Critical transitions
Matthew A. Barbour
2021-06-24
Last updated: 2021-06-24
Checks: 6 1
Knit directory: genes-to-foodweb-stability/
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Wrangle data
# Load and manage data
df <- read_csv("data/InsectAbundanceSurvival.csv") %>%
# renaming for brevity
rename(cage = Cage,
com = Composition,
week = Week,
temp = Temperature,
rich = Richness) %>%
mutate(cage = as.character(cage),
fweek = factor(ifelse(week < 10, paste("0", week, sep=""), week)),
temp = ifelse(temp=="20 C", 0, 1)) %>%
arrange(cage, week)
# create data for multi-state survival analysis
state_df <- df %>%
# counter information is not relevant (because it is the same), so we summarise across it
group_by(cage, fweek, week, temp, rich, Col, gsm1, AOP2, AOP2.gsoh, com) %>%
summarise_at(vars(BRBR_Survival, LYER_Survival, Mummy_Ptoids_Survival), list(mean)) %>%
ungroup() %>%
# create possible food-web states
mutate(BRBR = ifelse(BRBR_Survival == 1, "BRBR", ifelse(BRBR_Survival == 0, "0", NA)),
LYER = ifelse(LYER_Survival == 1, "LYER", ifelse(LYER_Survival == 0, "0", NA)),
Ptoid = ifelse(Mummy_Ptoids_Survival == 1, "Ptoid", ifelse(Mummy_Ptoids_Survival == 0, "0", NA))) %>%
mutate(state = paste(BRBR, LYER, Ptoid, sep = "-"),
cage = as.character(cage)) %>%
# these variables are no longer needed
select(-BRBR, -LYER, -Ptoid) %>%
# remove all instances where all species have been labelled extinct for more than 1 week "NA-NA-NA".
# also, only keep observations after 2 weeks when we added the parasitoid (full community)
filter(state != "NA-NA-NA", week > 2) %>%
mutate(week_since = week - 2)
# replace NA with zeros for state variable
state_df$state <- gsub("NA","0", state_df$state)
# everything appears in order
arrange(state_df, cage, week_since) %>% select(cage, week_since, BRBR_Survival, LYER_Survival, Mummy_Ptoids_Survival, state) # A tibble: 710 x 6
cage week_since BRBR_Survival LYER_Survival Mummy_Ptoids_Surviv… state
<chr> <dbl> <dbl> <dbl> <dbl> <chr>
1 1 1 1 1 1 BRBR-LYER-…
2 1 2 1 1 1 BRBR-LYER-…
3 1 3 1 1 1 BRBR-LYER-…
4 1 4 1 1 1 BRBR-LYER-…
5 1 5 0 0 1 0-0-Ptoid
6 1 6 NA NA 0 0-0-0
7 10 1 1 1 1 BRBR-LYER-…
8 10 2 1 1 1 BRBR-LYER-…
9 10 3 1 1 1 BRBR-LYER-…
10 10 4 1 1 1 BRBR-LYER-…
# … with 700 more rowsMulti-state Markov model with msm
# state transitions for all cages and time points
msm::statetable.msm(state = state, subject = cage, data = state_df) to
from 0-0-0 0-0-Ptoid 0-LYER-0 0-LYER-Ptoid BRBR-LYER-Ptoid
0-0-Ptoid 22 7 0 0 0
0-LYER-0 1 0 131 0 0
0-LYER-Ptoid 5 12 26 242 0
BRBR-LYER-Ptoid 0 10 0 50 144# turn state into numeric values, which is necessary for the analysis
state_df$state_type <- with(state_df, ifelse(state == "BRBR-LYER-Ptoid", 1,
ifelse(state == "0-LYER-Ptoid", 2,
ifelse(state == "0-LYER-0", 3,
ifelse(state == "0-0-Ptoid", 4,
ifelse(state == "0-0-0", 5, NA))))))
# no NAs
which(is.na(state_df$state_type) == T)integer(0)# inspect states
statetable.msm(state = state_type, subject = cage, data = state_df) to
from 1 2 3 4 5
1 144 50 0 10 0
2 0 242 26 12 5
3 0 0 131 0 1
4 0 0 0 7 22# specify allowed transitions
Q <- rbind(c(0,1,0,1,0),
c(0,0,1,1,0),
c(0,0,0,0,1),
c(0,0,0,0,1),
c(0,0,0,0,0))
# give informative labels
rownames(Q) <- colnames(Q) <- c("1-1-1","0-1-1","0-1-0","0-0-1","0-0-0")
# everything appears in order
Q 1-1-1 0-1-1 0-1-0 0-0-1 0-0-0
1-1-1 0 1 0 1 0
0-1-1 0 0 1 1 0
0-1-0 0 0 0 0 1
0-0-1 0 0 0 0 1
0-0-0 0 0 0 0 0# we use this initial transition matrix by specifying "gen.inits = T" in msm model
crudeinits.msm(state_type ~ week_since, subject = cage, data = state_df, qmatrix = Q) 1-1-1 0-1-1 0-1-0 0-0-1 0-0-0
1-1-1 -0.2941176 0.2450980 0.000000000 0.04901961 0.000000000
0-1-1 0.0000000 -0.1333333 0.091228070 0.04210526 0.000000000
0-1-0 0.0000000 0.0000000 -0.007575758 0.00000000 0.007575758
0-0-1 0.0000000 0.0000000 0.000000000 -0.75862069 0.758620690
0-0-0 0.0000000 0.0000000 0.000000000 0.00000000 0.000000000# fit model
AOP2_foodweb.msm <- msm(state_type ~ week_since,
subject = cage,
data = state_df,
qmatrix = Q,
gen.inits = TRUE,
# for "3-5" (aphid alone to collapse) and "4-5" (ptoid alone to collapse),
# I don't expect there to be any genetic effects, because the aphid alone
# will likely persist regardless of plant genetics. similarly, a parasitoid
# population without any aphids will inevitably go extinct.
covariates = list("1-2" =~ I(Col+gsm1) + I(AOP2+AOP2.gsoh),
"1-4" =~ I(Col+gsm1) + I(AOP2+AOP2.gsoh),
"2-3" =~ I(Col+gsm1) + I(AOP2+AOP2.gsoh),
"2-4" =~ I(Col+gsm1) + I(AOP2+AOP2.gsoh)),
obstype = 1)
# hazard ratios for each food-web transition
hazard.msm(AOP2_foodweb.msm)$`I(Col + gsm1)`
HR L U
1-1-1 - 0-1-1 0.9442035 0.6251704 1.4260437
1-1-1 - 0-0-1 0.9222300 0.2975583 2.8582907
0-1-1 - 0-1-0 0.8370570 0.4655484 1.5050303
0-1-1 - 0-0-1 0.3292210 0.1483872 0.7304303
0-1-0 - 0-0-0 1.0000000 1.0000000 1.0000000
0-0-1 - 0-0-0 1.0000000 1.0000000 1.0000000
$`I(AOP2 + AOP2.gsoh)`
HR L U
1-1-1 - 0-1-1 0.9732554 0.6506339 1.455851
1-1-1 - 0-0-1 1.2270368 0.3875724 3.884743
0-1-1 - 0-1-0 0.8579613 0.4747299 1.550561
0-1-1 - 0-0-1 0.7437616 0.2954229 1.872506
0-1-0 - 0-0-0 1.0000000 1.0000000 1.000000
0-0-1 - 0-0-0 1.0000000 1.0000000 1.000000Reproduce Fig. S4
# for coxph analysis (multistate), this may not be completely necessary
AJ_state_df <- state_df %>%
