(nrow(data1), nrow(data2))){
same.row.nb <- FALSE
}else{
same.row.nb <- TRUE
row.nb <- nrow(data1)
}
if( ! identical(ncol(data1), ncol(data2))){
same.col.nb <- FALSE
}else{
same.col.nb <- TRUE
col.nb <- ncol(data1)
}
# row and col names
if(is.null(dimnames(data1)) & is.null(dimnames(data2))){
same.row.name <- NULL
same.col.name <- NULL
# row and col names remain NULL
}else if((is.null(dimnames(data1)) & ! is.null(dimnames(data2))) | ( ! is.null(dimnames(data1)) & is.null(dimnames(data2)))){
same.row.name <- FALSE
same.col.name <- FALSE
# row and col names remain NULL
}else{
if( ! identical(dimnames(data1)[[1]], dimnames(data2)[[1]])){
same.row.name <- FALSE
# row names remain NULL
Gael  MILLOT's avatar
Gael MILLOT committed
1081
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
same.row.name <- TRUE
row.name <- dimnames(data1)[[1]]
}
# row names
any.id.row.name <- FALSE
if(any(dimnames(data1)[[1]] %in% dimnames(data2)[[1]])){
any.id.row.name <- TRUE
same.row.name.pos1 <- which(dimnames(data1)[[1]] %in% dimnames(data2)[[1]])
}
if(any(dimnames(data2)[[1]] %in% dimnames(data1)[[1]])){
any.id.row.name <- TRUE
same.row.name.pos2 <- which(dimnames(data2)[[1]] %in% dimnames(data1)[[1]])
}
if(any.id.row.name == TRUE){
common.row.names <- unique(c(dimnames(data1)[[1]][same.row.name.pos1], dimnames(data2)[[1]][same.row.name.pos2]))
}
# col names
any.id.col.name <- FALSE
if(any(dimnames(data1)[[2]] %in% dimnames(data2)[[2]])){
any.id.col.name <- TRUE
same.col.name.pos1 <- which(dimnames(data1)[[2]] %in% dimnames(data2)[[2]])
}
if(any(dimnames(data2)[[2]] %in% dimnames(data1)[[2]])){
any.id.col.name <- TRUE
same.col.name.pos2 <- which(dimnames(data2)[[2]] %in% dimnames(data1)[[2]])
}
if(any.id.col.name == TRUE){
common.col.names <- unique(c(dimnames(data1)[[2]][same.col.name.pos1], dimnames(data2)[[2]][same.col.name.pos2]))
}
if( ! identical(dimnames(data1)[[2]], dimnames(data2)[[2]])){
same.col.name <- FALSE
# col names remain NULL
}else{
same.col.name <- TRUE
col.name <- dimnames(data1)[[2]]
}
}
# identical row and col content
if(all(class(data1) == "table")){
as.data.frame(matrix(data1, ncol = ncol(data1)), stringsAsFactors = FALSE)
}else if(all(class(data1) == "matrix")){
data1 <- as.data.frame(data1, stringsAsFactors = FALSE)
}else if(all(class(data1) == "data.frame")){
data1 <- data.frame(lapply(data1, as.character), stringsAsFactors=FALSE)
}
if(all(class(data2) == "table")){
as.data.frame(matrix(data2, ncol = ncol(data2)), stringsAsFactors = FALSE)
}else if(all(class(data2) == "matrix")){
data2 <- as.data.frame(data2, stringsAsFactors = FALSE)
}else if(all(class(data2) == "data.frame")){
data2 <- data.frame(lapply(data2, as.character), stringsAsFactors=FALSE)
}
row.names(data1) <- paste0("A", 1:nrow(data1))
row.names(data2) <- paste0("A", 1:nrow(data2))
if(same.col.nb == TRUE){ # because if not the same col nb, the row cannot be identical
same.row.pos1 <- which(c(as.data.frame(t(data1), stringsAsFactors = FALSE)) %in% c(as.data.frame(t(data2), stringsAsFactors = FALSE)))
same.row.pos2 <- which(c(as.data.frame(t(data2), stringsAsFactors = FALSE)) %in% c(as.data.frame(t(data1), stringsAsFactors = FALSE)))
names(same.row.pos1) <- NULL
names(same.row.pos2) <- NULL
if(all(is.na(same.row.pos1))){
same.row.pos1 <- NULL
}else{
same.row.pos1 <- same.row.pos1[ ! is.na(same.row.pos1)]
any.id.row <- TRUE
Gael  MILLOT's avatar
Gael MILLOT committed
1146
}
Gael  MILLOT's avatar
Gael MILLOT committed
1147
1148
1149
1150
1151
1152
1153
1154
if(all(is.na(same.row.pos2))){
same.row.pos2 <- NULL
}else{
same.row.pos2 <- same.row.pos2[ ! is.na(same.row.pos2)]
any.id.row <- TRUE
}
if(is.null(same.row.pos1) & is.null(same.row.pos2)){
any.id.row <- FALSE
Gael  MILLOT's avatar
Gael MILLOT committed
1155
1156
}
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
any.id.row <- FALSE
# same.row.pos1 and 2 remain NULL
}
if(same.row.nb == TRUE){ # because if not the same row nb, the col cannot be identical
same.col.pos1 <- which(c(data1) %in% c(data2))
same.col.pos2 <- which(c(data2) %in% c(data1))
names(same.col.pos1) <- NULL
names(same.col.pos2) <- NULL
if(all(is.na(same.col.pos1))){
same.col.pos1 <- NULL
}else{
same.col.pos1 <- same.col.pos1[ ! is.na(same.col.pos1)]
any.id.col <- TRUE
Gael  MILLOT's avatar
Gael MILLOT committed
1170
}
Gael  MILLOT's avatar
Gael MILLOT committed
1171
1172
if(all(is.na(same.col.pos2))){
same.col.pos2 <- NULL
Gael  MILLOT's avatar
Gael MILLOT committed
1173
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1174
1175
1176
1177
1178
1179
same.col.pos2 <- same.col.pos2[ ! is.na(same.col.pos2)]
any.id.col <- TRUE
}
if(is.null(same.col.pos1) & is.null(same.col.pos2)){
any.id.col <- FALSE
}
Gael  MILLOT's avatar
Gael MILLOT committed
1180
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1181
1182
any.id.col <- FALSE
# same.col.pos1 and 2 remain NULL
Gael  MILLOT's avatar
Gael MILLOT committed
1183
}
Gael  MILLOT's avatar
Gael MILLOT committed
1184
1185
1186
1187
1188
if(same.dim == TRUE & ! all(is.null(same.row.pos1), is.null(same.row.pos2), is.null(same.col.pos1), is.null(same.col.pos2))){ # same.dim == TRUE means that same.row.nb == TRUE and same.col.nb == TRUE, meaning that row.nb != NULL and col.nb != NULL. Thus, no need to include these checkings
if(identical(same.row.pos1, 1:row.nb) & identical(same.row.pos2, 1:row.nb) & identical(same.col.pos1, 1:col.nb) & identical(same.col.pos2, 1:col.nb)){
identical.content <- TRUE
}else{
identical.content <- FALSE
Gael  MILLOT's avatar
Gael MILLOT committed
1189
1190
}
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
identical.content <- FALSE
}
}
output <- list(same.class = same.class, class = class, same.dim = same.dim, dim = dim, same.row.nb = same.row.nb, row.nb = row.nb, same.col.nb = same.col.nb , col.nb = col.nb, same.row.name = same.row.name, row.name = row.name, any.id.row.name = any.id.row.name, same.row.name.pos1 = same.row.name.pos1, same.row.name.pos2 = same.row.name.pos2, common.row.names = common.row.names, same.col.name = same.col.name, col.name = col.name,any.id.col.name = any.id.col.name, same.col.name.pos1 = same.col.name.pos1, same.col.name.pos2 = same.col.name.pos2, common.col.names = common.col.names, any.id.row = any.id.row, same.row.pos1 = same.row.pos1, same.row.pos2 = same.row.pos2, any.id.col = any.id.col, same.col.pos1 = same.col.pos1, same.col.pos2 = same.col.pos2, identical.object = identical.object, identical.content = identical.content)
return(output)
}


######## fun_comp_list() #### comparison of two lists


