-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathARCHIVE_SAM_GrowthData_Alloc_V2.R
358 lines (296 loc) · 13 KB
/
ARCHIVE_SAM_GrowthData_Alloc_V2.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
#use latest SamFilter as precusror to this file
# currently SamFilter050916.RData
library(car)
library(MASS)
library(boot)
library(plyr)
library(dtplyr)
library(gdata)
library(ggplot2)
library(ggrepel)
library(multcompView)
library(devtools)
library(lubridate)
#######RBIND ALL SUBSETS (function below for unmatch columns)
rbind.match.columns <- function(input1, input2) {
n.input1 <- ncol(input1)
n.input2 <- ncol(input2)
if (n.input2 < n.input1) {
TF.names <- which(names(input2) %in% names(input1))
column.names <- names(input2[, TF.names])
} else {
TF.names <- which(names(input1) %in% names(input2))
column.names <- names(input1[, TF.names])
}
return(rbind(input1[, column.names], input2[, column.names]))
}
#################################################################
# # LOAD SAM DATA
# load('c:/CloudStor/R_Stuff/SAM/Logistic/SamFilter190916.RData ')
# SamFiltered<-left_join(SamListKeep, SamFilter[,c(1,17:22,28:30)], by = "SiteCode")
load('c:/CloudStor/R_Stuff/SAM/Logistic/SamFilter131016.RData')
keep(SamFilter, SamResults, BlckPop, sure=T)
#recode database subblock errors
SamFilter$SubBlockNo[SamFilter$SubBlockNo==11] <- "11A"
#
###### CHOOSE OPTION ########
SamFilterIL<-SamFilter
#SamFilterIL<-SamFilterCI
# #================================================================
# # ADD IN SL DATA from raw SAM database file to SAMfilter
# #================================================================
SiteCodes<-unique(SamFilterIL$SiteCode)
pick <- which(BlckPop$SiteCode %in% SiteCodes)
BlckPopFilter<-BlckPop[pick,]
names(BlckPopFilter)[names(BlckPopFilter)=='SIT_StatBlock']<-"BlockNo"
names(BlckPopFilter)[names(BlckPopFilter)=='SIT_SubBlock']<-"SubBlockNo"
#Reformat SublockNo
BlckPopFilter$SubBlockNo<-paste(BlckPopFilter$BlockNo,BlckPopFilter$SubBlockNo, sep="")
SLSubBlockSum<-ddply(BlckPopFilter,.(SubBlockNo), summarize,
SLmax = max(SPC_ShellLength, na.rm=T), SLq95 = quantile(SPC_ShellLength, 0.95, na.rm=T))
#
#Match SLBlockSum to SamFilter by subblock
#
SamFilterIL<-left_join(SamFilterIL,SLSubBlockSum, by = 'SubBlockNo')
rm(SLSubBlockSum)
#drop SAM observations with odd low LD50
# OddLook<-subset(SamFilterIL, LD50 < 100 & SLmax > 183)
# OddSiteCodes<-unique(OddLook$SiteCode)
# pick <- which(SamFilterIL$SiteCode %in% OddSiteCodes)
# SamFilterIL<-SamFilterIL[-pick,]
# #================================================================
# # load Growth parameters
# #================================================================
load('c:/CloudStor/R_Stuff/SAM/Logistic/ILResults131016.Rdata')
IL.info<-ILResults
names(IL.info)[names(IL.info)=='Latitude']<-"Latitude.IL"
names(IL.info)[names(IL.info)=='Longitude']<-"Longitude.IL"
names(IL.info)[names(IL.info)=='StatBlock']<-"BlockNo.IL"
names(IL.info)[names(IL.info)=='NameSh']<-"GrowthSite"
names(IL.info)[names(IL.info)=='SiteId']<-"SIT_Id"
#Add zone
IL.info$Zone[IL.info$BlockNo %in% c(seq(13,30,1))] <- "E"
IL.info$Zone[IL.info$BlockNo %in% c(seq(7,12,1))] <- "W"
IL.info$Zone[IL.info$BlockNo %in% c(seq(6,6,1))] <- "CW"
IL.info$Zone[IL.info$BlockNo %in% c(seq(5,5,1))] <- "N"