# convert Ptoid only state to collapsed state, which is inevitable
mutate(state_adj = ifelse(state == "0-0-Ptoid", "0-0-0", state)) %>%
# convert state into a factor for analysis
mutate(fstate = factor(state_adj, levels = c("BRBR-LYER-Ptoid","0-LYER-Ptoid","0-LYER-0","0-0-0"))) %>%
mutate(rich_temp = paste(rich, temp, sep = "_")) %>%
mutate(aop2_genotypes = factor(Col+gsm1, levels = c(0,1,2), labels = c("AOP2\u2013 = 0", "AOP2\u2013 = 1", "AOP2\u2013 = 2")))
# get food-web transitions as a function of number of aop2 genotypes
aop2_AJ <- survfit(Surv(I(week_since-1), week_since, fstate) ~ aop2_genotypes, data = AJ_state_df, id = cage)
tidy_aop2_AJ <- tidy(aop2_AJ)
tidy_aop2_AJ$strata <- sub(pattern = "aop2_genotypes=", replacement = "", x = tidy_aop2_AJ$strata)
# plot
plot_aop2_genotypes_multistate <- ggplot(tidy_aop2_AJ, aes(x = time + 2, y = estimate)) +
geom_area(aes(fill = state)) +
facet_wrap(~strata) +
scale_fill_viridis_d(name = "Food-web state", labels = c("Arabidopsis only","Aphid only","Food chain","Initial")) +
xlab("Week of experiment") +
ylab("Proportion")
x11(); plot_aop2_genotypes_multistate
#ggsave(plot = plot_aop2_genotypes_multistate, filename = "figures/aop2-genotypes-multistate.pdf", width = 6, height = 5, device=cairo_pdf)
Assess robustness of AOP2 effect on food chain persistence
## Organize data for analysis
# LYER-Ptoid cages at least at one time point
LP_cages <- unique(filter(state_df, state == "0-LYER-Ptoid")$cage)
# should be 50 cages, and it is
length(LP_cages)[1] 50# filter and manage data
LP_transit_df <- state_df %>%
filter(cage %in% LP_cages, state != "BRBR-LYER-Ptoid") %>%
# omit BRBR from consideration
select(-BRBR_Survival) %>%
# omit rows where we already know either LYER or Ptoid went extinct
na.omit() %>%
mutate(# assume these two states are the same, i.e. to get to 0-0-0, had to go through 0-0-Ptoid
state_adj = ifelse(state %in% c("0-0-Ptoid","0-0-0"), "0-0-Ptoid", state))
# confirm levels
unique(LP_transit_df$state_adj) #fstate)[1] "0-LYER-Ptoid" "0-LYER-0" "0-0-Ptoid" # get start times after BRBR went extinct
get_LP_transit_start <- LP_transit_df %>%
group_by(cage) %>%
arrange(week_since) %>%
mutate(start = first(week_since))
# all looks in order
get_LP_transit_start %>% arrange(cage) %>% data.frame() cage fweek week temp rich Col gsm1 AOP2 AOP2.gsoh com
1 12 07 7 0 4 1 1 1 1 Poly
2 12 08 8 0 4 1 1 1 1 Poly
3 12 09 9 0 4 1 1 1 1 Poly
4 12 10 10 0 4 1 1 1 1 Poly
5 12 11 11 0 4 1 1 1 1 Poly
6 12 12 12 0 4 1 1 1 1 Poly
7 12 13 13 0 4 1 1 1 1 Poly
8 12 14 14 0 4 1 1 1 1 Poly
9 12 15 15 0 4 1 1 1 1 Poly
10 12 16 16 0 4 1 1 1 1 Poly
11 12 17 17 0 4 1 1 1 1 Poly
12 13 06 6 0 4 1 1 1 1 Poly
13 13 07 7 0 4 1 1 1 1 Poly
14 13 08 8 0 4 1 1 1 1 Poly
15 13 09 9 0 4 1 1 1 1 Poly
16 13 10 10 0 4 1 1 1 1 Poly
17 13 11 11 0 4 1 1 1 1 Poly
18 13 12 12 0 4 1 1 1 1 Poly
19 13 13 13 0 4 1 1 1 1 Poly
20 13 14 14 0 4 1 1 1 1 Poly
21 13 15 15 0 4 1 1 1 1 Poly
22 13 16 16 0 4 1 1 1 1 Poly
23 13 17 17 0 4 1 1 1 1 Poly
24 14 08 8 0 1 1 0 0 0 Col
25 14 09 9 0 1 1 0 0 0 Col
26 14 10 10 0 1 1 0 0 0 Col
27 15 07 7 0 1 0 0 0 1 AOP2.gsoh
28 15 08 8 0 1 0 0 0 1 AOP2.gsoh
29 15 09 9 0 1 0 0 0 1 AOP2.gsoh
30 15 10 10 0 1 0 0 0 1 AOP2.gsoh
31 15 11 11 0 1 0 0 0 1 AOP2.gsoh
32 15 12 12 0 1 0 0 0 1 AOP2.gsoh
33 15 13 13 0 1 0 0 0 1 AOP2.gsoh
34 15 14 14 0 1 0 0 0 1 AOP2.gsoh
35 15 15 15 0 1 0 0 0 1 AOP2.gsoh
36 17 08 8 0 2 0 1 1 0 gsm1_AOP2
37 17 09 9 0 2 0 1 1 0 gsm1_AOP2
38 18 07 7 0 2 1 0 0 1 Col_AOP2.gsoh
39 18 08 8 0 2 1 0 0 1 Col_AOP2.gsoh
40 18 09 9 0 2 1 0 0 1 Col_AOP2.gsoh
41 18 10 10 0 2 1 0 0 1 Col_AOP2.gsoh
42 18 11 11 0 2 1 0 0 1 Col_AOP2.gsoh
43 18 12 12 0 2 1 0 0 1 Col_AOP2.gsoh
44 18 13 13 0 2 1 0 0 1 Col_AOP2.gsoh
45 18 14 14 0 2 1 0 0 1 Col_AOP2.gsoh
46 18 15 15 0 2 1 0 0 1 Col_AOP2.gsoh
47 18 16 16 0 2 1 0 0 1 Col_AOP2.gsoh
48 20 07 7 0 2 0 1 1 0 gsm1_AOP2
49 20 08 8 0 2 0 1 1 0 gsm1_AOP2
50 20 09 9 0 2 0 1 1 0 gsm1_AOP2
51 20 10 10 0 2 0 1 1 0 gsm1_AOP2
52 20 11 11 0 2 0 1 1 0 gsm1_AOP2
53 20 12 12 0 2 0 1 1 0 gsm1_AOP2
54 20 13 13 0 2 0 1 1 0 gsm1_AOP2
55 22 07 7 0 1 0 0 0 1 AOP2.gsoh
56 22 08 8 0 1 0 0 0 1 AOP2.gsoh
57 23 07 7 0 2 0 0 1 1 AOP2_AOP2.gsoh
58 23 08 8 0 2 0 0 1 1 AOP2_AOP2.gsoh
59 23 09 9 0 2 0 0 1 1 AOP2_AOP2.gsoh
60 23 10 10 0 2 0 0 1 1 AOP2_AOP2.gsoh
61 23 11 11 0 2 0 0 1 1 AOP2_AOP2.gsoh
62 23 12 12 0 2 0 0 1 1 AOP2_AOP2.gsoh
63 23 13 13 0 2 0 0 1 1 AOP2_AOP2.gsoh
64 23 14 14 0 2 0 0 1 1 AOP2_AOP2.gsoh
65 23 15 15 0 2 0 0 1 1 AOP2_AOP2.gsoh
66 23 16 16 0 2 0 0 1 1 AOP2_AOP2.gsoh
67 25 06 6 0 1 0 0 1 0 AOP2
68 25 07 7 0 1 0 0 1 0 AOP2
69 25 08 8 0 1 0 0 1 0 AOP2
70 26 07 7 0 1 1 0 0 0 Col
71 26 08 8 0 1 1 0 0 0 Col
72 27 07 7 0 2 1 0 1 0 Col_AOP2
73 27 08 8 0 2 1 0 1 0 Col_AOP2
74 28 06 6 0 2 1 0 0 1 Col_AOP2.gsoh
75 28 07 7 0 2 1 0 0 1 Col_AOP2.gsoh
76 28 08 8 0 2 1 0 0 1 Col_AOP2.gsoh
77 29 06 6 0 2 0 1 0 1 gsm1_AOP2.gsoh
78 29 07 7 0 2 0 1 0 1 gsm1_AOP2.gsoh
79 29 08 8 0 2 0 1 0 1 gsm1_AOP2.gsoh
80 29 09 9 0 2 0 1 0 1 gsm1_AOP2.gsoh
81 29 10 10 0 2 0 1 0 1 gsm1_AOP2.gsoh
82 29 11 11 0 2 0 1 0 1 gsm1_AOP2.gsoh
83 29 12 12 0 2 0 1 0 1 gsm1_AOP2.gsoh
84 29 13 13 0 2 0 1 0 1 gsm1_AOP2.gsoh
85 29 14 14 0 2 0 1 0 1 gsm1_AOP2.gsoh
86 29 15 15 0 2 0 1 0 1 gsm1_AOP2.gsoh
87 30 08 8 0 2 1 1 0 0 Col_gsm1
88 30 09 9 0 2 1 1 0 0 Col_gsm1
89 30 10 10 0 2 1 1 0 0 Col_gsm1
90 30 11 11 0 2 1 1 0 0 Col_gsm1