# Check OK: clear to go Apollo
fun_comp_list <- function(data1, data2){
# AIM
# compare two lists. Check and report in a list if the 2 datasets have:
# same length
# common names
# common compartments
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# none
# ARGUMENTS
# data1: list
# data2: list
# RETURN
# a list containing:
# $same.length: logical. Are number of elements identical?
# $length: number of elements in the 2 datasets (NULL otherwise)
# $same.name: logical. Are element names identical ?
# $name: name of elements of the 2 datasets if identical (NULL otherwise)
# $any.id.name: logical. Is there any element names identical ?
# $same.name.pos1: position, in data1, of the element names identical in data2
# $same.name.pos2: position, in data2, of the compartment names identical in data1
# $any.id.compartment: logical. is there any identical compartments ?
# $same.compartment.pos1: position, in data1, of the compartments identical in data2
# $same.compartment.pos2: position, in data2, of the compartments identical in data1
# $identical.object: logical. Are objects identical (kind of object, compartment names and content)?
# $identical.content: logical. Are content objects identical (identical compartments excluding compartment names)?
# EXAMPLES
# obs1 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; obs2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; fun_comp_list(obs1, obs2)
# obs1 = list(1:5, LETTERS[1:2]) ; obs2 = list(a = 1:5, b = LETTERS[1:2]) ; fun_comp_list(obs1, obs2)
# obs1 = list(b = 1:5, c = LETTERS[1:2]) ; obs2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; fun_comp_list(obs1, obs2)
# obs1 = list(b = 1:5, c = LETTERS[1:2]) ; obs2 = list(LETTERS[5:9], matrix(1:6), 1:5) ; fun_comp_list(obs1, obs2)
# DEBUGGING
# data1 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; data2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) # for function debugging
# data1 = list(a = 1:5, b = LETTERS[1:2]) ; data2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# argument checking
if( ! any(class(data1) %in% "list")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A LIST\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if( ! any(class(data2) %in% "list")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A LIST\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) # activate this line and use the function to check arguments status
# end argument checking
# main code
same.length <- NULL
length <- NULL
same.name <- NULL
name <- NULL
any.id.name <- NULL
same.name.pos1 <- NULL
same.name.pos2 <- NULL
any.id.compartment <- NULL
same.compartment.pos1 <- NULL
same.compartment.pos2 <- NULL
identical.object <- NULL
identical.content <- NULL
if(identical(data1, data2)){
same.length <- TRUE
length <- length(data1)
if( ! is.null(names(data1))){
same.name <- TRUE
name <- names(data1)
any.id.name <- TRUE
same.name.pos1 <- 1:length(data1)
same.name.pos2 <- 1:length(data2)
}
any.id.compartment <- TRUE
same.compartment.pos1 <- 1:length(data1)
same.compartment.pos2 <- 1:length(data2)
identical.object <- TRUE
identical.content <- TRUE
}else{
identical.object <- FALSE
if( ! identical(length(data1), length(data2))){
same.length<- FALSE
}else{
same.length<- TRUE
length <- length(data1)
}
if( ! (is.null(names(data1)) & is.null(names(data2)))){
if( ! identical(names(data1), names(data2))){
same.name <- FALSE
}else{
same.name <- TRUE
name <- names(data1)
}
any.id.name <- FALSE
if(any(names(data1) %in% names(data2))){
any.id.name <- TRUE
same.name.pos1 <- which(names(data1) %in% names(data2))
}
if(any(names(data2) %in% names(data1))){
any.id.name <- TRUE
same.name.pos2 <- which(names(data2) %in% names(data1))
}
}
names(data1) <- NULL
names(data2) <- NULL
any.id.compartment <- FALSE
if(any(data1 %in% data2)){
any.id.compartment <- TRUE
same.compartment.pos1 <- which(data1 %in% data2)
}
if(any(data2 %in% data1)){
any.id.compartment <- TRUE
same.compartment.pos2 <- which(data2 %in% data1)
}
if(same.length == TRUE & ! all(is.null(same.compartment.pos1), is.null(same.compartment.pos2))){
if(identical(same.compartment.pos1, same.compartment.pos2)){
identical.content <- TRUE
}else{
identical.content <- FALSE
}
}else{
identical.content <- FALSE
}
}
output <- list(same.length = same.length, length = length, same.name = same.name, name = name, any.id.name = any.id.name, same.name.pos1 = same.name.pos1, same.name.pos2 = same.name.pos2, any.id.compartment = any.id.compartment, same.compartment.pos1 = same.compartment.pos1, same.compartment.pos2 = same.compartment.pos2, identical.object = identical.object, identical.content = identical.content)
return(output)
Gael  MILLOT's avatar
Gael MILLOT committed
1326
1327
1328
}


1329
######## fun_test() #### test combinations of argument values of a function and return errors (and graphs)
Gael  MILLOT's avatar
Gael MILLOT committed
1330
1331


Gael  MILLOT's avatar
Gael MILLOT committed
1332
1333
# add traceback https://stackoverflow.com/questions/47414119/how-to-read-a-traceback-in-r

Gael  MILLOT's avatar
Gael MILLOT committed
1334
# Check OK: clear to go Apollo
Gael  MILLOT's avatar
tempo    
Gael MILLOT committed
1335
fun_test <- function(fun, arg, val, expect.error = NULL, thread.nb = NULL, print.count = 10, plot.fun = FALSE, export = FALSE, res.path = NULL, lib.path = NULL, cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"){
Gael  MILLOT's avatar
Gael MILLOT committed
1336
1337
# AIM
# test combinations of argument values of a function
Gael  MILLOT's avatar
Gael MILLOT committed
1338
1339
# WARNING
# Limited to 43 arguments with at least 2 values each. The total number of arguments tested can be more if the additional arguments have a single value. The limit is due to nested "for" loops (https://stat.ethz.ch/pipermail/r-help/2008-March/157341.html), but it should not be a problem since the number of tests would be 2^43 > 8e12
Gael  MILLOT's avatar
Gael MILLOT committed
1340
# ARGUMENTS
1341
1342
# fun: character string indicating the name of the function tested (without brackets)
# arg: vector of character strings of arguments of fun. At least arguments that do not have default values must be present in this vector
Gael  MILLOT's avatar
Gael MILLOT committed
1343
# val: list with number of compartments equal to length of arg, each compartment containing values of the corresponding argument in arg. Each different value must be in a list or in a vector. For instance, argument 3 in arg is a logical argument (values accepted TRUE, FALSE, NA). Thus, compartment 3 of val can be either list(TRUE, FALSE, NA), or c(TRUE, FALSE, NA)
1344
# expect.error: list of exactly the same structure as val argument, but containing FALSE or TRUE, depending on whether error is expected (TRUE) or not (FALSE) for each corresponding value of val. A message is returned depending on discrepancies between the expected and observed errors. BEWARE: not always possible to write the expected errors for all the combination of argument values. Ignored if NULL
1345
# thread.nb: numeric value indicating the number of available threads. Write NULL if no parallelization wanted
Gael  MILLOT's avatar
Gael MILLOT committed
1346
# print.count: interger value. Print a working progress message every print.count during loops. BEWARE: can increase substentially the time to complete the process using a small value, like 10 for instance. Use Inf is no loop message desired