IL.info$Zone[IL.info$BlockNo %in% c(1, 2, 3, 4,47, 48, 49,39, 40)] <- "N"
IL.info$Zone[IL.info$BlockNo %in% c(seq(32, 38,1),seq(41,46,1), seq(50,57,1))] <- "BS"
IL.info<-droplevels(subset(IL.info, SIT_Id != "266"))#Louisa Bay
# IL.info<-droplevels(subset(IL.info, SIT_Id != "171"))#Sterile Island
# IL.info<-droplevels(subset(IL.info, SIT_Id != "172"))#Actaeon Island
# # IL.info<-droplevels(subset(IL.info, SIT_Id != "461"))# One Tree Point
# # IL.info<-droplevels(subset(IL.info, SIT_Id != "764"))#Duck holes
# IL.info<-droplevels(subset(IL.info, SIT_Id != "480"))#Gagens Point
# IL.info<-droplevels(subset(IL.info, SIT_Id != "478"))#Middle Grounds
# IL.info<-droplevels(subset(IL.info, SIT_Id != "337"))#Southerly Bottom
# IL.info<-droplevels(subset(IL.info, SIT_Id != "813"))#George III
IL.info$L95<-as.numeric(as.character(IL.info$L95))
IL.info$L50<-as.numeric(as.character(IL.info$L50))
IL.info$MaxDL<-as.numeric(as.character(IL.info$MaxDL))
IL.info$MaxSig<-as.numeric(as.character(IL.info$MaxSig))
# #================================================================
# # Match SAM and Growth ID's
# #================================================================
SamFilterIL$SIT_Id<-as.character(SamFilterIL$SIT_Id)
SAM.IL<-left_join(SamFilterIL,IL.info[,c(1:5,11,13)], by = 'SIT_Id')
SAMSites<-subset(SAM.IL, is.na(MaxDL))
SAMSites<-SAMSites[,1:49]
SAMGwthSitesRAW<-subset(SAM.IL, !is.na(MaxDL))
rm(SAM.IL)
#write.csv(SAMGwthSites, file='GrwthSAMmatched.csv')
hist(SAMGwthSitesRAW$Ld50BootRange)
mean(SAMGwthSitesRAW$Ld50BootRange)
sd(SAMGwthSitesRAW$Ld50BootRange)
quantile(SAMGwthSitesRAW$Ld50BootRange, 0.68)
SAMGwthSites<-subset(SAMGwthSitesRAW, Ld50BootRange <= quantile(SAMGwthSitesRAW$Ld50BootRange, 0.68))
SAMGwthSiteReject<-subset(SAMGwthSitesRAW, Ld50BootRange > quantile(SAMGwthSitesRAW$Ld50BootRange, 0.68))
SAMGwthSites$SAMYear.GwthYear<-paste(SAMGwthSites$FishYear,SAMGwthSites$Recap_Year, sep=".")
# # ================== LM =================================
boxcox(SAMGwthSites$LD50~SAMGwthSites$L50)
fit<-lm(LD50~L50, data=SAMGwthSites)
summary(fit)
anova(fit)
par(mfrow = c(2,2))
plot(fit)
par(mfrow = c(1,1))
# view the data l50 by ld50
ggplot(data = SAMGwthSites, aes(x=L50, y=LD50)) +
xlab(bquote(''~L50['']~'(mm)')) + ylab(bquote(''~LM['50%']~'(mm)'))+
geom_smooth(method=lm, se=F, color='grey', fullrange=F, size=1.2, color='black')+
geom_text_repel(aes(label=SAMYear.GwthYear), size=3)+
geom_errorbar(aes(ymin=SAMGwthSites$Ld50BootL95, ymax=SAMGwthSites$Ld50BootU95),
width=.2, colour = 'grey')+
geom_point(aes(colour=Zone), size=3)+
#ggtitle(paste(dum$SubBlockNo, FishYear))+
#labs(title= Yeardum$SubBlockNo, size=10)+
#geom_histogram(binwidth=50)+
theme_bw()+
#scale_color_identity()+ #this makes sure the color follows the color argument above in aes()
theme(legend.position=c(0.1, 0.8))+
theme(legend.title=element_blank())+
theme(legend.text = element_text(size=14))+
theme(axis.title.x = element_text(size=14),
axis.text.x = element_text(size=14))+
theme(axis.title.y = element_text(size=14),
axis.text.y = element_text(size=14))
# filter by duplicate matches
dupes<-SAMGwthSites[duplicated(SAMGwthSites$GrowthSite),]
dupe_names<-unique(dupes$GrowthSite)
dupe_records<-subset(SAMGwthSites, GrowthSite %in% dupe_names)