91 30 12 12 0 2 1 1 0 0 Col_gsm1
92 30 13 13 0 2 1 1 0 0 Col_gsm1
93 30 14 14 0 2 1 1 0 0 Col_gsm1
94 31 07 7 1 2 0 1 1 0 gsm1_AOP2
95 31 08 8 1 2 0 1 1 0 gsm1_AOP2
96 31 09 9 1 2 0 1 1 0 gsm1_AOP2
97 31 10 10 1 2 0 1 1 0 gsm1_AOP2
98 31 11 11 1 2 0 1 1 0 gsm1_AOP2
99 31 12 12 1 2 0 1 1 0 gsm1_AOP2
100 31 13 13 1 2 0 1 1 0 gsm1_AOP2
101 31 14 14 1 2 0 1 1 0 gsm1_AOP2
102 32 05 5 1 1 1 0 0 0 Col
103 32 06 6 1 1 1 0 0 0 Col
104 32 07 7 1 1 1 0 0 0 Col
105 32 08 8 1 1 1 0 0 0 Col
106 32 09 9 1 1 1 0 0 0 Col
107 32 10 10 1 1 1 0 0 0 Col
108 32 11 11 1 1 1 0 0 0 Col
109 32 12 12 1 1 1 0 0 0 Col
110 32 13 13 1 1 1 0 0 0 Col
111 32 14 14 1 1 1 0 0 0 Col
112 32 15 15 1 1 1 0 0 0 Col
113 33 05 5 1 1 1 0 0 0 Col
114 33 06 6 1 1 1 0 0 0 Col
115 33 07 7 1 1 1 0 0 0 Col
116 33 08 8 1 1 1 0 0 0 Col
117 33 09 9 1 1 1 0 0 0 Col
118 33 10 10 1 1 1 0 0 0 Col
119 34 06 6 1 2 1 0 0 1 Col_AOP2.gsoh
120 34 07 7 1 2 1 0 0 1 Col_AOP2.gsoh
121 34 08 8 1 2 1 0 0 1 Col_AOP2.gsoh
122 34 09 9 1 2 1 0 0 1 Col_AOP2.gsoh
123 35 06 6 1 2 0 0 1 1 AOP2_AOP2.gsoh
124 35 07 7 1 2 0 0 1 1 AOP2_AOP2.gsoh
125 36 04 4 1 2 0 1 0 1 gsm1_AOP2.gsoh
126 36 05 5 1 2 0 1 0 1 gsm1_AOP2.gsoh
127 36 06 6 1 2 0 1 0 1 gsm1_AOP2.gsoh
128 36 07 7 1 2 0 1 0 1 gsm1_AOP2.gsoh
129 36 08 8 1 2 0 1 0 1 gsm1_AOP2.gsoh
130 36 09 9 1 2 0 1 0 1 gsm1_AOP2.gsoh
131 36 10 10 1 2 0 1 0 1 gsm1_AOP2.gsoh
132 36 11 11 1 2 0 1 0 1 gsm1_AOP2.gsoh
133 36 12 12 1 2 0 1 0 1 gsm1_AOP2.gsoh
134 36 13 13 1 2 0 1 0 1 gsm1_AOP2.gsoh
135 36 14 14 1 2 0 1 0 1 gsm1_AOP2.gsoh
136 36 15 15 1 2 0 1 0 1 gsm1_AOP2.gsoh
137 37 06 6 1 2 0 1 0 1 gsm1_AOP2.gsoh
138 37 07 7 1 2 0 1 0 1 gsm1_AOP2.gsoh
139 37 08 8 1 2 0 1 0 1 gsm1_AOP2.gsoh
140 37 09 9 1 2 0 1 0 1 gsm1_AOP2.gsoh
141 37 10 10 1 2 0 1 0 1 gsm1_AOP2.gsoh
142 37 11 11 1 2 0 1 0 1 gsm1_AOP2.gsoh
143 37 12 12 1 2 0 1 0 1 gsm1_AOP2.gsoh
144 37 13 13 1 2 0 1 0 1 gsm1_AOP2.gsoh
145 37 14 14 1 2 0 1 0 1 gsm1_AOP2.gsoh
146 37 15 15 1 2 0 1 0 1 gsm1_AOP2.gsoh
147 37 16 16 1 2 0 1 0 1 gsm1_AOP2.gsoh
148 37 17 17 1 2 0 1 0 1 gsm1_AOP2.gsoh
149 38 04 4 1 4 1 1 1 1 Poly
150 38 05 5 1 4 1 1 1 1 Poly
151 38 06 6 1 4 1 1 1 1 Poly
152 38 07 7 1 4 1 1 1 1 Poly
153 38 08 8 1 4 1 1 1 1 Poly
154 38 09 9 1 4 1 1 1 1 Poly
155 38 10 10 1 4 1 1 1 1 Poly
156 38 11 11 1 4 1 1 1 1 Poly
157 38 12 12 1 4 1 1 1 1 Poly
158 38 13 13 1 4 1 1 1 1 Poly
159 38 14 14 1 4 1 1 1 1 Poly
160 39 07 7 1 1 0 1 0 0 gsm1
161 39 08 8 1 1 0 1 0 0 gsm1
162 39 09 9 1 1 0 1 0 0 gsm1
163 4 07 7 0 1 0 0 1 0 AOP2
164 4 08 8 0 1 0 0 1 0 AOP2
165 4 09 9 0 1 0 0 1 0 AOP2
166 40 04 4 1 2 0 1 0 1 gsm1_AOP2.gsoh
167 40 05 5 1 2 0 1 0 1 gsm1_AOP2.gsoh
168 40 06 6 1 2 0 1 0 1 gsm1_AOP2.gsoh
169 40 07 7 1 2 0 1 0 1 gsm1_AOP2.gsoh
170 40 08 8 1 2 0 1 0 1 gsm1_AOP2.gsoh
171 40 09 9 1 2 0 1 0 1 gsm1_AOP2.gsoh
172 40 10 10 1 2 0 1 0 1 gsm1_AOP2.gsoh
173 40 11 11 1 2 0 1 0 1 gsm1_AOP2.gsoh
174 40 12 12 1 2 0 1 0 1 gsm1_AOP2.gsoh
175 40 13 13 1 2 0 1 0 1 gsm1_AOP2.gsoh
176 40 14 14 1 2 0 1 0 1 gsm1_AOP2.gsoh
177 40 15 15 1 2 0 1 0 1 gsm1_AOP2.gsoh
178 40 16 16 1 2 0 1 0 1 gsm1_AOP2.gsoh
179 41 08 8 1 2 1 0 1 0 Col_AOP2
180 41 09 9 1 2 1 0 1 0 Col_AOP2
181 41 10 10 1 2 1 0 1 0 Col_AOP2
182 42 06 6 1 2 1 0 1 0 Col_AOP2
183 42 07 7 1 2 1 0 1 0 Col_AOP2
184 43 06 6 1 4 1 1 1 1 Poly
185 43 07 7 1 4 1 1 1 1 Poly
186 43 08 8 1 4 1 1 1 1 Poly
187 43 09 9 1 4 1 1 1 1 Poly
188 43 10 10 1 4 1 1 1 1 Poly
189 43 11 11 1 4 1 1 1 1 Poly
190 43 12 12 1 4 1 1 1 1 Poly
191 45 06 6 1 2 1 1 0 0 Col_gsm1
192 45 07 7 1 2 1 1 0 0 Col_gsm1
193 45 08 8 1 2 1 1 0 0 Col_gsm1
194 45 09 9 1 2 1 1 0 0 Col_gsm1
195 45 10 10 1 2 1 1 0 0 Col_gsm1
196 45 11 11 1 2 1 1 0 0 Col_gsm1
197 45 12 12 1 2 1 1 0 0 Col_gsm1
198 45 13 13 1 2 1 1 0 0 Col_gsm1
199 45 14 14 1 2 1 1 0 0 Col_gsm1
200 45 15 15 1 2 1 1 0 0 Col_gsm1
201 45 16 16 1 2 1 1 0 0 Col_gsm1
202 45 17 17 1 2 1 1 0 0 Col_gsm1
203 46 06 6 1 4 1 1 1 1 Poly
204 46 07 7 1 4 1 1 1 1 Poly
205 46 08 8 1 4 1 1 1 1 Poly
206 47 04 4 1 2 0 1 1 0 gsm1_AOP2
207 47 05 5 1 2 0 1 1 0 gsm1_AOP2
208 47 06 6 1 2 0 1 1 0 gsm1_AOP2
209 47 07 7 1 2 0 1 1 0 gsm1_AOP2
210 47 08 8 1 2 0 1 1 0 gsm1_AOP2
211 47 09 9 1 2 0 1 1 0 gsm1_AOP2
212 47 10 10 1 2 0 1 1 0 gsm1_AOP2
213 47 11 11 1 2 0 1 1 0 gsm1_AOP2
214 47 12 12 1 2 0 1 1 0 gsm1_AOP2
215 47 13 13 1 2 0 1 1 0 gsm1_AOP2
216 47 14 14 1 2 0 1 1 0 gsm1_AOP2
217 47 15 15 1 2 0 1 1 0 gsm1_AOP2
218 48 06 6 1 2 0 0 1 1 AOP2_AOP2.gsoh
219 48 07 7 1 2 0 0 1 1 AOP2_AOP2.gsoh
220 48 08 8 1 2 0 0 1 1 AOP2_AOP2.gsoh
221 48 09 9 1 2 0 0 1 1 AOP2_AOP2.gsoh
222 49 07 7 1 2 1 1 0 0 Col_gsm1
223 49 08 8 1 2 1 1 0 0 Col_gsm1
224 49 09 9 1 2 1 1 0 0 Col_gsm1
225 49 10 10 1 2 1 1 0 0 Col_gsm1
226 49 11 11 1 2 1 1 0 0 Col_gsm1
227 49 12 12 1 2 1 1 0 0 Col_gsm1
228 49 13 13 1 2 1 1 0 0 Col_gsm1
229 5 08 8 0 1 0 1 0 0 gsm1
230 5 09 9 0 1 0 1 0 0 gsm1
231 5 10 10 0 1 0 1 0 0 gsm1
232 5 11 11 0 1 0 1 0 0 gsm1
233 5 12 12 0 1 0 1 0 0 gsm1
234 5 13 13 0 1 0 1 0 0 gsm1
235 5 14 14 0 1 0 1 0 0 gsm1
236 5 15 15 0 1 0 1 0 0 gsm1
237 5 16 16 0 1 0 1 0 0 gsm1
238 50 06 6 1 2 1 0 1 0 Col_AOP2
239 50 07 7 1 2 1 0 1 0 Col_AOP2
240 50 08 8 1 2 1 0 1 0 Col_AOP2
241 50 09 9 1 2 1 0 1 0 Col_AOP2
242 50 10 10 1 2 1 0 1 0 Col_AOP2
243 50 11 11 1 2 1 0 1 0 Col_AOP2
244 50 12 12 1 2 1 0 1 0 Col_AOP2
245 50 13 13 1 2 1 0 1 0 Col_AOP2
246 50 14 14 1 2 1 0 1 0 Col_AOP2
247 50 15 15 1 2 1 0 1 0 Col_AOP2
