|
1
|
R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes"
|
|
2
|
Copyright (C) 2016 The R Foundation for Statistical Computing
|
|
3
|
Platform: x86_64-pc-linux-gnu (64-bit)
|
|
4
|
|
|
5
|
R is free software and comes with ABSOLUTELY NO WARRANTY.
|
|
6
|
You are welcome to redistribute it under certain conditions.
|
|
7
|
Type 'license()' or 'licence()' for distribution details.
|
|
8
|
|
|
9
|
R is a collaborative project with many contributors.
|
|
10
|
Type 'contributors()' for more information and
|
|
11
|
'citation()' on how to cite R or R packages in publications.
|
|
12
|
|
|
13
|
Type 'demo()' for some demos, 'help()' for on-line help, or
|
|
14
|
'help.start()' for an HTML browser interface to help.
|
|
15
|
Type 'q()' to quit R.
|
|
16
|
|
|
17
|
> setwd("/home/gcube/tomcat/webapps/wps/config/../ecocfg/rscr_19ecc1bf-8b5e-4350-bc38-2e4c4ae7ac64/catches_by_gear")
|
|
18
|
> source('/home/gcube/tomcat/webapps/wps/config/../ecocfg/rscr_19ecc1bf-8b5e-4350-bc38-2e4c4ae7ac64/catches_by_gear/4b814d63-5d3f-4a75-887f-d633d90955b7main.R')
|
|
19
|
let's begin
|
|
20
|
> if (is.null(time_aggregation)) {
|
|
21
|
+ time_start <- as.Date(time_start)
|
|
22
|
+ time_end <- as.Date(time_end)
|
|
23
|
+ time_frame <- time_end - time_sta .... [TRUNCATED]
|
|
24
|
|
|
25
|
> if (!is.null(tableToUse)) {
|
|
26
|
+ if (tableToUse == "total_catches") {
|
|
27
|
+ dbTable <- "tunaatlas.total_catches_ird_labels"
|
|
28
|
+ }
|
|
29
|
+ if (t .... [TRUNCATED]
|
|
30
|
|
|
31
|
> if (is.null(tableToUse)) {
|
|
32
|
+ if (is.null(time_aggregation)) {
|
|
33
|
+ if (time_frame >= 730 & !substr(area_filter, (nchar(area_filter) +
|
|
34
|
+ .... [TRUNCATED]
|
|
35
|
|
|
36
|
> if (!is.null(species_filter)) {
|
|
37
|
+ sp_filter <- unlist(strsplit(species_filter, split = ","))
|
|
38
|
+ if (nchar(sp_filter) == 3) {
|
|
39
|
+ specie .... [TRUNCATED]
|
|
40
|
|
|
41
|
> if (species_AggregationLevel == "speciesgroup_tunaatlas") {
|
|
42
|
+ col_species <- paste("id_", species_AggregationLevel, sep = "")
|
|
43
|
+ }
|
|
44
|
|
|
45
|
> if (species_AggregationLevel == "species") {
|
|
46
|
+ col_species <- paste("id_", species_AggregationLevel, "_",
|
|
47
|
+ codelistRef, sep = "")
|
|
48
|
+ }
|
|
49
|
|
|
50
|
> if (gear_AggregationLevel == "geargroup_tunaatlas") {
|
|
51
|
+ col_gear <- paste("id_", gear_AggregationLevel, sep = "")
|
|
52
|
+ }
|
|
53
|
|
|
54
|
> if (gear_AggregationLevel == "gear") {
|
|
55
|
+ col_gear <- paste("id_", gear_AggregationLevel, "_", codelistRef,
|
|
56
|
+ sep = "")
|
|
57
|
+ }
|
|
58
|
|
|
59
|
> col_flag <- paste("id_flag_", codelistRef, sep = "")
|
|
60
|
|
|
61
|
> if (is.null(time_aggregation)) {
|
|
62
|
+ if (time_frame < 730) {
|
|
63
|
+ time_aggregation = "month"
|
|
64
|
+ }
|
|
65
|
+ else {
|
|
66
|
+ time_aggregation .... [TRUNCATED]
|
|
67
|
|
|
68
|
> if (time_aggregation %in% c("month", "quarter", "semester")) {
|
|
69
|
+ col_time <- paste("time.", time_aggregation, ",time.year",
|
|
70
|
+ sep = "") .... [TRUNCATED]
|
|
71
|
|
|
72
|
> if (time_aggregation %in% c("year", "decade")) {
|
|
73
|
+ col_time <- paste("time.", time_aggregation, sep = "")
|
|
74
|
+ }
|
|
75
|
|
|
76
|
> select_column_query <- paste(col_gear, " AS gear,",
|
|
77
|
+ col_time, sep = "")
|
|
78
|
|
|
79
|
> where_clause_function <- function(column_name, filter) {
|
|
80
|
+ if (!is.null(filter)) {
|
|
81
|
+ filter = gsub(",", "','", filter)
|
|
82
|
+ filter .... [TRUNCATED]
|
|
83
|
|
|
84
|
> time_query_where_clause <- paste("time.time_start>='",
|
|
85
|