dupe_pick<-dupe_records[c(2,3,5,7, 11, 13, 14, 17),]
SAMGwthSites<-SAMGwthSites[!SAMGwthSites$GrowthSite %in% dupe_names,]
SAMGwthSites<-rbind(SAMGwthSites, dupe_pick)
# #drop SAM observations with odd low LD50
# OddLook<-subset(SAMGwthSites, L50 < 110 & LD50 > 120)
# OddSiteCodes<-unique(OddLook$SiteCode)
# pick <- which(SamFilterIL$SiteCode %in% OddSiteCodes)
# SamFilterIL<-SamFilterIL[-pick,]
#
# #================================================================
# #
# # Growth data allocation with zone
# #
# #================================================================
#############################
names(SAMGwthSites)[names(SAMGwthSites)=='LD50']<-"GwthLD50"
SAMSite.BS<-droplevels(subset(SAMSites, Zone == 'BS'))
SAMSite.Z<-droplevels(subset(SAMSites, Zone != 'BS'))
Zones<-unique(SAMSite.Z$Zone)
#####
if (exists("SAMjoin"))
rm(SAMjoin)
for(z in Zones){
Samchoice<-subset(SAMSite.Z, Zone == z)
ILchoice<-subset(SAMGwthSites, Zone == z)
Samchoice$match<-sapply(Samchoice$LD50,function(x)which.min(abs(x - ILchoice$GwthLD50)))
Samchoice$match<-as.numeric(Samchoice$match)
ILchoice$match<-1:nrow(ILchoice)
Zonejoin<-left_join(Samchoice,ILchoice[,c(6,50:52,55, 57)], by = 'match')
if (exists("SAMjoin"))
SAMjoin <- rbind(SAMjoin, Zonejoin)
else
SAMjoin <- Zonejoin
}
ggplot(data = SAMjoin, aes(x=L50, y=LD50)) +
xlab(bquote(''~L50['']~'(mm)')) + ylab(bquote(''~LM['50%']~'(mm)'))+
geom_smooth(method=lm, se=F, color='grey', fullrange=F, size=1.2, color='black')+
#geom_text_repel(aes(label=GrowthSite), size=3)+
# geom_errorbar(aes(ymin=SAMGwthSites$Ld50BootL95, ymax=SAMGwthSites$Ld50BootU95),
# width=.2, colour = 'grey')+
geom_point(aes(colour=Zone), size=3)+
#ggtitle(paste(dum$SubBlockNo, FishYear))+
#labs(title= Yeardum$SubBlockNo, size=10)+
#geom_histogram(binwidth=50)+
theme_bw()+
#scale_color_identity()+ #this makes sure the color follows the color argument above in aes()
theme(legend.position=c(0.1, 0.8))+
theme(legend.title=element_blank())+
theme(legend.text = element_text(size=14))+
theme(axis.title.x = element_text(size=14),
axis.text.x = element_text(size=14))+
theme(axis.title.y = element_text(size=14),
axis.text.y = element_text(size=14))
# names(SAMjoin)[names(SAMjoin)=='LD50.x']<-"LD50"
# names(SAMjoin)[names(SAMjoin)=='LD50.y']<-"GrowthLD50"
# #
# #TREAT BSZ grwth data as mean values as no direct matches by SIT_ID
BS.IL.Info<-droplevels(subset(IL.info, Zone == "BS"))
SAMSite.BS$match<-sapply(SAMSite.BS$BlockNo,function(x)which.min(abs(x - as.integer(BS.IL.Info$BlockNo.IL))))
SAMSite.BS$match<-as.numeric(SAMSite.BS$match)
BS.IL.Info$match<-1:nrow(BS.IL.Info)
BSjoin<-left_join(SAMSite.BS, BS.IL.Info[,c(2:4,13,15)], by = 'match')
BSjoin$GrowthLD50<-BSjoin$LD50
SAMGwthSites$LD50<-SAMGwthSites$GwthLD50
SAMGwthOutPut<-rbind.match.columns(SAMjoin, BSjoin)
SAMILResults<-rbind.match.columns(SAMGwthSites,SAMGwthOutPut)
SamSites_Test<-SAMSites
SAMGwthSites_Test<-SAMGwthSites
SamSites_Test$match<-sapply(SamSites_Test$LD50,function(x)which.min(abs(x - SAMGwthSites_Test$GwthLD50)))
SamSites_Test$match<-as.numeric(SamSites_Test$match)
SAMGwthSites_Test$match<-1:nrow(SAMGwthSites_Test)
Zonejoin_test<-left_join(SamSites_Test,SAMGwthSites_Test[,c(6,50:52,55, 57)], by = 'match')