248 50 16 16 1 2 1 0 1 0 Col_AOP2
249 50 17 17 1 2 1 0 1 0 Col_AOP2
250 51 05 5 1 1 0 1 0 0 gsm1
251 51 06 6 1 1 0 1 0 0 gsm1
252 51 07 7 1 1 0 1 0 0 gsm1
253 52 05 5 1 1 0 0 1 0 AOP2
254 52 06 6 1 1 0 0 1 0 AOP2
255 52 07 7 1 1 0 0 1 0 AOP2
256 52 08 8 1 1 0 0 1 0 AOP2
257 52 09 9 1 1 0 0 1 0 AOP2
258 52 10 10 1 1 0 0 1 0 AOP2
259 52 11 11 1 1 0 0 1 0 AOP2
260 53 08 8 1 4 1 1 1 1 Poly
261 53 09 9 1 4 1 1 1 1 Poly
262 53 10 10 1 4 1 1 1 1 Poly
263 53 11 11 1 4 1 1 1 1 Poly
264 53 12 12 1 4 1 1 1 1 Poly
265 53 13 13 1 4 1 1 1 1 Poly
266 53 14 14 1 4 1 1 1 1 Poly
267 53 15 15 1 4 1 1 1 1 Poly
268 53 16 16 1 4 1 1 1 1 Poly
269 53 17 17 1 4 1 1 1 1 Poly
270 54 04 4 1 1 0 0 0 1 AOP2.gsoh
271 54 05 5 1 1 0 0 0 1 AOP2.gsoh
272 54 06 6 1 1 0 0 0 1 AOP2.gsoh
273 54 07 7 1 1 0 0 0 1 AOP2.gsoh
274 54 08 8 1 1 0 0 0 1 AOP2.gsoh
275 54 09 9 1 1 0 0 0 1 AOP2.gsoh
276 54 10 10 1 1 0 0 0 1 AOP2.gsoh
277 54 11 11 1 1 0 0 0 1 AOP2.gsoh
278 54 12 12 1 1 0 0 0 1 AOP2.gsoh
279 54 13 13 1 1 0 0 0 1 AOP2.gsoh
280 54 14 14 1 1 0 0 0 1 AOP2.gsoh
281 54 15 15 1 1 0 0 0 1 AOP2.gsoh
282 55 07 7 1 2 1 0 0 1 Col_AOP2.gsoh
283 55 08 8 1 2 1 0 0 1 Col_AOP2.gsoh
284 56 06 6 1 1 0 0 0 1 AOP2.gsoh
285 56 07 7 1 1 0 0 0 1 AOP2.gsoh
286 57 06 6 1 2 0 0 1 1 AOP2_AOP2.gsoh
287 57 07 7 1 2 0 0 1 1 AOP2_AOP2.gsoh
288 58 05 5 1 2 1 0 0 1 Col_AOP2.gsoh
289 58 06 6 1 2 1 0 0 1 Col_AOP2.gsoh
290 58 07 7 1 2 1 0 0 1 Col_AOP2.gsoh
291 58 08 8 1 2 1 0 0 1 Col_AOP2.gsoh
292 58 09 9 1 2 1 0 0 1 Col_AOP2.gsoh
293 58 10 10 1 2 1 0 0 1 Col_AOP2.gsoh
294 58 11 11 1 2 1 0 0 1 Col_AOP2.gsoh
295 58 12 12 1 2 1 0 0 1 Col_AOP2.gsoh
296 58 13 13 1 2 1 0 0 1 Col_AOP2.gsoh
297 58 14 14 1 2 1 0 0 1 Col_AOP2.gsoh
298 58 15 15 1 2 1 0 0 1 Col_AOP2.gsoh
299 58 16 16 1 2 1 0 0 1 Col_AOP2.gsoh
300 58 17 17 1 2 1 0 0 1 Col_AOP2.gsoh
301 59 05 5 1 2 1 1 0 0 Col_gsm1
302 59 06 6 1 2 1 1 0 0 Col_gsm1
303 59 07 7 1 2 1 1 0 0 Col_gsm1
304 59 08 8 1 2 1 1 0 0 Col_gsm1
305 59 09 9 1 2 1 1 0 0 Col_gsm1
306 59 10 10 1 2 1 1 0 0 Col_gsm1
307 59 11 11 1 2 1 1 0 0 Col_gsm1
308 59 12 12 1 2 1 1 0 0 Col_gsm1
309 6 07 7 0 2 1 0 1 0 Col_AOP2
310 6 08 8 0 2 1 0 1 0 Col_AOP2
311 6 09 9 0 2 1 0 1 0 Col_AOP2
312 6 10 10 0 2 1 0 1 0 Col_AOP2
313 6 11 11 0 2 1 0 1 0 Col_AOP2
314 6 12 12 0 2 1 0 1 0 Col_AOP2
315 6 13 13 0 2 1 0 1 0 Col_AOP2
316 6 14 14 0 2 1 0 1 0 Col_AOP2
317 6 15 15 0 2 1 0 1 0 Col_AOP2
318 6 16 16 0 2 1 0 1 0 Col_AOP2
319 60 05 5 1 2 0 1 1 0 gsm1_AOP2
320 60 06 6 1 2 0 1 1 0 gsm1_AOP2
321 60 07 7 1 2 0 1 1 0 gsm1_AOP2
322 7 07 7 0 4 1 1 1 1 Poly
323 7 08 8 0 4 1 1 1 1 Poly
324 8 06 6 0 2 1 0 0 1 Col_AOP2.gsoh
325 8 07 7 0 2 1 0 0 1 Col_AOP2.gsoh
326 8 08 8 0 2 1 0 0 1 Col_AOP2.gsoh
327 9 07 7 0 2 1 1 0 0 Col_gsm1
328 9 08 8 0 2 1 1 0 0 Col_gsm1
329 9 09 9 0 2 1 1 0 0 Col_gsm1
330 9 10 10 0 2 1 1 0 0 Col_gsm1
331 9 11 11 0 2 1 1 0 0 Col_gsm1
332 9 12 12 0 2 1 1 0 0 Col_gsm1
333 9 13 13 0 2 1 1 0 0 Col_gsm1
334 9 14 14 0 2 1 1 0 0 Col_gsm1
335 9 15 15 0 2 1 1 0 0 Col_gsm1
LYER_Survival Mummy_Ptoids_Survival state week_since state_type
1 1 1 0-LYER-Ptoid 5 2
2 1 1 0-LYER-Ptoid 6 2
3 1 1 0-LYER-Ptoid 7 2
4 1 1 0-LYER-Ptoid 8 2
5 1 1 0-LYER-Ptoid 9 2
6 1 1 0-LYER-Ptoid 10 2
7 1 1 0-LYER-Ptoid 11 2
8 1 1 0-LYER-Ptoid 12 2
9 1 1 0-LYER-Ptoid 13 2
10 1 1 0-LYER-Ptoid 14 2
11 1 1 0-LYER-Ptoid 15 2
12 1 1 0-LYER-Ptoid 4 2
13 1 1 0-LYER-Ptoid 5 2
14 1 1 0-LYER-Ptoid 6 2
15 1 1 0-LYER-Ptoid 7 2
16 1 1 0-LYER-Ptoid 8 2
17 1 1 0-LYER-Ptoid 9 2
18 1 1 0-LYER-Ptoid 10 2
19 1 1 0-LYER-Ptoid 11 2
20 1 1 0-LYER-Ptoid 12 2
21 1 1 0-LYER-Ptoid 13 2
22 1 1 0-LYER-Ptoid 14 2
23 1 1 0-LYER-Ptoid 15 2
24 1 1 0-LYER-Ptoid 6 2
25 1 1 0-LYER-Ptoid 7 2
26 1 0 0-LYER-0 8 3
27 1 1 0-LYER-Ptoid 5 2
28 1 1 0-LYER-Ptoid 6 2
29 1 1 0-LYER-Ptoid 7 2
30 1 1 0-LYER-Ptoid 8 2
31 1 1 0-LYER-Ptoid 9 2
32 1 1 0-LYER-Ptoid 10 2
33 1 1 0-LYER-Ptoid 11 2
34 1 1 0-LYER-Ptoid 12 2
35 0 1 0-0-Ptoid 13 4
36 1 1 0-LYER-Ptoid 6 2
37 1 0 0-LYER-0 7 3
38 1 1 0-LYER-Ptoid 5 2
39 1 1 0-LYER-Ptoid 6 2
40 1 1 0-LYER-Ptoid 7 2
41 1 1 0-LYER-Ptoid 8 2
42 1 1 0-LYER-Ptoid 9 2
43 1 1 0-LYER-Ptoid 10 2
44 1 1 0-LYER-Ptoid 11 2
45 1 1 0-LYER-Ptoid 12 2
46 1 1 0-LYER-Ptoid 13 2
47 0 1 0-0-Ptoid 14 4
48 1 1 0-LYER-Ptoid 5 2
49 1 1 0-LYER-Ptoid 6 2
50 1 1 0-LYER-Ptoid 7 2
51 1 1 0-LYER-Ptoid 8 2
52 1 1 0-LYER-Ptoid 9 2
53 1 1 0-LYER-Ptoid 10 2
54 1 0 0-LYER-0 11 3
55 1 1 0-LYER-Ptoid 5 2
56 1 0 0-LYER-0 6 3
57 1 1 0-LYER-Ptoid 5 2
58 1 1 0-LYER-Ptoid 6 2
59 1 1 0-LYER-Ptoid 7 2
60 1 1 0-LYER-Ptoid 8 2
61 1 1 0-LYER-Ptoid 9 2
62 1 1 0-LYER-Ptoid 10 2
63 1 1 0-LYER-Ptoid 11 2
64 1 1 0-LYER-Ptoid 12 2
65 1 1 0-LYER-Ptoid 13 2
66 1 0 0-LYER-0 14 3
67 1 1 0-LYER-Ptoid 4 2
68 1 1 0-LYER-Ptoid 5 2
69 0 1 0-0-Ptoid 6 4
70 1 1 0-LYER-Ptoid 5 2
71 0 1 0-0-Ptoid 6 4
72 1 1 0-LYER-Ptoid 5 2
73 0 1 0-0-Ptoid 6 4
74 1 1 0-LYER-Ptoid 4 2
75 1 1 0-LYER-Ptoid 5 2
76 0 1 0-0-Ptoid 6 4
77 1 1 0-LYER-Ptoid 4 2
78 1 1 0-LYER-Ptoid 5 2
79 1 1 0-LYER-Ptoid 6 2
80 1 1 0-LYER-Ptoid 7 2
81 1 1 0-LYER-Ptoid 8 2
82 1 1 0-LYER-Ptoid 9 2
83 1 1 0-LYER-Ptoid 10 2
84 1 1 0-LYER-Ptoid 11 2
85 1 1 0-LYER-Ptoid 12 2
86 0 0 0-0-0 13 5
87 1 1 0-LYER-Ptoid 6 2
88 1 1 0-LYER-Ptoid 7 2
89 1 1 0-LYER-Ptoid 8 2
90 1 1 0-LYER-Ptoid 9 2
91 1 1 0-LYER-Ptoid 10 2
92 1 1 0-LYER-Ptoid 11 2
93 1 0 0-LYER-0 12 3
94 1 1 0-LYER-Ptoid 5 2
95 1 1 0-LYER-Ptoid 6 2
96 1 1 0-LYER-Ptoid 7 2
97 1 1 0-LYER-Ptoid 8 2