Gael  MILLOT's avatar
Gael MILLOT committed
1347
# plot.fun: logical. Plot the plotting function tested for each test?
1348
1349
# export: logical. Export the results into a .RData file and into a .txt file? If FALSE, return a list into the console (see below). BEWARE: will be automatically set to TRUE if thread.nb is not NULL. This means that when using parallelization, the results are systematically exported, not returned into the console
# res.path: character string indicating the absolute pathway of folder where the txt results and pdfs, containing all the plots, will be saved. Several txt and pdf, one per thread, if parallelization. Ignored if export is FALSE. Must be specified if thread.nb is not NULL or if export is TRUE
1350
# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
Gael  MILLOT's avatar
Gael MILLOT committed
1351
# cute.path: character string indicating the absolute path of the cute.R file. Will be remove when cute will be a package. Not considered if thread.nb is NULL
Gael  MILLOT's avatar
Gael MILLOT committed
1352
# REQUIRED PACKAGES
Gael  MILLOT's avatar
Gael MILLOT committed
1353
# lubridate
Gael  MILLOT's avatar
Gael MILLOT committed
1354
# parallel if thread.nb argument is not NULL
Gael  MILLOT's avatar
Gael MILLOT committed
1355
# if the tested function is in a package, this package must be imported first (no parallelization) or must be in the classical R package folder indicated by the lib.path argument (parallelization)
Gael  MILLOT's avatar
Gael MILLOT committed
1356
1357
1358
1359
1360
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# fun_get_message()
# fun_pack()
# RETURN
Gael  MILLOT's avatar
Gael MILLOT committed
1361
# if export is FALSE a list containing:
Gael  MILLOT's avatar
Gael MILLOT committed
1362
1363
1364
1365
1366
# $fun: the tested function
# $data: a data frame of all the combination tested, containing the following columns:
# the different values tested, named by arguments
# $kind: a vector of character strings indicating the kind of test result: either "ERROR", or "WARNING", or "OK"
# $problem: a logical vector indicating if error or not
1367
# $expected.error: optional logical vector indicating the expected error specified in the expect.error argument
1368
1369
# $message: either NULL if $kind is always "OK", or the messages
# $instruction: the initial instruction
Gael  MILLOT's avatar
Gael MILLOT committed
1370
# $sys.info: system and packages info
1371
# if export is TRUE 1) the same list object into a .RData file, 2) also the $data data frame into a .txt file, and 3) if expect.error is non NULL and if any discrepancy, the $data data frame into a .txt file but containing only the rows with discrepancies between expected and observed errors
Gael  MILLOT's avatar
Gael MILLOT committed
1372
1373
1374
1375
# one or several pdf if a plotting function is tested and if the plot.fun argument is TRUE
# EXAMPLES
# fun_test(fun = "unique", arg = c("x", "incomparables"), val = list(x = list(1:10, c(1,1,2,8), NA), incomparable = c(TRUE, FALSE, NA)))
# fun_test(fun = "fun_round", arg = c("data", "dec.nb", "after.lead.zero"), val = list(L1 = list(c(1, 1.0002256, 1.23568), "a", NA), L2 = list(2, c(1,3), NA), L3 = c(TRUE, FALSE, NA)))
1376
# fun_test(fun = "plot", arg = c("x", "y"), val = list(x = list(1:10, 12:13, NA, (1:10)^2), y = list(1:10, NA, NA)),  expect.error = list(x = list(FALSE, TRUE, TRUE, FALSE), y = list(FALSE, TRUE, TRUE)), thread.nb = NULL, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = NULL)
Gael  MILLOT's avatar
Gael MILLOT committed
1377
# fun_test(fun = "plot", arg = c("x", "y"), val = list(x = list(1:10, 12:13, NA, (1:10)^2), y = list(1:10, NA, NA)), thread.nb = 4, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = "C:\\Program Files\\R\\R-3.6.1\\library\\")
Gael  MILLOT's avatar
Gael MILLOT committed
1378
# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10)) ; fun_test(fun = "fun_gg_boxplot", arg = c("data1", "y", "categ"), val = list(L1 = list(L1 = obs1), L2 = list(L1 = "Time"), L3 = list(L1 = "Group1")))
Gael  MILLOT's avatar
Gael MILLOT committed
1379
1380
# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10)) ; fun_test(fun = "fun_gg_boxplot", arg = c("data1", "y", "categ"), val = list(L1 = list(obs1), L2 = "Time", L3 = "Group1"), thread.nb = NULL, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = "C:\\Program Files\\R\\R-3.6.1\\library\\")
# library(ggplot2) ; fun_test(fun = "geom_histogram", arg = c("data", "mapping"), val = list(x = list(data.frame(X = "a")), y = list(ggplot2::aes(x = X))), thread.nb = NULL, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = "C:\\Program Files\\R\\R-3.6.1\\library\\") # BEWARE: ggplot2::geom_histogram does not work
Gael  MILLOT's avatar
Gael MILLOT committed
1381
# DEBUGGING
1382
1383
1384
1385
# fun = "unique" ; arg = "x" ; val = list(x = list(1:10, c(1,1,2,8), NA)) ; expect.error = list(x = list(FALSE, FALSE, TRUE)) ; thread.nb = NULL ; plot.fun = FALSE ; export = FALSE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL ; print.count = 1 ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R" # for function debugging
# fun = "unique" ; arg = c("x", "incomparables") ; val = list(x = list(1:10, c(1,1,2,8), NA), incomparable = c(TRUE, FALSE, NA)) ; expect.error = NULL ; thread.nb = 2 ; plot.fun = FALSE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL ; print.count = 10 ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R" # for function debugging
# fun = "plot" ; arg = c("x", "y") ; val = list(x = list(1:10, 12:13, NA), y = list(1:10, NA, NA)) ; expect.error = list(x = list(FALSE, FALSE, TRUE, FALSE), y = list(FALSE, TRUE, TRUE)) ; print.count = 10 ; thread.nb = NULL ; plot.fun = TRUE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL # for function debugging
# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10)) ; fun = "fun_gg_boxplot" ; arg = c("data1", "y", "categ") ; val = list(L1 = list(L1 = obs1), L2 = list(L1 = "Time"), L3 = list(L1 = "Group1")) ; expect.error = NULL ; print.count = 10 ; thread.nb = NULL ; plot.fun = TRUE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL # for function debugging
Gael  MILLOT's avatar
Gael MILLOT committed
1386
1387
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
1388
instruction <- match.call()
Gael  MILLOT's avatar
Gael MILLOT committed
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
# end function name
# required function checking
req.function <- c(
"fun_check", 
"fun_get_message", 
"fun_pack"
)
for(i1 in req.function){
if(length(find(i1, mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED ", i1, "() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat)
