Chiriqui benthic cover
Ana Palacio-Castro
2020-11-02
- Setup
- Coral cover data
- Explore data
- Data analysis (Aggregated data)
- Aggregated categories? Plot algae as well?
- Mean (stacked) coral cover by dataset
- Stats Pocillopora repeated measurements per transect?
- Packages used
Setup
Coral cover data
(Wide format)
Select target data (Panama)
- Remove data from Galapagos
cover<-subset(cover, Region!="Galapagos")Pocillopora
- Pocillopora % cover in all Panama datasets
“Massive” species
- Massives % cover in all Panama datasets.
Note: Includes P.stellata, which I would not say it is massive, but this probably does not matter.
Remove datasets from Panama
- Remove DgFr_, UvRd_, Sa_10, Uva_Millep
- Remove “Secas_Chains”, because transects VII, VIII, and IX are crazy in 2005. Maybe only that year needs to be removed?
# Data sets
DataSets<-as.data.frame(c("4x5", "Canal de Afuera Reef","Uva_1m2",
"UvRf-Chains"))
colnames(DataSets)<-"Location"
# Select datasets
cover<-droplevels(cover %>%
filter(Location %in% DataSets$Location))
summary(cover$Location)## 4x5 Canal de Afuera Reef Uva_1m2
## 40 18 213
## UvRf-Chains
## 309- Remove UvRf before 1980
# Remove UvRf before 1980
cover<-subset(cover, YEAR>=1980)- Remove CPCe data
# Remove Uva-Reef Uva_1m2 CPCe
cover<-filter(cover,
!(Location == "Uva_1m2" & Processing == "CPCe over Image"))
cover<-filter(cover,
!(Location == "4x5" &
YEAR == "2015" & Processing == "Photo"))
cover<-filter(cover,
!(Location == "Uva_1m2" &
YEAR == "2015" & Processing == "Image Overlay"))Check transects/sample units
Notes:
- 4x5, Uva1m2 sampled 2 times in 2015 (2015-08)
- Secas_Chains sampled 2 times in 1978 (1978-02), year will be removed anyways
- Secas Secas_Chains (1974) was sampled 4 times
- Secas Secas_Chains (1975) was sampled 3 times
Secas Secas_Chains (1978) was sampled 5 times
- 4x5 was sampled 6 times in 1984 and 1985
Changed Secas_ _chains Arabic numbers to Roman (2015, CPCe data by different researcher)
Explore data
Pocillopora
- Pre-1982 Pocillopora cover in 4*5 = 77% manually added
- Line = mean
- Boxplots = median
- Pocillopora individual transects (all data)
There seem to be some weird transects (wrong labels?). If there are swap this issue can be ignored for stats as far as we are not doing repeated measurements within each transect.
Check individual datasets
- Pocillopora 1m2 data
- Pocillopora chain data
Non-Pocillopora scleractinians
- Line = mean
- Boxplots = median
- Non-Pocillopora individual transects
Check individual datasets
- Non-Pocillopora 1m2 data
Millepora
- Millepora (individual transects)
Data analysis (Aggregated data)
Aggregate data (Pocillopora)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location <- aggregate(Pocillopora ~ YEAR+Month+Site+Location,
FUN=mean,data=cover)
aggr.location$Year_F<-as.factor(aggr.location$YEAR)Pocillopora (model 1)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR is a continuous variable
- Location as a random factor
Data does not look normally distributed, which is ok, since the coral cover cannot be linear (Year as continuous), unless pre-1982 is removed?
Model is signif., but clearly BS (see model prediction below). If we want a continuous model need to start after 1983
# All years 1980_2018
model1 <- lme(
Pocillopora ~ -1 + YEAR, random = ~1|Location, data=aggr.location)
summary(model1)## Linear mixed-effects model fit by REML
## Data: aggr.location
## AIC BIC logLik
## 850.127 857.6596 -422.0635
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 18.38621 21.53904
##
## Fixed effects: Pocillopora ~ -1 + YEAR
## Value Std.Error DF t-value p-value
## YEAR 0.01561409 0.004878674 88 3.200479 0.0019
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.2651464 -0.7754878 -0.2833085 0.5231233 2.4325067
##
## Number of Observations: 92
## Number of Groups: 4 anova(model1) plot(ranef(model1)) # Symmetrical scatter effects around zero?
plot(model1) # plot residuals vs fitted
resnorm1 <- resid(model1)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model1))) # Coefficients of the model
plot(model1, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model1, Pocillopora ~ fitted(.), abline = c(0,1))
Model 1 (data) plot
Model 1 (predicted values) plot
- Extract model 1 predicted values
# Create a new data frame for independent variables
NewData_1 <- expand.grid(Location=unique(aggr.location$Location),
YEAR=seq((min(aggr.location$YEAR)), (max(aggr.location$YEAR))))
pred_1 <- predict(model1 , newdata=NewData_1, level=0)
#summary(pred_1)
#length(pred_1)- Plot model predictions
Pocillopora model 2 (+ multiple comparisons among years)
This model includes data from Chiriqui
- Aggregated by location
- Year is a factor
- Location as a random factor
# All years 1980_2018
model2 <- lme(
Pocillopora ~ -1 + Year_F, random = ~1|Location, data=aggr.location)
#summary(model2)
anova(model2) plot(ranef(model2)) # Symmetrical scatter effects around zero?
plot(model2) # plot residuals vs fitted
resnorm1 <- resid(model2)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model2))) # Coefficients of the model
plot(model2, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model2, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(model2, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups# Effect plot
plot(emmeans(model2, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw()
- Model is significant
- Better normality
Model 2 plot (data)
Multiple comparisons among years
- Too many lines!