98 1 1 0-LYER-Ptoid 9 2
99 1 1 0-LYER-Ptoid 10 2
100 1 1 0-LYER-Ptoid 11 2
101 1 0 0-LYER-0 12 3
102 1 1 0-LYER-Ptoid 3 2
103 1 1 0-LYER-Ptoid 4 2
104 1 1 0-LYER-Ptoid 5 2
105 1 1 0-LYER-Ptoid 6 2
106 1 1 0-LYER-Ptoid 7 2
107 1 1 0-LYER-Ptoid 8 2
108 1 1 0-LYER-Ptoid 9 2
109 1 1 0-LYER-Ptoid 10 2
110 1 1 0-LYER-Ptoid 11 2
111 1 1 0-LYER-Ptoid 12 2
112 1 0 0-LYER-0 13 3
113 1 1 0-LYER-Ptoid 3 2
114 1 1 0-LYER-Ptoid 4 2
115 1 1 0-LYER-Ptoid 5 2
116 1 1 0-LYER-Ptoid 6 2
117 1 1 0-LYER-Ptoid 7 2
118 1 0 0-LYER-0 8 3
119 1 1 0-LYER-Ptoid 4 2
120 1 1 0-LYER-Ptoid 5 2
121 1 1 0-LYER-Ptoid 6 2
122 1 0 0-LYER-0 7 3
123 1 1 0-LYER-Ptoid 4 2
124 1 0 0-LYER-0 5 3
125 1 1 0-LYER-Ptoid 2 2
126 1 1 0-LYER-Ptoid 3 2
127 1 1 0-LYER-Ptoid 4 2
128 1 1 0-LYER-Ptoid 5 2
129 1 1 0-LYER-Ptoid 6 2
130 1 1 0-LYER-Ptoid 7 2
131 1 1 0-LYER-Ptoid 8 2
132 1 1 0-LYER-Ptoid 9 2
133 1 1 0-LYER-Ptoid 10 2
134 1 1 0-LYER-Ptoid 11 2
135 1 1 0-LYER-Ptoid 12 2
136 0 0 0-0-0 13 5
137 1 1 0-LYER-Ptoid 4 2
138 1 1 0-LYER-Ptoid 5 2
139 1 1 0-LYER-Ptoid 6 2
140 1 1 0-LYER-Ptoid 7 2
141 1 1 0-LYER-Ptoid 8 2
142 1 1 0-LYER-Ptoid 9 2
143 1 1 0-LYER-Ptoid 10 2
144 1 1 0-LYER-Ptoid 11 2
145 1 1 0-LYER-Ptoid 12 2
146 1 1 0-LYER-Ptoid 13 2
147 1 1 0-LYER-Ptoid 14 2
148 1 1 0-LYER-Ptoid 15 2
149 1 1 0-LYER-Ptoid 2 2
150 1 1 0-LYER-Ptoid 3 2
151 1 1 0-LYER-Ptoid 4 2
152 1 1 0-LYER-Ptoid 5 2
153 1 1 0-LYER-Ptoid 6 2
154 1 1 0-LYER-Ptoid 7 2
155 1 1 0-LYER-Ptoid 8 2
156 1 1 0-LYER-Ptoid 9 2
157 1 1 0-LYER-Ptoid 10 2
158 1 1 0-LYER-Ptoid 11 2
159 1 0 0-LYER-0 12 3
160 1 1 0-LYER-Ptoid 5 2
161 1 1 0-LYER-Ptoid 6 2
162 1 0 0-LYER-0 7 3
163 1 1 0-LYER-Ptoid 5 2
164 1 1 0-LYER-Ptoid 6 2
165 1 0 0-LYER-0 7 3
166 1 1 0-LYER-Ptoid 2 2
167 1 1 0-LYER-Ptoid 3 2
168 1 1 0-LYER-Ptoid 4 2
169 1 1 0-LYER-Ptoid 5 2
170 1 1 0-LYER-Ptoid 6 2
171 1 1 0-LYER-Ptoid 7 2
172 1 1 0-LYER-Ptoid 8 2
173 1 1 0-LYER-Ptoid 9 2
174 1 1 0-LYER-Ptoid 10 2
175 1 1 0-LYER-Ptoid 11 2
176 1 1 0-LYER-Ptoid 12 2
177 1 1 0-LYER-Ptoid 13 2
178 1 0 0-LYER-0 14 3
179 1 1 0-LYER-Ptoid 6 2
180 1 1 0-LYER-Ptoid 7 2
181 1 0 0-LYER-0 8 3
182 1 1 0-LYER-Ptoid 4 2
183 0 0 0-0-0 5 5
184 1 1 0-LYER-Ptoid 4 2
185 1 1 0-LYER-Ptoid 5 2
186 1 1 0-LYER-Ptoid 6 2
187 1 1 0-LYER-Ptoid 7 2
188 1 1 0-LYER-Ptoid 8 2
189 1 1 0-LYER-Ptoid 9 2
190 1 0 0-LYER-0 10 3
191 1 1 0-LYER-Ptoid 4 2
192 1 1 0-LYER-Ptoid 5 2
193 1 1 0-LYER-Ptoid 6 2
194 1 1 0-LYER-Ptoid 7 2
195 1 1 0-LYER-Ptoid 8 2
196 1 1 0-LYER-Ptoid 9 2
197 1 1 0-LYER-Ptoid 10 2
198 1 1 0-LYER-Ptoid 11 2
199 1 1 0-LYER-Ptoid 12 2
200 1 1 0-LYER-Ptoid 13 2
201 1 1 0-LYER-Ptoid 14 2
202 1 1 0-LYER-Ptoid 15 2
203 1 1 0-LYER-Ptoid 4 2
204 1 1 0-LYER-Ptoid 5 2
205 1 0 0-LYER-0 6 3
206 1 1 0-LYER-Ptoid 2 2
207 1 1 0-LYER-Ptoid 3 2
208 1 1 0-LYER-Ptoid 4 2
209 1 1 0-LYER-Ptoid 5 2
210 1 1 0-LYER-Ptoid 6 2
211 1 1 0-LYER-Ptoid 7 2
212 1 1 0-LYER-Ptoid 8 2
213 1 1 0-LYER-Ptoid 9 2
214 1 1 0-LYER-Ptoid 10 2
215 1 1 0-LYER-Ptoid 11 2
216 1 1 0-LYER-Ptoid 12 2
217 1 0 0-LYER-0 13 3
218 1 1 0-LYER-Ptoid 4 2
219 1 1 0-LYER-Ptoid 5 2
220 1 1 0-LYER-Ptoid 6 2
221 1 0 0-LYER-0 7 3
222 1 1 0-LYER-Ptoid 5 2
223 1 1 0-LYER-Ptoid 6 2
224 1 1 0-LYER-Ptoid 7 2
225 1 1 0-LYER-Ptoid 8 2
226 1 1 0-LYER-Ptoid 9 2
227 1 1 0-LYER-Ptoid 10 2
228 1 0 0-LYER-0 11 3
229 1 1 0-LYER-Ptoid 6 2
230 1 1 0-LYER-Ptoid 7 2
231 1 1 0-LYER-Ptoid 8 2
232 1 1 0-LYER-Ptoid 9 2
233 1 1 0-LYER-Ptoid 10 2
234 1 1 0-LYER-Ptoid 11 2
235 1 1 0-LYER-Ptoid 12 2
236 1 1 0-LYER-Ptoid 13 2
237 1 0 0-LYER-0 14 3
238 1 1 0-LYER-Ptoid 4 2
239 1 1 0-LYER-Ptoid 5 2
240 1 1 0-LYER-Ptoid 6 2
241 1 1 0-LYER-Ptoid 7 2
242 1 1 0-LYER-Ptoid 8 2
243 1 1 0-LYER-Ptoid 9 2
244 1 1 0-LYER-Ptoid 10 2
245 1 1 0-LYER-Ptoid 11 2
246 1 1 0-LYER-Ptoid 12 2
247 1 1 0-LYER-Ptoid 13 2
248 1 1 0-LYER-Ptoid 14 2
249 1 1 0-LYER-Ptoid 15 2
250 1 1 0-LYER-Ptoid 3 2
251 1 1 0-LYER-Ptoid 4 2
252 0 1 0-0-Ptoid 5 4
253 1 1 0-LYER-Ptoid 3 2
254 1 1 0-LYER-Ptoid 4 2
255 1 1 0-LYER-Ptoid 5 2
256 1 1 0-LYER-Ptoid 6 2
257 1 1 0-LYER-Ptoid 7 2
258 1 1 0-LYER-Ptoid 8 2
259 1 0 0-LYER-0 9 3
260 1 1 0-LYER-Ptoid 6 2
261 1 1 0-LYER-Ptoid 7 2
262 1 1 0-LYER-Ptoid 8 2
263 1 1 0-LYER-Ptoid 9 2
264 1 1 0-LYER-Ptoid 10 2
265 1 1 0-LYER-Ptoid 11 2
266 1 1 0-LYER-Ptoid 12 2
267 1 1 0-LYER-Ptoid 13 2
268 1 1 0-LYER-Ptoid 14 2
269 1 1 0-LYER-Ptoid 15 2
270 1 1 0-LYER-Ptoid 2 2
271 1 1 0-LYER-Ptoid 3 2
272 1 1 0-LYER-Ptoid 4 2
273 1 1 0-LYER-Ptoid 5 2
274 1 1 0-LYER-Ptoid 6 2
275 1 1 0-LYER-Ptoid 7 2
276 1 1 0-LYER-Ptoid 8 2
277 1 1 0-LYER-Ptoid 9 2
278 1 1 0-LYER-Ptoid 10 2
279 1 1 0-LYER-Ptoid 11 2
280 1 1 0-LYER-Ptoid 12 2
281 0 1 0-0-Ptoid 13 4
282 1 1 0-LYER-Ptoid 5 2
283 0 1 0-0-Ptoid 6 4
284 1 1 0-LYER-Ptoid 4 2
285 0 1 0-0-Ptoid 5 4
286 1 1 0-LYER-Ptoid 4 2
287 0 1 0-0-Ptoid 5 4
288 1 1 0-LYER-Ptoid 3 2
289 1 1 0-LYER-Ptoid 4 2
290 1 1 0-LYER-Ptoid 5 2
291 1 1 0-LYER-Ptoid 6 2
292 1 1 0-LYER-Ptoid 7 2
293 1 1 0-LYER-Ptoid 8 2
294 1 1 0-LYER-Ptoid 9 2
295 1 1 0-LYER-Ptoid 10 2
296 1 1 0-LYER-Ptoid 11 2
297 1 1 0-LYER-Ptoid 12 2
298 1 1 0-LYER-Ptoid 13 2
299 1 1 0-LYER-Ptoid 14 2
300 1 1 0-LYER-Ptoid 15 2
301 1 1 0-LYER-Ptoid 3 2
302 1 1 0-LYER-Ptoid 4 2
303 1 1 0-LYER-Ptoid 5 2
304 1 1 0-LYER-Ptoid 6 2
305 1 1 0-LYER-Ptoid 7 2
306 1 1 0-LYER-Ptoid 8 2
307 1 1 0-LYER-Ptoid 9 2
308 1 0 0-LYER-0 10 3
309 1 1 0-LYER-Ptoid 5 2
310 1 1 0-LYER-Ptoid 6 2
311 1 1 0-LYER-Ptoid 7 2