}
}
# end required function checking
Gael  MILLOT's avatar
Gael MILLOT committed
1403
# argument primary checking
1404
1405
1406
1407
1408
1409
1410
# arg with no default values
if(any(missing(fun) | missing(arg) | missing(val))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ARGUMENTS fun, arg AND val HAVE NO DEFAULT VALUE AND REQUIRE ONE\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end arg with no default values
# using fun_check()
Gael  MILLOT's avatar
Gael MILLOT committed
1411
1412
1413
1414
1415
1416
1417
1418
1419
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = fun, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
if(grepl(x = fun, pattern = "()$")){ # remove ()
fun <- sub(x = fun, pattern = "()$", replacement = "")
}
Gael  MILLOT's avatar
Gael MILLOT committed
1420
1421
if( ! exists(fun)){
tempo.cat <- paste0("ERROR IN ", function.name, ": CHARACTER STRING IN fun ARGUMENT DOES NOT EXIST IN THE R WORKING ENVIRONMENT: ", paste(fun, collapse = "\n"))
Gael  MILLOT's avatar
Gael MILLOT committed
1422
1423
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
Gael  MILLOT's avatar
Gael MILLOT committed
1424
}else if( ! all(class(get(fun)) == "function")){
1425
tempo.cat <- paste0("ERROR IN ", function.name, ": fun ARGUMENT IS NOT CLASS \"function\" BUT: ", paste(class(get(fun)), collapse = "\n"), "\nCHECK IF ANY CREATED OBJECT WOULD HAVE THE NAME OF THE TESTED FUNCTION")
Gael  MILLOT's avatar
Gael MILLOT committed
1426
1427
1428
1429
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1430
tempo <- fun_check(data = arg, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
1431
1432
1433
1434
1435
if(tempo$problem == FALSE & length(arg) == 0){
tempo.cat <- paste0("ERROR IN ", function.name, ": arg ARGUMENT CANNOT BE LENGTH 0")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
Gael  MILLOT's avatar
Gael MILLOT committed
1436
1437
tempo <- fun_check(data = val, class = "list", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
1438
1439
1440
for(i2 in 1:length(val)){
tempo1 <- fun_check(data = val[[i2]], class = "vector", na.contain = TRUE, fun.name = function.name, print = FALSE)
tempo2 <- fun_check(data = val[[i2]], class = "list", na.contain = TRUE, fun.name = function.name, print = FALSE)
Gael  MILLOT's avatar
Gael MILLOT committed
1441
if(tempo1$problem == TRUE & tempo2$problem == TRUE){
1442
tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i2, " OF val ARGUMENT MUST BE A VECTOR OR A LIST")
Gael  MILLOT's avatar
Gael MILLOT committed
1443
1444
1445
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else if(tempo1$problem == FALSE){ # vector split into list compartments
1446
val[[i2]] <- split(x = val[[i2]], f = 1:length(val[[i2]]))
Gael  MILLOT's avatar
Gael MILLOT committed
1447
1448
1449
}
}
}
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
if( ! is.null(expect.error)){
tempo <- fun_check(data = expect.error, class = "list", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
for(i3 in 1:length(expect.error)){
tempo1 <- fun_check(data = expect.error[[i3]], class = "vector",  mode = "logical", fun.name = function.name, print = FALSE)
tempo2 <- fun_check(data =  expect.error[[i3]], class = "list", fun.name = function.name, print = FALSE)
if(tempo1$problem == TRUE & tempo2$problem == TRUE){
tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i3, " OF expect.error ARGUMENT MUST BE TRUE OR FALSE")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else if(tempo1$problem == FALSE){ # vector split into list compartments
expect.error[[i3]] <- split(x = expect.error[[i3]], f = 1:length(expect.error[[i3]]))
}
}
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1466
1467
1468
1469
1470
1471
1472
1473
if( ! is.null(thread.nb)){
tempo <- fun_check(data = thread.nb, typeof = "integer", double.as.integer.allowed = TRUE, neg.values = FALSE, length = 1, fun.name = "SLITHERINE") ; eval(ee)
if(tempo$problem == FALSE & thread.nb < 1){
tempo.cat <- paste0("ERROR IN ", function.name, ": thread.nb PARAMETER MUST EQUAL OR GREATER THAN 1: ", thread.nb)
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1474
tempo <- fun_check(data = print.count, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
Gael  MILLOT's avatar
Gael MILLOT committed
1475
tempo <- fun_check(data = plot.fun, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
Gael  MILLOT's avatar
Gael MILLOT committed
1476
1477
tempo <- fun_check(data = export, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(res.path)){
Gael  MILLOT's avatar
Gael MILLOT committed
1478
1479
1480
1481
tempo <- fun_check(data = res.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
if( ! all(dir.exists(res.path))){ # separation to avoid the problem of tempo$problem == FALSE and res.path == NA
tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE res.path ARGUMENT DOES NOT EXISTS:\n", paste(res.path, collapse = "\n"))
Gael  MILLOT's avatar
Gael MILLOT committed
1482
1483
1484
1485
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1486
}
Gael  MILLOT's avatar
Gael MILLOT committed
1487
if( ! is.null(lib.path)){
Gael  MILLOT's avatar
Gael MILLOT committed
1488
1489
1490
1491
tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
Gael  MILLOT's avatar
Gael MILLOT committed
1492
1493
1494
1495
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1496
}
Gael  MILLOT's avatar
Gael MILLOT committed
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
if( ! is.null(thread.nb)){
tempo <- fun_check(data = cute.path, class = "vector", typeof = "character", length = 1, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
if( ! file.exists(cute.path)){
tempo.cat <- paste0("ERROR IN ", function.name, ": FILE PATH INDICATED IN THE cute.path PARAMETER DOES NOT EXISTS:\n", cute.path)
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1507
1508
1509
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
1510
# end using fun_check()
Gael  MILLOT's avatar
Gael MILLOT committed
1511
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
Gael  MILLOT's avatar
Gael MILLOT committed
1512
# end argument primary checking
Gael  MILLOT's avatar
Gael MILLOT committed
1513
# second round of checking and data preparation
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
# dealing with NA
if(any(is.na(fun)) | any(is.na(arg)) | any(is.na(expect.error)) | any(is.na(thread.nb)) | any(is.na(print.count)) | any(is.na(plot.fun)) | any(is.na(export)) | any(is.na(res.path)) | any(is.na(lib.path))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": NO ARGUMENT EXCEPT val CAN HAVE NA VALUES\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end dealing with NA
