Friday, September 19, 2014

9 19 2014 oyster bay fall maintenance

Kamilche wa

High 60s low 70s cloudy to mostly sunny

Participants: Sean Bennett,  Jonathan Allen,  and Jake heare.

Took live dead counts for all remaining trays. Then moved remaining oysters from trays to new hexagonal hanging cages. Then tied the cages together and hung them off the same hanging ropes. Very high survival in all trays, less than 2% mortality. Food growth in all trays. Some oysters look market size now. Mussel incursion was much better than expected with very little in most trays. More red rock crabs than I expected but seemed to have little effect on survival. Also lots of oyster spat in all trays. Collected spat for DNA workup if desired.

Numbers as follow

1S9-12
Live.           3
Dead.         3
Sampled     3

1H13-16
Live.           12
Dead.          2
Sample.      12

1N1-4
Live.           72
Dead.         0
Sample.      20

1H5-8
Live.          49
Dead.         7
Sample.      13

1S1-4
Live.          80
Dead.         4
Sample.      24

1S13-16
Live.          71
Dead.          2
Sample.      23

1N5-8
Live.          51
Dead.         0
Sample.      10

1H9-12.     
Live.          80
Dead.         3
Sample.      15

1H1-4
Live.         67
Dead.        3
Sample.     10

1N9-12
Live.          77
Dead.         1
Sample.      20

Pics below. 1S1-4 tray with 3 live on it is actually 1S9-12. 

Sunday, September 14, 2014

9 14 2014 Kaplan Meier Graphs Improved

KMgraphsWorking.R
library(survival)
## Loading required package: splines
kmdab=read.csv("KMdataDabob.csv")
names(kmdab)    
## [1] "Animal"     "Population" "Death"      "Status"
with(kmdab, tapply(Death[Status==1],Population[Status==1],mean))
##     H     N     S 
## 4.385 4.522 4.715
with(kmdab, tapply(Death[Status==1],Population[Status==1],var))
##      H      N      S 
## 0.4524 0.9786 1.6039
fit1=with(kmdab,survfit(Surv(Death,Status)~Population))
plot(fit1, col=c(1:3), xlab="Survival Time from Outplant in Months", ylab="% Surviving")
legend("bottomleft", title="Population", c("Dabob","Fidalgo","Oyster Bay"), fill=c(1:3))

plot of chunk unnamed-chunk-1

kmman=read.csv("KMdataMan.csv")
names(kmman)
## [1] "Animal"     "Population" "Death"      "Status"
with(kmman, tapply(Death[Status==1],Population[Status==1],mean))
##      H      N      S 
## 10.540  9.368  9.197
with(kmman, tapply(Death[Status==1],Population[Status==1],var))
##     H     N     S 
## 1.519 6.468 6.321
fit2=with(kmman, survfit(Surv(Death,Status)~Population))
plot(fit2, col=c(1:3), xlab="Survival Time from Outplant in Months", ylab="% Surviving")
legend("bottomleft", title="Population", c("Dabob","Fidalgo","Oyster Bay"), fill=c(1:3))

plot of chunk unnamed-chunk-1

kmfid=read.csv("KMdataFid.csv")
with(kmfid, tapply(Death[Status==1],Population[Status==1],mean))
##     H     N     S 
## 5.921 5.754 6.897
with(kmfid, tapply(Death[Status==1],Population[Status==1],var))
##     H     N     S 
## 2.554 2.189 3.989
fit3=with(kmfid, survfit(Surv(Death,Status)~Population))
plot(fit3, col=c(1:3), xlab="Survival Time from Outplant in Months", ylab="% Surviving")
legend("bottomleft", title="Population", c("Dabob","Fidalgo","Oyster Bay"), fill=c(1:3))

plot of chunk unnamed-chunk-1

kmoys=read.csv("KMdataOys.csv")
with(kmoys, tapply(Death[Status==1],Population[Status==1],mean))
##     H     N     S 
## 7.550 8.069 8.396
with(kmoys, tapply(Death[Status==1],Population[Status==1],var))
##     H     N     S 
## 7.774 5.805 5.814
fit4=with(kmoys, survfit(Surv(Death,Status)~Population))
plot(fit4, col=c(1:3), xlab="Survival Time from Outplant in Months", ylab="% Surviving")
legend("bottomleft", title="Population", c("Dabob","Fidalgo","Oyster Bay"), fill=c(1:3))

plot of chunk unnamed-chunk-1