312 1 1 0-LYER-Ptoid 8 2
313 1 1 0-LYER-Ptoid 9 2
314 1 1 0-LYER-Ptoid 10 2
315 1 1 0-LYER-Ptoid 11 2
316 1 1 0-LYER-Ptoid 12 2
317 1 1 0-LYER-Ptoid 13 2
318 0 0 0-0-0 14 5
319 1 1 0-LYER-Ptoid 3 2
320 1 1 0-LYER-Ptoid 4 2
321 0 1 0-0-Ptoid 5 4
322 1 1 0-LYER-Ptoid 5 2
323 1 0 0-LYER-0 6 3
324 1 1 0-LYER-Ptoid 4 2
325 1 1 0-LYER-Ptoid 5 2
326 0 0 0-0-0 6 5
327 1 1 0-LYER-Ptoid 5 2
328 1 1 0-LYER-Ptoid 6 2
329 1 1 0-LYER-Ptoid 7 2
330 1 1 0-LYER-Ptoid 8 2
331 1 1 0-LYER-Ptoid 9 2
332 1 1 0-LYER-Ptoid 10 2
333 1 1 0-LYER-Ptoid 11 2
334 1 1 0-LYER-Ptoid 12 2
335 1 0 0-LYER-0 13 3
state_adj start
1 0-LYER-Ptoid 5
2 0-LYER-Ptoid 5
3 0-LYER-Ptoid 5
4 0-LYER-Ptoid 5
5 0-LYER-Ptoid 5
6 0-LYER-Ptoid 5
7 0-LYER-Ptoid 5
8 0-LYER-Ptoid 5
9 0-LYER-Ptoid 5
10 0-LYER-Ptoid 5
11 0-LYER-Ptoid 5
12 0-LYER-Ptoid 4
13 0-LYER-Ptoid 4
14 0-LYER-Ptoid 4
15 0-LYER-Ptoid 4
16 0-LYER-Ptoid 4
17 0-LYER-Ptoid 4
18 0-LYER-Ptoid 4
19 0-LYER-Ptoid 4
20 0-LYER-Ptoid 4
21 0-LYER-Ptoid 4
22 0-LYER-Ptoid 4
23 0-LYER-Ptoid 4
24 0-LYER-Ptoid 6
25 0-LYER-Ptoid 6
26 0-LYER-0 6
27 0-LYER-Ptoid 5
28 0-LYER-Ptoid 5
29 0-LYER-Ptoid 5
30 0-LYER-Ptoid 5
31 0-LYER-Ptoid 5
32 0-LYER-Ptoid 5
33 0-LYER-Ptoid 5
34 0-LYER-Ptoid 5
35 0-0-Ptoid 5
36 0-LYER-Ptoid 6
37 0-LYER-0 6
38 0-LYER-Ptoid 5
39 0-LYER-Ptoid 5
40 0-LYER-Ptoid 5
41 0-LYER-Ptoid 5
42 0-LYER-Ptoid 5
43 0-LYER-Ptoid 5
44 0-LYER-Ptoid 5
45 0-LYER-Ptoid 5
46 0-LYER-Ptoid 5
47 0-0-Ptoid 5
48 0-LYER-Ptoid 5
49 0-LYER-Ptoid 5
50 0-LYER-Ptoid 5
51 0-LYER-Ptoid 5
52 0-LYER-Ptoid 5
53 0-LYER-Ptoid 5
54 0-LYER-0 5
55 0-LYER-Ptoid 5
56 0-LYER-0 5
57 0-LYER-Ptoid 5
58 0-LYER-Ptoid 5
59 0-LYER-Ptoid 5
60 0-LYER-Ptoid 5
61 0-LYER-Ptoid 5
62 0-LYER-Ptoid 5
63 0-LYER-Ptoid 5
64 0-LYER-Ptoid 5
65 0-LYER-Ptoid 5
66 0-LYER-0 5
67 0-LYER-Ptoid 4
68 0-LYER-Ptoid 4
69 0-0-Ptoid 4
70 0-LYER-Ptoid 5
71 0-0-Ptoid 5
72 0-LYER-Ptoid 5
73 0-0-Ptoid 5
74 0-LYER-Ptoid 4
75 0-LYER-Ptoid 4
76 0-0-Ptoid 4
77 0-LYER-Ptoid 4
78 0-LYER-Ptoid 4
79 0-LYER-Ptoid 4
80 0-LYER-Ptoid 4
81 0-LYER-Ptoid 4
82 0-LYER-Ptoid 4
83 0-LYER-Ptoid 4
84 0-LYER-Ptoid 4
85 0-LYER-Ptoid 4
86 0-0-Ptoid 4
87 0-LYER-Ptoid 6
88 0-LYER-Ptoid 6
89 0-LYER-Ptoid 6
90 0-LYER-Ptoid 6
91 0-LYER-Ptoid 6
92 0-LYER-Ptoid 6
93 0-LYER-0 6
94 0-LYER-Ptoid 5
95 0-LYER-Ptoid 5
96 0-LYER-Ptoid 5
97 0-LYER-Ptoid 5
98 0-LYER-Ptoid 5
99 0-LYER-Ptoid 5
100 0-LYER-Ptoid 5
101 0-LYER-0 5
102 0-LYER-Ptoid 3
103 0-LYER-Ptoid 3
104 0-LYER-Ptoid 3
105 0-LYER-Ptoid 3
106 0-LYER-Ptoid 3
107 0-LYER-Ptoid 3
108 0-LYER-Ptoid 3
109 0-LYER-Ptoid 3
110 0-LYER-Ptoid 3
111 0-LYER-Ptoid 3
112 0-LYER-0 3
113 0-LYER-Ptoid 3
114 0-LYER-Ptoid 3
115 0-LYER-Ptoid 3
116 0-LYER-Ptoid 3
117 0-LYER-Ptoid 3
118 0-LYER-0 3
119 0-LYER-Ptoid 4
120 0-LYER-Ptoid 4
121 0-LYER-Ptoid 4
122 0-LYER-0 4
123 0-LYER-Ptoid 4
124 0-LYER-0 4
125 0-LYER-Ptoid 2
126 0-LYER-Ptoid 2
127 0-LYER-Ptoid 2
128 0-LYER-Ptoid 2
129 0-LYER-Ptoid 2
130 0-LYER-Ptoid 2
131 0-LYER-Ptoid 2
132 0-LYER-Ptoid 2
133 0-LYER-Ptoid 2
134 0-LYER-Ptoid 2
135 0-LYER-Ptoid 2
136 0-0-Ptoid 2
137 0-LYER-Ptoid 4
138 0-LYER-Ptoid 4
139 0-LYER-Ptoid 4
140 0-LYER-Ptoid 4
141 0-LYER-Ptoid 4
142 0-LYER-Ptoid 4
143 0-LYER-Ptoid 4
144 0-LYER-Ptoid 4
145 0-LYER-Ptoid 4
146 0-LYER-Ptoid 4
147 0-LYER-Ptoid 4
148 0-LYER-Ptoid 4
149 0-LYER-Ptoid 2
150 0-LYER-Ptoid 2
151 0-LYER-Ptoid 2
152 0-LYER-Ptoid 2
153 0-LYER-Ptoid 2
154 0-LYER-Ptoid 2
155 0-LYER-Ptoid 2
156 0-LYER-Ptoid 2
157 0-LYER-Ptoid 2
158 0-LYER-Ptoid 2
159 0-LYER-0 2
160 0-LYER-Ptoid 5
161 0-LYER-Ptoid 5
162 0-LYER-0 5
163 0-LYER-Ptoid 5
164 0-LYER-Ptoid 5
165 0-LYER-0 5
166 0-LYER-Ptoid 2
167 0-LYER-Ptoid 2
168 0-LYER-Ptoid 2
169 0-LYER-Ptoid 2
170 0-LYER-Ptoid 2
171 0-LYER-Ptoid 2
172 0-LYER-Ptoid 2
173 0-LYER-Ptoid 2
174 0-LYER-Ptoid 2
175 0-LYER-Ptoid 2
176 0-LYER-Ptoid 2
177 0-LYER-Ptoid 2
178 0-LYER-0 2
179 0-LYER-Ptoid 6
180 0-LYER-Ptoid 6
181 0-LYER-0 6
182 0-LYER-Ptoid 4
183 0-0-Ptoid 4
184 0-LYER-Ptoid 4
185 0-LYER-Ptoid 4
186 0-LYER-Ptoid 4
187 0-LYER-Ptoid 4
188 0-LYER-Ptoid 4
189 0-LYER-Ptoid 4
190 0-LYER-0 4
191 0-LYER-Ptoid 4
192 0-LYER-Ptoid 4
193 0-LYER-Ptoid 4
194 0-LYER-Ptoid 4
195 0-LYER-Ptoid 4
196 0-LYER-Ptoid 4
197 0-LYER-Ptoid 4
198 0-LYER-Ptoid 4
199 0-LYER-Ptoid 4
200 0-LYER-Ptoid 4
201 0-LYER-Ptoid 4
202 0-LYER-Ptoid 4
203 0-LYER-Ptoid 4
204 0-LYER-Ptoid 4
205 0-LYER-0 4
206 0-LYER-Ptoid 2
207 0-LYER-Ptoid 2
208 0-LYER-Ptoid 2
209 0-LYER-Ptoid 2
210 0-LYER-Ptoid 2
211 0-LYER-Ptoid 2
212 0-LYER-Ptoid 2
213 0-LYER-Ptoid 2
214 0-LYER-Ptoid 2
215 0-LYER-Ptoid 2
216 0-LYER-Ptoid 2
217 0-LYER-0 2
218 0-LYER-Ptoid 4
219 0-LYER-Ptoid 4
220 0-LYER-Ptoid 4
221 0-LYER-0 4
222 0-LYER-Ptoid 5
223 0-LYER-Ptoid 5
224 0-LYER-Ptoid 5
225 0-LYER-Ptoid 5
226 0-LYER-Ptoid 5
227 0-LYER-Ptoid 5
228 0-LYER-0 5
229 0-LYER-Ptoid 6
230 0-LYER-Ptoid 6
231 0-LYER-Ptoid 6
232 0-LYER-Ptoid 6
233 0-LYER-Ptoid 6
234 0-LYER-Ptoid 6
235 0-LYER-Ptoid 6
236 0-LYER-Ptoid 6
237 0-LYER-0 6
238 0-LYER-Ptoid 4
239 0-LYER-Ptoid 4
240 0-LYER-Ptoid 4
241 0-LYER-Ptoid 4
242 0-LYER-Ptoid 4
243 0-LYER-Ptoid 4
244 0-LYER-Ptoid 4
245 0-LYER-Ptoid 4
246 0-LYER-Ptoid 4
247 0-LYER-Ptoid 4
248 0-LYER-Ptoid 4
249 0-LYER-Ptoid 4
250 0-LYER-Ptoid 3
251 0-LYER-Ptoid 3
252 0-0-Ptoid 3
253 0-LYER-Ptoid 3
254 0-LYER-Ptoid 3
255 0-LYER-Ptoid 3
256 0-LYER-Ptoid 3
257 0-LYER-Ptoid 3
258 0-LYER-Ptoid 3
259 0-LYER-0 3
260 0-LYER-Ptoid 6