# dealing with NULL
if(is.null(fun) | is.null(arg) | is.null(val) | is.null(print.count) | is.null(plot.fun) | is.null(export)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THESE ARGUMENTS fun, arg, val, print.count, plot.fun AND export CANNOT BE NULL\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end dealing with NULL
Gael  MILLOT's avatar
Gael MILLOT committed
1526
if(length(arg) != length(val)){
1527
tempo.cat <- paste0("ERROR IN ", function.name, ": LENGTH OF arg ARGUMENT MUST BE IDENTICAL TO LENGTH OF val ARGUMENT:\nHERE IT IS: ", length(arg), " VERSUS ", length(val))
Gael  MILLOT's avatar
Gael MILLOT committed
1528
1529
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
}
Gael  MILLOT's avatar
Gael MILLOT committed
1530
1531
1532
args <- names(formals(get(fun)))
if( ! all(arg %in% args)){
tempo.cat <- paste0("ERROR IN ", function.name, ": SOME OF THE STRINGS IN arg ARE NOT ARGUMENTS OF fun\nfun ARGUMENTS: ", paste(args, collapse = " "),"\nPROBLEMATIC STRINGS IN arg: ", paste(arg[ ! arg %in% args], collapse = " "))
1533
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
Gael  MILLOT's avatar
Gael MILLOT committed
1534
}
Gael  MILLOT's avatar
Gael MILLOT committed
1535
1536
if(sum(sapply(val, FUN = length) > 1) > 43){
tempo.cat <- paste0("ERROR IN ", function.name, ": CANNOT TEST MORE THAN 43 ARGUMENTS IF THEY ALL HAVE AT LEAST 2 VALUES EACH\nHERE THE NUMBER IS: ", sum(sapply(val, FUN = length) > 1))
1537
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
Gael  MILLOT's avatar
Gael MILLOT committed
1538
}
1539
1540
1541
1542
1543
1544
if( ! is.null(expect.error)){
if(length(val) != length(expect.error)){
tempo.cat <- paste0("ERROR IN ", function.name, ": LENGTH OF val ARGUMENT MUST BE IDENTICAL TO LENGTH OF expect.error ARGUMENT:\nHERE IT IS: ", length(val), " VERSUS ", length(expect.error))
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1545
1546
1547
1548
1549
1550
1551
1552
1553
if( ! is.null(thread.nb) & is.null(res.path)){
tempo.cat <- paste0("ERROR IN ", function.name, ": res.path ARGUMENT MUST BE SPECIFIED IF thread.nb ARGUMENT IS NOT NULL")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
}
if(is.null(res.path) & export == TRUE){
tempo.cat <- paste0("ERROR IN ", function.name, ": res.path ARGUMENT MUST BE SPECIFIED IF export ARGUMENT TRUE")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
}
if( ! is.null(thread.nb) & export == FALSE){
Gael  MILLOT's avatar
Gael MILLOT committed
1554
export <- TRUE
Gael  MILLOT's avatar
Gael MILLOT committed
1555
1556
1557
1558
tempo.cat <- paste0("WARNING FROM ", function.name, ": export ARGUMENT CONVERTED TO TRUE BECAUSE thread.nb ARGUMENT IS NOT NULL")
warning(paste0("\n", tempo.cat, "\n"), call. = FALSE)
}
# end second round of checking and data preparation
Gael  MILLOT's avatar
Gael MILLOT committed
1559
# package checking
Gael  MILLOT's avatar
Gael MILLOT committed
1560
fun_pack(req.package = c("lubridate"), lib.path = lib.path)
Gael  MILLOT's avatar
Gael MILLOT committed
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
if( ! is.null(thread.nb)){
fun_pack(req.package = c("parallel"), lib.path = lib.path)
}
# end package checking
# declaration of special plot functions
sp.plot.fun <- c("fun_gg_scatter", "fun_gg_bar", "fun_gg_boxplot")
# end declaration of special plot functions
# main code
cat("\nfun_test JOB IGNITION\n")
ini.date <- Sys.time()
ini.time <- as.numeric(ini.date) # time of process begin, converted into seconds
Gael  MILLOT's avatar
Gael MILLOT committed
1572
if(export == TRUE){
Gael  MILLOT's avatar
Gael MILLOT committed
1573
res.path <- paste0(res.path, "/fun_test_res_", trunc(ini.time))
Gael  MILLOT's avatar
Gael MILLOT committed
1574
1575
1576
1577
1578
1579
1580
if(dir.exists(res.path)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": FOLDER ALREADY EXISTS\n", res.path, "\nPLEASE RERUN ONCE\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}else{
dir.create(res.path)
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1581
1582
total.comp.nb <- prod(sapply(val, FUN = "length"))
cat(paste0("\nTHE TOTAL NUMBER OF TESTS IS: ", total.comp.nb, "\n"))
Gael  MILLOT's avatar
Gael MILLOT committed
1583
# creation of the txt instruction that includes several loops
Gael  MILLOT's avatar
Gael MILLOT committed
1584
1585
1586
1587
loop.string <- NULL
end.loop.string <- NULL
fun.args <- NULL
fun.args2 <- NULL
1588
error.values <- NULL
Gael  MILLOT's avatar
Gael MILLOT committed
1589
1590
arg.values <- "list("
for(i1 in 1:length(arg)){
Gael  MILLOT's avatar
Gael MILLOT committed
1591
if(is.null(thread.nb)){
Gael  MILLOT's avatar
Gael MILLOT committed
1592
if(length(val[[i1]]) > 1){ # loop only if more than one value in length(val[[i1]])
Gael  MILLOT's avatar
Gael MILLOT committed
1593
1594
loop.string <- paste0(loop.string, "for(i", i1, " in 1:", length(val[[i1]]), "){")
end.loop.string <- paste0(end.loop.string, "}")
Gael  MILLOT's avatar
Gael MILLOT committed
1595
}
Gael  MILLOT's avatar
Gael MILLOT committed
1596
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1597
loop.string <- "for(i in x){"
Gael  MILLOT's avatar
Gael MILLOT committed
1598
end.loop.string <- "}"
Gael  MILLOT's avatar
Gael MILLOT committed
1599
}
Gael  MILLOT's avatar
Gael MILLOT committed
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
fun.args <- paste0(
fun.args, 
ifelse(i1 == 1, "", ", "), 
arg[i1], 
" = val[[", 
i1, 
"]][[", 
if(is.null(thread.nb)){
if(length(val[[i1]]) > 1){
paste0("i", i1)
}else{
"1" # a unique element in val[[i1]]
}
}else{
paste0("i.list[[", i1, "]][i]")
}, 
"]]"
)
fun.args2 <- paste0(
fun.args2, 
ifelse(i1 == 1, "", ", "), 
arg[i1], 
" = val[[", 
i1, 
"]][[', ", 
if(is.null(thread.nb)){
if(length(val[[i1]]) > 1){
paste0("i", i1)
}else{
"1" # a unique element in val[[i1]]
}
}else{
paste0("i.list[[", i1, "]][i]")
}, 
", ']]"
)
arg.values <- paste0(
arg.values, 
"val[[", i1, "]][[", 
if(is.null(thread.nb)){
if(length(val[[i1]]) > 1){
paste0("i", i1)
}else{
"1" # a unique element in val[[i1]]
}
}else{
paste0("i.list[[", i1, "]][i]")
}, 
"]]", 
ifelse(i1 == length(arg), "", ", ")
)
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
error.values <- paste0(
error.values, 
ifelse(i1 == 1, "", " | "), 
"expect.error[[", i1, "]][[", 
if(is.null(thread.nb)){
if(length(expect.error[[i1]]) > 1){
paste0("i", i1)
}else{
"1" # a unique element in expect.error[[i1]]
}
}else{
paste0("i.list[[", i1, "]][i]")
}, 
"]]"
)
Gael  MILLOT's avatar
Gael MILLOT committed
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
}
arg.values <- paste0(arg.values, ")")