ggplot(data = Nzones.SAM.IL, aes(x=L50, y=LD50)) +
xlab(bquote(''~L50['']~'(mm)')) + ylab(bquote(''~LM['50%']~'(mm)'))+
geom_smooth(method=lm, se=F, color='grey', fullrange=F, size=1.2, color='black')+
#geom_text_repel(aes(label=GrowthSite), size=3)+
# geom_errorbar(aes(ymin=SAMGwthSites$Ld50BootL95, ymax=SAMGwthSites$Ld50BootU95),
# width=.2, colour = 'grey')+
geom_point(aes(colour=Zone), size=3)+
#ggtitle(paste(dum$SubBlockNo, FishYear))+
#labs(title= Yeardum$SubBlockNo, size=10)+
#geom_histogram(binwidth=50)+
theme_bw()+
#scale_color_identity()+ #this makes sure the color follows the color argument above in aes()
theme(legend.position=c(0.1, 0.8))+
theme(legend.title=element_blank())+
theme(legend.text = element_text(size=14))+
theme(axis.title.x = element_text(size=14),
axis.text.x = element_text(size=14))+
theme(axis.title.y = element_text(size=14),
axis.text.y = element_text(size=14))
SAMILResults_Test<-rbind.match.columns(SAMGwthSites,Zonejoin_test)
# GrwthAllocations<-SAMjoin[,c(6, 18, 21, 22,29, 36,41)]
# E_GrwthAllocations<-droplevels(subset(GrwthAllocations, Zone =='E'))
#
# write.csv(GrwthAllocations, file='GrwthAllocations.csv')
########GROWTH ALLOCATION OPTIONS NOT USED###############
# 1. #ALLOCATE THE GROWTH DATA BY LD50 without zone retrictions
# SAMSite.Z$match<-sapply(SAMSite.Z$LD50,function(x)which.min(abs(x - SAMGwthSites$LD50)))
# SAMGwthSites$match<-c(1:20)
# SAMjoin<-left_join(SAMSite.Z,SAMGwthSites[,c(6,35:41)], by = 'match')
# names(SAMjoin)[names(SAMjoin)=='LD50.x']<-"LD50"
# names(SAMjoin)[names(SAMjoin)=='LD50.y']<-"GrowthLD50"
# 2. #ALLOCATE GROWTH DATA ONLY KEEPING MAXIMUM REULST FOR EACH MATCH OF GROWTH AND SAM
#SAMGwthSites<-do.call(rbind,lapply(split(SAMGwthSites,SAMGwthSites$SIT_Id),function(chunk) chunk[which.min(chunk$LD50),]))
# 3. #ALLOCATE GROWTH DATA VIA Producing LD50t for each of the growth data from Growth data with matching LD50range < 5 mm
# fit2<-lm(LD50~L50, data=SAMGwthSites)
# summary(fit2)
#
# anova(fit2)
# par(mfrow = c(2,2))
# plot(fit2)
# par(mfrow = c(1,1))
# #shapiro.test(fit2)
#
#
# IL.info$LD50t<-fit2$coef[1]+fit2$coef[2]*IL.info$L50
#
# # #================================================================
# # #
# # # Growth data allocation with zone
# # #
# # #================================================================
# #############################
# SAMSite.BS<-droplevels(subset(SamFilter, Zone == 'BS'))
# SAMSite.Z<-droplevels(subset(SamFilter, Zone != 'BS'))
#
# Zones<-unique(SAMSite.Z$Zone)
# #####
# if (exists("SAMjoin"))
# rm(SAMjoin)
#
# for(z in Zones){
# Samchoice<-subset(SamFilter, Zone == z)
# ILchoice<-subset(IL.info, Zone == z)
# Samchoice$match<-sapply(Samchoice$LD50,function(x)which.min(abs(x - ILchoice$LD50t)))
# Samchoice$match<-as.numeric(Samchoice$match)
# ILchoice$match<-1:nrow(ILchoice)
#
# Zonejoin<-left_join(Samchoice,ILchoice[,c(2:5,7,14)], by = 'match')
#
# if (exists("SAMjoin"))
# SAMjoin <- rbind(SAMjoin, Zonejoin)
# else
# SAMjoin <- Zonejoin
# }
#
# #TREAT BSZ grwth data as mean values as no direct matches by SIT_ID
# BS.IL.Info<-droplevels(subset(IL.info, SIT_Id == "315"))
# BSjoin<-left_join(SAMSite.BS, BS.IL.Info[,c(2:6,12)], by = 'Zone')
#
#
#
# SAMGwthOutPut<-rbind.match.columns(SAMjoin, BSjoin)
#
# SAMILResults<-SAMGwthOutPut
#