261 0-LYER-Ptoid 6
262 0-LYER-Ptoid 6
263 0-LYER-Ptoid 6
264 0-LYER-Ptoid 6
265 0-LYER-Ptoid 6
266 0-LYER-Ptoid 6
267 0-LYER-Ptoid 6
268 0-LYER-Ptoid 6
269 0-LYER-Ptoid 6
270 0-LYER-Ptoid 2
271 0-LYER-Ptoid 2
272 0-LYER-Ptoid 2
273 0-LYER-Ptoid 2
274 0-LYER-Ptoid 2
275 0-LYER-Ptoid 2
276 0-LYER-Ptoid 2
277 0-LYER-Ptoid 2
278 0-LYER-Ptoid 2
279 0-LYER-Ptoid 2
280 0-LYER-Ptoid 2
281 0-0-Ptoid 2
282 0-LYER-Ptoid 5
283 0-0-Ptoid 5
284 0-LYER-Ptoid 4
285 0-0-Ptoid 4
286 0-LYER-Ptoid 4
287 0-0-Ptoid 4
288 0-LYER-Ptoid 3
289 0-LYER-Ptoid 3
290 0-LYER-Ptoid 3
291 0-LYER-Ptoid 3
292 0-LYER-Ptoid 3
293 0-LYER-Ptoid 3
294 0-LYER-Ptoid 3
295 0-LYER-Ptoid 3
296 0-LYER-Ptoid 3
297 0-LYER-Ptoid 3
298 0-LYER-Ptoid 3
299 0-LYER-Ptoid 3
300 0-LYER-Ptoid 3
301 0-LYER-Ptoid 3
302 0-LYER-Ptoid 3
303 0-LYER-Ptoid 3
304 0-LYER-Ptoid 3
305 0-LYER-Ptoid 3
306 0-LYER-Ptoid 3
307 0-LYER-Ptoid 3
308 0-LYER-0 3
309 0-LYER-Ptoid 5
310 0-LYER-Ptoid 5
311 0-LYER-Ptoid 5
312 0-LYER-Ptoid 5
313 0-LYER-Ptoid 5
314 0-LYER-Ptoid 5
315 0-LYER-Ptoid 5
316 0-LYER-Ptoid 5
317 0-LYER-Ptoid 5
318 0-0-Ptoid 5
319 0-LYER-Ptoid 3
320 0-LYER-Ptoid 3
321 0-0-Ptoid 3
322 0-LYER-Ptoid 5
323 0-LYER-0 5
324 0-LYER-Ptoid 4
325 0-LYER-Ptoid 4
326 0-0-Ptoid 4
327 0-LYER-Ptoid 5
328 0-LYER-Ptoid 5
329 0-LYER-Ptoid 5
330 0-LYER-Ptoid 5
331 0-LYER-Ptoid 5
332 0-LYER-Ptoid 5
333 0-LYER-Ptoid 5
334 0-LYER-Ptoid 5
335 0-LYER-0 5# convert to Cox data frame for analysis
LP_transit_cox_df <- get_LP_transit_start %>%
arrange(cage, week_since, state_adj) %>%
select(cage, start, week_since, temp:com, state_adj) %>%
group_by(cage) %>%
summarise(across(everything(), last)) %>%
mutate(#any_event = ifelse(state_adj == "0-LYER-Ptoid", 0, 1),
fstate = factor(state_adj, levels = c("0-LYER-Ptoid","0-LYER-0","0-0-Ptoid")))
# all looks good, 50 data points
LP_transit_cox_df %>% data.frame() cage start week_since temp rich Col gsm1 AOP2 AOP2.gsoh com
1 12 5 15 0 4 1 1 1 1 Poly
2 13 4 15 0 4 1 1 1 1 Poly
3 14 6 8 0 1 1 0 0 0 Col
4 15 5 13 0 1 0 0 0 1 AOP2.gsoh
5 17 6 7 0 2 0 1 1 0 gsm1_AOP2
6 18 5 14 0 2 1 0 0 1 Col_AOP2.gsoh
7 20 5 11 0 2 0 1 1 0 gsm1_AOP2
8 22 5 6 0 1 0 0 0 1 AOP2.gsoh
9 23 5 14 0 2 0 0 1 1 AOP2_AOP2.gsoh
10 25 4 6 0 1 0 0 1 0 AOP2
11 26 5 6 0 1 1 0 0 0 Col
12 27 5 6 0 2 1 0 1 0 Col_AOP2
13 28 4 6 0 2 1 0 0 1 Col_AOP2.gsoh
14 29 4 13 0 2 0 1 0 1 gsm1_AOP2.gsoh
15 30 6 12 0 2 1 1 0 0 Col_gsm1
16 31 5 12 1 2 0 1 1 0 gsm1_AOP2
17 32 3 13 1 1 1 0 0 0 Col
18 33 3 8 1 1 1 0 0 0 Col
19 34 4 7 1 2 1 0 0 1 Col_AOP2.gsoh
20 35 4 5 1 2 0 0 1 1 AOP2_AOP2.gsoh
21 36 2 13 1 2 0 1 0 1 gsm1_AOP2.gsoh
22 37 4 15 1 2 0 1 0 1 gsm1_AOP2.gsoh
23 38 2 12 1 4 1 1 1 1 Poly
24 39 5 7 1 1 0 1 0 0 gsm1
25 4 5 7 0 1 0 0 1 0 AOP2
26 40 2 14 1 2 0 1 0 1 gsm1_AOP2.gsoh
27 41 6 8 1 2 1 0 1 0 Col_AOP2
28 42 4 5 1 2 1 0 1 0 Col_AOP2
29 43 4 10 1 4 1 1 1 1 Poly
30 45 4 15 1 2 1 1 0 0 Col_gsm1
31 46 4 6 1 4 1 1 1 1 Poly
32 47 2 13 1 2 0 1 1 0 gsm1_AOP2
33 48 4 7 1 2 0 0 1 1 AOP2_AOP2.gsoh
34 49 5 11 1 2 1 1 0 0 Col_gsm1
35 5 6 14 0 1 0 1 0 0 gsm1
36 50 4 15 1 2 1 0 1 0 Col_AOP2
37 51 3 5 1 1 0 1 0 0 gsm1
38 52 3 9 1 1 0 0 1 0 AOP2
39 53 6 15 1 4 1 1 1 1 Poly
40 54 2 13 1 1 0 0 0 1 AOP2.gsoh
41 55 5 6 1 2 1 0 0 1 Col_AOP2.gsoh
42 56 4 5 1 1 0 0 0 1 AOP2.gsoh
43 57 4 5 1 2 0 0 1 1 AOP2_AOP2.gsoh
44 58 3 15 1 2 1 0 0 1 Col_AOP2.gsoh
45 59 3 10 1 2 1 1 0 0 Col_gsm1
46 6 5 14 0 2 1 0 1 0 Col_AOP2
47 60 3 5 1 2 0 1 1 0 gsm1_AOP2
48 7 5 6 0 4 1 1 1 1 Poly
49 8 4 6 0 2 1 0 0 1 Col_AOP2.gsoh
50 9 5 13 0 2 1 1 0 0 Col_gsm1
state_adj fstate
1 0-LYER-Ptoid 0-LYER-Ptoid
2 0-LYER-Ptoid 0-LYER-Ptoid
3 0-LYER-0 0-LYER-0
4 0-0-Ptoid 0-0-Ptoid
5 0-LYER-0 0-LYER-0
6 0-0-Ptoid 0-0-Ptoid
7 0-LYER-0 0-LYER-0
8 0-LYER-0 0-LYER-0
9 0-LYER-0 0-LYER-0
10 0-0-Ptoid 0-0-Ptoid
11 0-0-Ptoid 0-0-Ptoid
12 0-0-Ptoid 0-0-Ptoid
13 0-0-Ptoid 0-0-Ptoid
14 0-0-Ptoid 0-0-Ptoid
15 0-LYER-0 0-LYER-0
16 0-LYER-0 0-LYER-0
17 0-LYER-0 0-LYER-0
18 0-LYER-0 0-LYER-0
19 0-LYER-0 0-LYER-0
20 0-LYER-0 0-LYER-0
21 0-0-Ptoid 0-0-Ptoid
22 0-LYER-Ptoid 0-LYER-Ptoid
23 0-LYER-0 0-LYER-0
24 0-LYER-0 0-LYER-0
25 0-LYER-0 0-LYER-0
26 0-LYER-0 0-LYER-0
27 0-LYER-0 0-LYER-0
28 0-0-Ptoid 0-0-Ptoid
29 0-LYER-0 0-LYER-0
30 0-LYER-Ptoid 0-LYER-Ptoid
31 0-LYER-0 0-LYER-0
32 0-LYER-0 0-LYER-0
33 0-LYER-0 0-LYER-0
34 0-LYER-0 0-LYER-0
35 0-LYER-0 0-LYER-0
36 0-LYER-Ptoid 0-LYER-Ptoid
37 0-0-Ptoid 0-0-Ptoid
38 0-LYER-0 0-LYER-0
39 0-LYER-Ptoid 0-LYER-Ptoid
40 0-0-Ptoid 0-0-Ptoid
41 0-0-Ptoid 0-0-Ptoid
42 0-0-Ptoid 0-0-Ptoid
43 0-0-Ptoid 0-0-Ptoid
44 0-LYER-Ptoid 0-LYER-Ptoid
45 0-LYER-0 0-LYER-0
46 0-0-Ptoid 0-0-Ptoid
47 0-0-Ptoid 0-0-Ptoid
48 0-LYER-0 0-LYER-0
49 0-0-Ptoid 0-0-Ptoid
50 0-LYER-0 0-LYER-0# multi-state model
LP_multi_coxph <- coxph(Surv(start, week_since, fstate) ~ I(Col+gsm1) + I(AOP2+AOP2.gsoh), LP_transit_cox_df, id = cage) # clear effect of AOP2-
LP_multi_cox.zph <- cox.zph(LP_multi_coxph)
LP_multi_cox.zph # AOP2+ appears to violate cox assumption for food-chain to aphid transition chisq df p
I(Col + gsm1)_1:2 0.1859 1 0.666
I(AOP2 + AOP2.gsoh)_1:2 6.0580 1 0.014
I(Col + gsm1)_1:3 0.5699 1 0.450
I(AOP2 + AOP2.gsoh)_1:3 0.0761 1 0.783
GLOBAL 6.6677 4 0.155plot(LP_multi_cox.zph[2]) # if anything, it appears we are underestimating the destabilizing effect of AOP2+, as it appears to initially increase the likelihood of a transition to the aphid only food web.