fun.test <- paste0(fun, "(", fun.args, ")")
fun.test2 <- paste0("paste0('", fun, "(", fun.args2, ")')")
# plot title for special plot functions
if(plot.fun == TRUE){
plot.kind <- "classic"
if(fun %in% sp.plot.fun){
plot.kind <- "special"
if(any(arg %in% "title")){ # this is for the special functions
tempo.match <- regmatches(x = fun.test, m = regexpr(text = fun.test, pattern = "title = .+[,)]"))
tempo.match <- substring(tempo.match , 1, nchar(tempo.match) - 1)
fun.test <- sub(x = fun.test, pattern = tempo.match, replacement = paste0(tempo.match, "\ntempo.title"))
}else{
fun.test <- sub(x = fun.test, pattern = ")$", replacement = ", title = tempo.title)")
}
}
}
# end plot title for special plot functions
kind <- character()
problem <- logical()
1687
expected.error <- logical()
Gael  MILLOT's avatar
Gael MILLOT committed
1688
1689
res <- character()
count <- 0
Gael  MILLOT's avatar
Gael MILLOT committed
1690
print.count.loop <- 0
Gael  MILLOT's avatar
Gael MILLOT committed
1691
plot.count <- 0
1692
1693
1694
1695
1696
if(length(arg) == 1){
data <- data.frame()
}else{ # length(arg) == 0 already tested above
data <- data.frame(t(vector("character", length(arg))), stringsAsFactors = FALSE)[-1, ] # -1 to remove the single row created and to have an empty data frame with length(arg) columns
}
Gael  MILLOT's avatar
Gael MILLOT committed
1697
1698
1699
code <- paste(
loop.string, '
count <- count + 1
Gael  MILLOT's avatar
Gael MILLOT committed
1700
print.count.loop <- print.count.loop + 1
Gael  MILLOT's avatar
Gael MILLOT committed
1701
data <- rbind(data, as.character(sapply(eval(parse(text = arg.values)), FUN = "paste", collapse = " ")), stringsAsFactors = FALSE) # each colum is a test
Gael  MILLOT's avatar
Gael MILLOT committed
1702
1703
tempo.try.error <- fun_get_message(data = eval(parse(text = fun.test2)), kind = "error", header = FALSE, env = get(env.name)) # data argument needs a character string but eval(parse(text = fun.test2)) provides it (eval parse replace the i1, i2, etc., by the correct values, meaning that only val is required in the env.name environment)
tempo.try.warning <- fun_get_message(data = eval(parse(text = fun.test2)), kind = "warning", header = FALSE, env = get(env.name), print.no = TRUE) # data argument needs a character string but eval(parse(text = fun.test2)) provides it (eval parse replace the i1, i2, etc., by the correct values, meaning that only val is required in the env.name environment)
1704
1705
1706
if( ! is.null(expect.error)){
expected.error <- c(expected.error, eval(parse(text = error.values)))
}
Gael  MILLOT's avatar
Gael MILLOT committed
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
if( ! is.null(tempo.try.error)){
kind <- c(kind, "ERROR")
problem <- c(problem, TRUE)
res <- c(res, tempo.try.error)
}else{
if( ! is.null(tempo.try.warning)){
kind <- c(kind, "WARNING")
problem <- c(problem, FALSE)
res <- c(res, tempo.try.warning)
}else{
kind <- c(kind, "OK")
problem <- c(problem, FALSE)
res <- c(res, "")
}
if(plot.fun == TRUE){
1722
invisible(dev.set(window.nb))
Gael  MILLOT's avatar
Gael MILLOT committed
1723
plot.count <- plot.count + 1
Gael  MILLOT's avatar
Gael MILLOT committed
1724
tempo.title <- paste0("test_", sprintf(paste0("%0", nchar(total.comp.nb), "d"), ifelse(is.null(thread.nb), count, x[count])))
Gael  MILLOT's avatar
Gael MILLOT committed
1725
1726
1727
1728
1729
1730
1731
1732
if(plot.kind == "classic"){
eval(parse(text = fun.test))
tempo <- fun_post_plot(corner.text = tempo.title)
}else if(plot.kind == "special"){
eval(parse(text = fun.test))
}else{
tempo.cat <- paste0("\n\n================\n\nINTERNAL CODE ERROR 1 IN ", function.name, ": CODE HAS TO BE MODIFIED\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
Gael  MILLOT's avatar
Gael MILLOT committed
1733
1734
1735
}
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1736
1737
if(print.count.loop == print.count){
print.count.loop <- 0
Gael  MILLOT's avatar
Gael MILLOT committed
1738
1739
tempo.time <- as.numeric(Sys.time())
tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
Gael  MILLOT's avatar
Gael MILLOT committed
1740
1741
1742
1743
final.loop <- (tempo.time - ini.time) / count * ifelse(is.null(thread.nb), total.comp.nb, length(x)) # intra nb.compar loop lapse: time lapse / cycles done * cycles remaining
final.exp <- as.POSIXct(final.loop, origin = ini.date)
cat(paste0(ifelse(is.null(thread.nb), "\n", paste0("\nIN PROCESS ", process.id, " | ")), "LOOP ", format(count, big.mark=","), " / ", format(ifelse(is.null(thread.nb), total.comp.nb, length(x)), big.mark=","), " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
}
Gael  MILLOT's avatar
Gael MILLOT committed
1744
1745
1746
1747
if(count == ifelse(is.null(thread.nb), total.comp.nb, length(x))){
tempo.time <- as.numeric(Sys.time())
tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
cat(paste0(ifelse(is.null(thread.nb), "\nLOOP PROCESS ENDED | ", paste0("\nPROCESS ", process.id, " ENDED | ")), "LOOP ", format(count, big.mark=","), " / ", format(ifelse(is.null(thread.nb), total.comp.nb, length(x)), big.mark=","), " | TIME SPENT: ", tempo.lapse, "\n\n"))
Gael  MILLOT's avatar
Gael MILLOT committed
1748
}
Gael  MILLOT's avatar
Gael MILLOT committed
1749
1750
1751
', 
end.loop.string
)
Gael  MILLOT's avatar
Gael MILLOT committed
1752
1753
1754
1755
# end creation of the txt instruction that includes several loops
if( ! is.null(thread.nb)){
# list of i numbers that will be split
i.list <- vector("list", length(val)) # positions to split in parallel jobs
1756
1757
1758
1759
1760
for(i2 in 1:length(arg)){
if(i2 == 1){
tempo.divisor <- total.comp.nb / length(val[[i2]])
i.list[[i2]] <- rep(1:length(val[[i2]]), each = as.integer(tempo.divisor))
tempo.multi <- length(val[[i2]])
Gael  MILLOT's avatar
Gael MILLOT committed
1761
}else{
1762
1763
1764
tempo.divisor <- tempo.divisor / length(val[[i2]])
i.list[[i2]] <- rep(rep(1:length(val[[i2]]), each = as.integer(tempo.divisor)), time = as.integer(tempo.multi))
tempo.multi <- tempo.multi * length(val[[i2]])
Gael  MILLOT's avatar
Gael MILLOT committed
1765
1766
1767
1768
1769
1770
1771
}
}
# end list of i numbers that will be split
tempo.cat <- paste0("PARALLELIZATION INITIATED AT: ", ini.date)
cat(paste0("\n", tempo.cat, "\n"))
tempo.thread.nb = parallel::detectCores(all.tests = FALSE, logical = TRUE) # detect the number of threads
if(tempo.thread.nb < thread.nb){
Gael  MILLOT's avatar
Gael MILLOT committed
1772
thread.nb <- tempo.thread.nb
Gael  MILLOT's avatar
Gael MILLOT committed
1773
1774
1775
}
tempo.cat <- paste0("NUMBER OF THREADS USED: ", thread.nb)
cat(paste0("\n    ", tempo.cat, "\n"))