+ time_start, "' AND time.time_end<='", time_end, "'", sep = "")
|
|
86
|
|
|
87
|
> species_query_where_clause <- where_clause_function(col_species,
|
|
88
|
+ species_filter)
|
|
89
|
|
|
90
|
> flag_query_where_clause <- where_clause_function(col_flag,
|
|
91
|
+ flag_filter)
|
|
92
|
|
|
93
|
> if (substr(area_filter, (nchar(area_filter) + 1) -
|
|
94
|
+ 1, nchar(area_filter)) == ")") {
|
|
95
|
+ col_area = "geom"
|
|
96
|
+ area_query_where_clause <- .... [TRUNCATED]
|
|
97
|
|
|
98
|
> where_clause <- paste("WHERE ", time_query_where_clause,
|
|
99
|
+ species_query_where_clause, flag_query_where_clause, area_query_where_clause)
|
|
100
|
|
|
101
|
> if (time_aggregation %in% c("month", "quarter", "semester")) {
|
|
102
|
+ groupby_clause_time <- paste("time.", time_aggregation, ",time.year",
|
|
103
|
+ .... [TRUNCATED]
|
|
104
|
|
|
105
|
> if (time_aggregation %in% c("year", "decade")) {
|
|
106
|
+ groupby_clause_time <- paste("time.", time_aggregation, sep = "")
|
|
107
|
+ }
|
|
108
|
|
|
109
|
> groupby_clause <- paste("GROUP BY ", col_gear, ",",
|
|
110
|
+ groupby_clause_time, sep = "")
|
|
111
|
|
|
112
|
> query <- paste("SELECT trunc(sum(v_catch)::numeric,2) as var,",
|
|
113
|
+ select_column_query, " FROM ", dbTable, " JOIN time.time USING (id_time) ",
|
|
114
|
.... [TRUNCATED]
|
|
115
|
|
|
116
|
> library(ggplot2)
|
|
117
|
|
|
118
|
> library(cowplot)
|
|
119
|
|
|
120
|
> library(pryr)
|
|
121
|
|
|
122
|
> library(RPostgreSQL)
|
|
123
|
|
|
124
|
> library(scales)
|
|
125
|
|
|
126
|
> options(warn = -1)
|
|
127
|
|
|
128
|
> if (time_aggregation %in% c("month", "quarter", "semester")) {
|
|
129
|
+ df_plot$time <- as.Date(paste(df_plot[, "year"], "-", df_plot[,
|
|
130
|
+ time .... [TRUNCATED]
|
|
131
|
|
|
132
|
> message("ok1")
|
|
133
|
|
|
134
|
> if (time_aggregation %in% c("year", "decade")) {
|
|
135
|
+ df_plot$time <- df_plot$year
|
|
136
|
+ df_plot$year <- NULL
|
|
137
|
+ }
|
|
138
|
|
|
139
|
> message("ok2")
|
|
140
|
|
|
141
|
> df_plot <- df_plot[order(df_plot$time, df_plot$gear),
|
|
142
|
+ ]
|
|
143
|
|
|
144
|
> message("ok3")
|
|
145
|
|
|
146
|
> resplt <- ggplot(df_plot, aes(x = time, y = var, ymax = max(var) *
|
|
147
|
+ 1.05, group = gear)) + xlab("time") + ylab("catches (t)") +
|
|
148
|
+ geom_ar .... [TRUNCATED]
|
|
149
|
|
|
150
|
> message("ok4")
|
|
151
|
|
|
152
|
> filename <- "plot.png"
|
|
153
|
|
|
154
|
> ggsave(filename = filename, plot = resplt, dpi = 300)
|
|
155
|
|
|
156
|
> resplt <- filename
|
|
157
|
|
|
158
|
> message("ok5")
|
|
159
|
adding: plot.png (deflated 12%)
|
|
160
|
null
|
|
161
|
Attaching package: ‘cowplot’
|
|
162
|
|
|
163
|
The following object is masked from ‘package:ggplot2’:
|
|
164
|
|
|
165
|
ggsave
|
|
166
|
|
|
167
|
Loading required package: DBI
|
|
168
|
Ok21
|
|
169
|
trying URL 'http://mdst-macroes.ird.fr/BlueBridge/Tuna_Atlas/plot1_libraryIRDTunaAtlas.zip'
|
|
170
|
Content type 'application/zip' length 4580 bytes
|
|
171
|
==================================================
|
|
172
|
downloaded 4580 bytes
|
|
173
|
|
|
174
|
Ok22
|
|
175
|
Ok23
|
|
176
|
ok10
|
|
177
|
ok11
|
|
178
|
ok12
|
|
179
|
ok1
|
|
180
|
ok2
|
|
181
|
ok3
|
|
182
|
ok4
|
|
183
|
Saving 7 x 7 in image
|
|
184
|
ok5
|
|
185
|
ok13
|
|
186
|
ok14
|
|
187
|
Ok24
|
|
188
|
Ok25
|
|
189
|
Ok26
|
|
190
|
Ok27
|
|
191
|
Ok28
|
|
192
|
Ok29
|
|
193
|
Ok30
|
|
194
|
Error in eval(expr, envir, enclos) : object 'gfsd' not found
|
|
195
|
Calls: source -> withVisible -> eval -> eval
|
|
196
|
Execution halted
|
|
197
|
null
|