coxph(list(Surv(start, week_since, fstate) ~ 1,
1:2 ~ I(Col+gsm1),
1:3 ~ I(Col+gsm1) + I(AOP2+AOP2.gsoh)), LP_transit_cox_df, id = cage)Call:
coxph(formula = list(Surv(start, week_since, fstate) ~ 1, 1:2 ~
I(Col + gsm1), 1:3 ~ I(Col + gsm1) + I(AOP2 + AOP2.gsoh)),
data = LP_transit_cox_df, id = cage)
1:2 coef exp(coef) se(coef) robust se z p
I(Col + gsm1) -0.2036 0.8158 0.2993 0.3115 -0.653 0.513
1:3 coef exp(coef) se(coef) robust se z p
I(Col + gsm1) -1.0565 0.3477 0.4442 0.2881 -3.667 0.000246
I(AOP2 + AOP2.gsoh) -0.5170 0.5963 0.4577 0.4004 -1.291 0.196658
States: 1= (s0), 2= 0-LYER-0, 3= 0-0-Ptoid
Likelihood ratio test=7.5 on 3 df, p=0.05758
n= 50, number of events= 43 # even after dropping AOP2+ effect on 1:2 transition, doesn't affect previously identified effect on food-chain to collapse.
coxph(Surv(start, week_since, fstate) ~ strata(temp) + I(Col+gsm1) + I(AOP2+AOP2.gsoh), LP_transit_cox_df, id = cage) # still a clear effect of AOP2- after stratifying by temperatureCall:
coxph(formula = Surv(start, week_since, fstate) ~ strata(temp) +
I(Col + gsm1) + I(AOP2 + AOP2.gsoh), data = LP_transit_cox_df,
id = cage)
1:2 coef exp(coef) se(coef) robust se z p
I(Col + gsm1) -0.2150 0.8066 0.3102 0.3245 -0.662 0.508
I(AOP2 + AOP2.gsoh) -0.1750 0.8395 0.3112 0.3023 -0.579 0.563
1:3 coef exp(coef) se(coef) robust se z p
I(Col + gsm1) -0.8798 0.4149 0.4245 0.2805 -3.136 0.00171
I(AOP2 + AOP2.gsoh) -0.5574 0.5727 0.4290 0.3847 -1.449 0.14742
States: 1= (s0), 2= 0-LYER-0, 3= 0-0-Ptoid
Likelihood ratio test=6.68 on 4 df, p=0.154
n= 50, number of events= 43 # note we can reproduce the multi-state model by focusing piecewise on this hazard rate
coxph(Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~ strata(temp) + I(Col+gsm1) + I(AOP2+AOP2.gsoh), LP_transit_cox_df) # id = cage no longer needed, including it gives the same results.Call:
coxph(formula = Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~
strata(temp) + I(Col + gsm1) + I(AOP2 + AOP2.gsoh), data = LP_transit_cox_df)
coef exp(coef) se(coef) z p
I(Col + gsm1) -0.8798 0.4149 0.4245 -2.072 0.0382
I(AOP2 + AOP2.gsoh) -0.5574 0.5727 0.4290 -1.299 0.1939
Likelihood ratio test=5.91 on 2 df, p=0.05202
n= 50, number of events= 17 # this is good because then we can see what happens if we account for other sources of non-independence
coxph(Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~ strata(temp) + I(Col+gsm1), LP_transit_cox_df) # effect persists when we have a more favorable event-to-variable ratio, although the coefficient has a slightly different meaning alone, so we retain both in the model.Call:
coxph(formula = Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~
strata(temp) + I(Col + gsm1), data = LP_transit_cox_df)
coef exp(coef) se(coef) z p
I(Col + gsm1) -0.7242 0.4847 0.3663 -1.977 0.048
Likelihood ratio test=4.15 on 1 df, p=0.0416
n= 50, number of events= 17 coxph(Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~ strata(temp) + I(Col+gsm1) + I(AOP2+AOP2.gsoh) + cluster(com), LP_transit_cox_df) # as before, we observe potentially anti-conservative results when clustering at com level.Call:
coxph(formula = Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~
strata(temp) + I(Col + gsm1) + I(AOP2 + AOP2.gsoh), data = LP_transit_cox_df,
cluster = com)
coef exp(coef) se(coef) robust se z p
I(Col + gsm1) -0.8798 0.4149 0.4245 0.3372 -2.609 0.00907
I(AOP2 + AOP2.gsoh) -0.5574 0.5727 0.4290 0.2783 -2.003 0.04522
Likelihood ratio test=5.91 on 2 df, p=0.05202
n= 50, number of events= 17 # results are robust to mixed-effect models
coxme(Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~ strata(temp) + I(Col+gsm1) + I(AOP2+AOP2.gsoh) + (1|com), LP_transit_cox_df)Cox mixed-effects model fit by maximum likelihood
Data: LP_transit_cox_df
events, n = 17, 50
Iterations= 2 14
NULL Integrated Fitted
Log-likelihood -43.95128 -40.99597 -40.99107
Chisq df p AIC BIC
Integrated loglik 5.91 3 0.116040 -0.09 -2.59
Penalized loglik 5.92 2 0.052038 1.91 0.24
Model: Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~ strata(temp) + I(Col + gsm1) + I(AOP2 + AOP2.gsoh) + (1 | com)
Fixed coefficients
coef exp(coef) se(coef) z p
I(Col + gsm1) -0.8798872 0.4148297 0.4246916 -2.07 0.038
I(AOP2 + AOP2.gsoh) -0.5573989 0.5726967 0.4292309 -1.30 0.190
Random effects
Group Variable Std Dev Variance
com Intercept 0.0199914171 0.0003996568coxme(Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~ strata(temp) + I(Col+gsm1) + I(AOP2+AOP2.gsoh) + (1|com/temp), LP_transit_cox_df)Cox mixed-effects model fit by maximum likelihood
Data: LP_transit_cox_df
events, n = 17, 50
Iterations= 2 14
NULL Integrated Fitted
Log-likelihood -43.95128 -40.99625 -40.98585
Chisq df p AIC BIC
Integrated loglik 5.91 4.00 0.205970 -2.09 -5.42
Penalized loglik 5.93 2.01 0.052023 1.91 0.24
Model: Surv(start, week_since, fstate %in% c("0-0-Ptoid")) ~ strata(temp) + I(Col + gsm1) + I(AOP2 + AOP2.gsoh) + (1 | com/temp)
Fixed coefficients
coef exp(coef) se(coef) z p
I(Col + gsm1) -0.8799935 0.4147856 0.4247821 -2.07 0.038
I(AOP2 + AOP2.gsoh) -0.5574958 0.5726412 0.4293484 -1.30 0.190
Random effects
Group Variable Std Dev Variance
com/temp (Intercept) 0.0199972339 0.0003998894
com (Intercept) 0.0199914116 0.0003996565
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.7 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] coxme_2.2-16 bdsmatrix_1.3-4 broom_0.7.6 survival_3.2-11
[5] msm_1.6.8 cowplot_1.1.1 forcats_0.5.1 stringr_1.4.0
[9] dplyr_1.0.6 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3
[13] tibble_3.1.2 ggplot2_3.3.3 tidyverse_1.3.1 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] httr_1.4.2 sass_0.4.0 jsonlite_1.7.2 viridisLite_0.4.0
[5] splines_4.1.0 modelr_0.1.8 bslib_0.2.5.1 assertthat_0.2.1
[9] expm_0.999-6 highr_0.9 cellranger_1.1.0 yaml_2.2.1
[13] pillar_1.6.1 backports_1.2.1 lattice_0.20-44 glue_1.4.2
[17] digest_0.6.27 promises_1.2.0.1 rvest_1.0.0 colorspace_2.0-1
[21] htmltools_0.5.1.1 httpuv_1.6.1 Matrix_1.3-4 pkgconfig_2.0.3
[25] haven_2.4.1 mvtnorm_1.1-2 scales_1.1.1 later_1.2.0
[29] git2r_0.28.0 generics_0.1.0 farver_2.1.0 ellipsis_0.3.2
[33] withr_2.4.2 cli_2.5.0 magrittr_2.0.1 crayon_1.4.1
[37] readxl_1.3.1 evaluate_0.14 fs_1.5.0 fansi_0.5.0
[41] nlme_3.1-152 xml2_1.3.2 tools_4.1.0 hms_1.1.0
[45] lifecycle_1.0.0 munsell_0.5.0 reprex_2.0.0 compiler_4.1.0
[49] jquerylib_0.1.4 rlang_0.4.11 grid_4.1.0 rstudioapi_0.13
[53] labeling_0.4.2 rmarkdown_2.8 gtable_0.3.0 DBI_1.1.1
[57] R6_2.5.0 lubridate_1.7.10 knitr_1.33 utf8_1.2.1
[61] rprojroot_2.0.2 stringi_1.6.2 Rcpp_1.0.6 vctrs_0.3.8
[65] dbplyr_2.1.1 tidyselect_1.1.1 xfun_0.23