1776
Clust <- parallel::makeCluster(thread.nb, outfile = paste0(res.path, "/fun_test_parall_log.txt")) # outfile to print or cat during parallelization (only possible in a file, outfile = "" do not work on windows)
1777
tempo.cat <- paste0("SPLIT OF TEST NUMBERS IN PARALLELISATION:")
Gael  MILLOT's avatar
Gael MILLOT committed
1778
cat(paste0("\n    ", tempo.cat, "\n"))
1779
1780
cluster.list <- parallel::clusterSplit(Clust, 1:total.comp.nb) # split according to the number of cluster
str(cluster.list) # using print(str()) add a NULL below the result
1781
cat("\n")
Gael  MILLOT's avatar
Gael MILLOT committed
1782
1783
paral.output.list <- parallel::clusterApply( # paral.output.list is a list made of thread.nb compartments, each made of n / thread.nb (mat theo column number) compartment. Each compartment receive the corresponding results of fun_permut(), i.e., data (permuted mat1.perm), warning message, cor (final correlation) and count (number of permutations)
cl = Clust,
1784
x = cluster.list,
Gael  MILLOT's avatar
Gael MILLOT committed
1785
function.name = function.name, 
1786
instruction = instruction, 
Gael  MILLOT's avatar
Gael MILLOT committed
1787
1788
thread.nb = thread.nb, 
print.count = print.count, 
Gael  MILLOT's avatar
Gael MILLOT committed
1789
1790
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
1801
1802
1803
1804
1805
1806
1807
1808
total.comp.nb = total.comp.nb, 
sp.plot.fun = sp.plot.fun,
i.list = i.list, 
fun.tested = fun,
arg.values = arg.values,
fun.test = fun.test,
fun.test2 = fun.test2,
kind = kind,
problem = problem,
res = res,
count = count,
plot.count = plot.count,
data = data,
code = code,
plot.fun = plot.fun, 
res.path = res.path, 
lib.path = lib.path, 
cute.path = cute.path, 
fun = function(
x, 
Gael  MILLOT's avatar
Gael MILLOT committed
1809
function.name, 
1810
instruction, 
Gael  MILLOT's avatar
Gael MILLOT committed
1811
1812
thread.nb, 
print.count, 
Gael  MILLOT's avatar
Gael MILLOT committed
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822
1823
1824
1825
1826
1827
1828
1829
1830
1831
1832
total.comp.nb, 
sp.plot.fun, 
i.list, 
fun.tested, 
arg.values, 
fun.test, 
fun.test2, 
kind, 
problem, 
res, 
count, 
plot.count, 
data, 
code, 
plot.fun, 
res.path, 
lib.path, 
cute.path
){
# check again: very important because another R
Gael  MILLOT's avatar
Gael MILLOT committed
1833
1834
process.id <- Sys.getpid()
cat(paste0("\nPROCESS ID ", process.id, " -> TESTS ", x[1], " TO ", x[length(x)], "\n"))
Gael  MILLOT's avatar
Gael MILLOT committed
1835
1836
1837
1838
1839
1840
1841
1842
1843
1844
source(cute.path, local = .GlobalEnv)
fun_pack(req.package = "lubridate", lib.path = lib.path, load = TRUE) # load = TRUE to be sure that functions are present in the environment. And this prevent to use R.lib.path argument of fun_python_pack()
# end check again: very important because another R
# plot management
if(plot.fun == TRUE){
pdf(file = paste0(res.path, "/plots_from_fun_test_", x[1], ifelse(length(x) == 1, ".pdf", paste0("-", x[length(x)], ".pdf"))))
}else{
pdf(file = NULL) # send plots into a NULL file, no pdf file created
}
window.nb <- dev.cur()
1845
invisible(dev.set(window.nb))
Gael  MILLOT's avatar
Gael MILLOT committed
1846
1847
1848
1849
1850
1851
1852
1853
# end plot management
# new environment
env.name <- paste0("env", ini.time)
if(exists(env.name, where = -1)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}else{
assign(env.name, new.env())
1854
assign("val", val, envir = get(env.name)) # var replaced by val
Gael  MILLOT's avatar
Gael MILLOT committed
1855
1856
1857
1858
}
# end new environment
ini.date <- Sys.time()
ini.time <- as.numeric(ini.date) # time of process begin, converted into 
Gael  MILLOT's avatar
Gael MILLOT committed
1859
print.count.loop <- 0
Gael  MILLOT's avatar
Gael MILLOT committed
1860
1861
suppressMessages(suppressWarnings(eval(parse(text = code))))
colnames(data) <- arg
1862
1863
1864
if( ! is.null(expect.error)){
data <- data.frame(data, kind = kind, problem = problem, expected.error = expected.error, message = res, stringsAsFactors = FALSE)
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1865
data <- data.frame(data, kind = kind, problem = problem, message = res, stringsAsFactors = FALSE)
1866
}
Gael  MILLOT's avatar
Gael MILLOT committed
1867
row.names(data) <- paste0("test_", sprintf(paste0("%0", nchar(total.comp.nb), "d"), x))
Gael  MILLOT's avatar
Gael MILLOT committed
1868
sys.info <- sessionInfo()
1869
sys.info$loadedOnly <- sys.info$loadedOnly[order(names(sys.info$loadedOnly))] # sort the packages
Gael  MILLOT's avatar
Gael MILLOT committed
1870
1871
1872
invisible(dev.off(window.nb))
rm(env.name) # optional, because should disappear at the end of the function execution
# output
1873
output <- list(fun = fun, data = data, instruction = instruction, sys.info = sys.info)
Gael  MILLOT's avatar
Gael MILLOT committed
1874
1875
save(output, file = paste0(res.path, "/fun_test_", x[1], ifelse(length(x) == 1, ".RData", paste0("-", x[length(x)], ".RData"))))
if(plot.fun == TRUE & plot.count == 0){
Gael  MILLOT's avatar
Gael MILLOT committed
1876
warning(paste0("\nWARNING FROM ", function.name, " IN PROCESS ", process.id, ": NO PDF PLOT BECAUSE ONLY ERRORS REPORTED\n"), call. = FALSE)
Gael  MILLOT's avatar
Gael MILLOT committed
1877
1878
1879
file.remove(paste0(res.path, "/plots_from_fun_test_", x[1], ifelse(length(x) == 1, ".pdf", paste0("-", x[length(x)], ".pdf"))))
}
table.out <- as.matrix(output$data)
1880
# table.out[table.out == ""] <- " " # does not work # because otherwise read.table() converts "" into NA
Gael  MILLOT's avatar
Gael MILLOT committed
1881
1882
1883
1884
1885
table.out <- gsub(table.out, pattern = "\n", replacement = " ")
write.table(table.out, file = paste0(res.path, "/table_from_fun_test_", x[1], ifelse(length(x) == 1, ".txt", paste0("-", x[length(x)], ".txt"))), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n")
}
)
parallel::stopCluster(Clust)
1886
1887
1888
1889
# txt files assembly
if(length(cluster.list) > 1){
for(i2 in 1:length(cluster.list)){
tempo.name <- paste0(res.path, "/table_from_fun_test_", min(cluster.list[[i2]], na.rm = TRUE), ifelse(length(cluster.list[[i2]]) == 1, ".txt", paste0("-", max(cluster.list[[i2]], na.rm = TRUE), ".txt")))
1890
tempo <- read.table(file = tempo.name, header = TRUE, stringsAsFactors = FALSE, sep = "\t", row.names = 1, comment.char = "", colClasses = "character") #  row.names = 1 (1st column) because now read.table() adds a NA in the header if the header starts by a tabulation, comment.char = "" because colors with #, colClasses = "character" otherwise convert "" (from NULL) into NA
1891
1892
1893
1894
1895
1896
1897
1898
file.remove(tempo.name)
if(i2 == 1){
final.file <- tempo
}else{
final.file <- rbind(final.file, tempo)
}
}
write.table(final.file, file = paste0(res.path, "/table_from_fun_test_1-", total.comp.nb, ".txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n")
1899
1900
1901
1902
1903
1904
1905
1906
1907
if( ! is.null(expect.error)){
final.file <- final.file[ ! final.file$problem == final.file$expected.error, ]
if(nrow(final.file) == 0){
cat(paste0("NO DISCREPANCY BETWEEN EXPECTED AND OBSERVED ERRORS\n\n"))
}else{
cat(paste0("DISCREPANCIES BETWEEN EXPECTED AND OBSERVED ERRORS (SEE THE discrepancy_table_from_fun_test_1-", total.comp.nb, ".txt FILE)\n\n"))
write.table(final.file, file = paste0(res.path, "/discrepancy_table_from_fun_test_1-", total.comp.nb, ".txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n")
}
}
1908
1909
}
# end txt files assembly
Gael  MILLOT's avatar
Gael MILLOT committed
1910
1911
1912
1913
1914
1915
1916
1917
}else{
# plot management
if(plot.fun == TRUE){
pdf(file = paste0(res.path, "/plots_from_fun_test_1", ifelse(total.comp.nb == 1, ".pdf", paste0("-", total.comp.nb, ".pdf"))))
}else{
pdf(file = NULL) # send plots into a NULL file, no pdf file created
}
window.nb <- dev.cur()
1918
invisible(dev.set(window.nb))
Gael  MILLOT's avatar
Gael MILLOT committed
1919
1920
1921
1922
1923
1924
1925
1926
# end plot management
# new environment
env.name <- paste0("env", ini.time)
if(exists(env.name, where = -1)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}else{
assign(env.name, new.env())
1927
assign("val", val, envir = get(env.name)) # var replaced by val
Gael  MILLOT's avatar
Gael MILLOT committed
1928
1929
}
# end new environment
Gael  MILLOT's avatar
Gael MILLOT committed
1930
1931
suppressMessages(suppressWarnings(eval(parse(text = code))))
colnames(data) <- arg
1932
1933
1934
1935
expect.data <- data.frame()
if( ! is.null(expect.error)){
data <- data.frame(data, kind = kind, problem = problem, expected.error = expected.error, message = res, stringsAsFactors = FALSE)
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1936
data <- data.frame(data, kind = kind, problem = problem, message = res, stringsAsFactors = FALSE)
1937
}
Gael  MILLOT's avatar
Gael MILLOT committed
1938
1939
row.names(data) <- paste0("test_", sprintf(paste0("%0", nchar(total.comp.nb), "d"), 1:total.comp.nb))
sys.info <- sessionInfo()
1940
sys.info$loadedOnly <- sys.info$loadedOnly[order(names(sys.info$loadedOnly))] # sort the packages
Gael  MILLOT's avatar
Gael MILLOT committed
1941
1942
1943
invisible(dev.off(window.nb))
rm(env.name) # optional, because should disappear at the end of the function execution
# output
1944
output <- list(fun = fun, data = data, instruction = instruction, sys.info = sys.info)
Gael  MILLOT's avatar
Gael MILLOT committed
1945
if(plot.fun == TRUE & plot.count == 0){
Gael  MILLOT's avatar
Gael MILLOT committed
1946
warning(paste0("\nWARNING FROM ", function.name, ": NO PDF PLOT BECAUSE ONLY ERRORS REPORTED\n"), call. = FALSE)
Gael  MILLOT's avatar
Gael MILLOT committed
1947
file.remove(paste0(res.path, "/plots_from_fun_test_1", ifelse(total.comp.nb == 1, ".pdf", paste0("-", total.comp.nb, ".pdf"))))
Gael  MILLOT's avatar
Gael MILLOT committed
1948
}
1949
1950
1951
1952
1953
1954
1955
1956
1957
1958
1959
1960
1961
if( ! is.null(expect.error)){
expect.data <- output$data[ ! output$data$problem == output$data$expected.error, ]
if(nrow(expect.data) == 0){
cat(paste0("NO DISCREPANCY BETWEEN EXPECTED AND OBSERVED ERRORS\n\n"))
}else{
cat(paste0("DISCREPANCIES BETWEEN EXPECTED AND OBSERVED ERRORS (SEE THE ", if(export == TRUE){paste0("discrepancy_table_from_fun_test_1", ifelse(total.comp.nb == 1, "", paste0("-", total.comp.nb)), ".txt FILE")}else{"$data RESULT"}, ")\n\n"))
if(export == TRUE){
expect.data <- as.matrix(expect.data)
expect.data <- gsub(expect.data, pattern = "\n", replacement = "  ")
write.table(expect.data, file = paste0(res.path, "/discrepancy_table_from_fun_test_1", ifelse(total.comp.nb == 1, ".txt", paste0("-", total.comp.nb, ".txt"))), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n")
}
}
}
Gael  MILLOT's avatar
Gael MILLOT committed
1962
1963
1964
if(export == TRUE){
save(output, file = paste0(res.path, "/fun_test_1", ifelse(total.comp.nb == 1, ".RData", paste0("-", total.comp.nb, ".RData"))))
table.out <- as.matrix(output$data)
1965
table.out <- gsub(table.out, pattern = "\n", replacement = "  ")
Gael  MILLOT's avatar
Gael MILLOT committed
1966
1967
write.table(table.out, file = paste0(res.path, "/table_from_fun_test_1", ifelse(total.comp.nb == 1, ".txt", paste0("-", total.comp.nb, ".txt"))), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n")
}else{
Gael  MILLOT's avatar
Gael MILLOT committed
1968
return(output)
Gael  MILLOT's avatar
Gael MILLOT committed
1969
}
Gael  MILLOT's avatar
Gael MILLOT committed
1970
}
Gael  MILLOT's avatar
Gael MILLOT committed
1971
1972
1973
end.date <- Sys.time()
end.time <- as.numeric(end.date)
total.lapse <- round(lubridate::seconds_to_period(end.time - ini.time))
1974
cat(paste0("fun_test JOB END\n\nTIME: ", end.date, "\n\nTOTAL TIME LAPSE: ", total.lapse, "\n\n\n"))
Gael  MILLOT's avatar
Gael MILLOT committed
1975
}
Gael  MILLOT's avatar
Gael MILLOT committed
1976

Gael  MILLOT's avatar
Gael MILLOT committed
1977

Gael  MILLOT's avatar
Gael MILLOT committed
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
################ Object modification


######## fun_name_change() #### check a vector of character strings and modify any string if present in another vector


# Check OK: clear to go Apollo
fun_name_change <- function(data1, data2, added.string = "_modif"){
# AIM
# this function allow to check if a vector of character strings, like column names of a data frame, has elements present in another vector (vector of reserved words or column names of another data frame before merging)
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS
# data1: vector of character strings to check and modify
# data2: reference vector of character strings
# added.string: string added at the end of the modified string in data1 if present in data2
# RETURN
# a list containing
1996
# $data: the modified data1 (in the same order as in the initial data1)
Gael  MILLOT's avatar
Gael MILLOT committed
1997
1998
1999
2000
# $ini: the initial elements before modification. NULL if no modification
# $post: the modified elements in the same order as in ini. NULL if no modification
# EXAMPLES
# obs1 <- c("A", "B", "C", "D") ; obs2 <- c("A", "C") ; fun_name_change(obs1, obs2)