Summary:
- 1980 is different from 1983-2001) -> Coral cover lose after 1981-82 ENSO
- “Recovery” by ~2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
m.comp_Pocillopora <- glht(model2, linfct = mcp(Year_F = "Tukey"))
Model2_multipcomp<-summary(m.comp_Pocillopora, test = univariate())
Model2_multipcomp##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = Pocillopora ~ -1 + Year_F, data = aggr.location,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -27.5310 10.4850 -2.626 0.008646 **
## 1984 - 1980 == 0 -51.2233 9.1795 -5.580 2.40e-08 ***
## 1985 - 1980 == 0 -48.7396 9.0228 -5.402 6.60e-08 ***
## 1986 - 1980 == 0 -43.2738 11.3764 -3.804 0.000142 ***
## 1987 - 1980 == 0 -43.0244 11.3764 -3.782 0.000156 ***
## 1988 - 1980 == 0 -42.0687 11.3764 -3.698 0.000217 ***
## 1989 - 1980 == 0 -46.4415 10.3964 -4.467 7.93e-06 ***
## 1990 - 1980 == 0 -45.3114 10.3964 -4.358 1.31e-05 ***
## 1992 - 1980 == 0 -40.1390 11.3764 -3.528 0.000418 ***
## 1993 - 1980 == 0 -39.4649 11.3764 -3.469 0.000522 ***
## 1994 - 1980 == 0 -40.4588 10.4417 -3.875 0.000107 ***
## 1995 - 1980 == 0 -34.2451 10.4417 -3.280 0.001039 **
## 1997 - 1980 == 0 -30.4044 9.6113 -3.163 0.001559 **
## 1998 - 1980 == 0 -28.9079 11.5153 -2.510 0.012060 *
## 2000 - 1980 == 0 -24.7482 10.4417 -2.370 0.017782 *
## 2001 - 1980 == 0 -23.8384 11.5142 -2.070 0.038420 *
## 2002 - 1980 == 0 -15.3991 10.4417 -1.475 0.140273
## 2003 - 1980 == 0 -13.0172 10.4417 -1.247 0.212525
## 2004 - 1980 == 0 -7.9947 11.3764 -0.703 0.482218
## 2005 - 1980 == 0 -9.4519 10.4417 -0.905 0.365358
## 2006 - 1980 == 0 -0.9469 11.5142 -0.082 0.934457
## 2007 - 1980 == 0 -6.0651 10.4417 -0.581 0.561339
## 2010 - 1980 == 0 -1.0775 10.4417 -0.103 0.917813
## 2014 - 1980 == 0 -1.8503 9.8926 -0.187 0.851628
## 2015 - 1980 == 0 3.3410 10.0415 0.333 0.739348
## 2016 - 1980 == 0 -2.5693 10.0415 -0.256 0.798056
## 2017 - 1980 == 0 10.3875 10.4417 0.995 0.319829
## 2018 - 1980 == 0 12.9677 10.0415 1.291 0.196562
## 1984 - 1983 == 0 -23.6922 8.2311 -2.878 0.003997 **
## 1985 - 1983 == 0 -21.2086 8.0003 -2.651 0.008026 **
## 1986 - 1983 == 0 -15.7427 10.4850 -1.501 0.133239
## 1987 - 1983 == 0 -15.4934 10.4850 -1.478 0.139497
## 1988 - 1983 == 0 -14.5376 10.4850 -1.387 0.165590
## 1989 - 1983 == 0 -18.9105 9.4860 -1.994 0.046206 *
## 1990 - 1983 == 0 -17.7804 9.4860 -1.874 0.060878 .
## 1992 - 1983 == 0 -12.6079 10.4850 -1.202 0.229181
## 1993 - 1983 == 0 -11.9339 10.4850 -1.138 0.255045
## 1994 - 1983 == 0 -12.9278 9.4617 -1.366 0.171838
## 1995 - 1983 == 0 -6.7140 9.4617 -0.710 0.477953
## 1997 - 1983 == 0 -2.8734 8.4874 -0.339 0.734950
## 1998 - 1983 == 0 -1.3769 10.5360 -0.131 0.896024
## 2000 - 1983 == 0 2.7829 9.4617 0.294 0.768666
## 2001 - 1983 == 0 3.6926 10.7306 0.344 0.730755
## 2002 - 1983 == 0 12.1319 9.4617 1.282 0.199769
## 2003 - 1983 == 0 14.5139 9.4617 1.534 0.125040
## 2004 - 1983 == 0 19.5364 10.4850 1.863 0.062425 .
## 2005 - 1983 == 0 18.0792 9.4617 1.911 0.056034 .
## 2006 - 1983 == 0 26.5841 10.7306 2.477 0.013234 *
## 2007 - 1983 == 0 21.4659 9.4617 2.269 0.023286 *
## 2010 - 1983 == 0 26.4536 9.4617 2.796 0.005176 **
## 2014 - 1983 == 0 25.6807 8.7932 2.921 0.003495 **
## 2015 - 1983 == 0 30.8720 9.0182 3.423 0.000619 ***
## 2016 - 1983 == 0 24.9618 9.0182 2.768 0.005641 **
## 2017 - 1983 == 0 37.9185 9.4617 4.008 6.13e-05 ***
## 2018 - 1983 == 0 40.4987 9.0182 4.491 7.10e-06 ***
## 1985 - 1984 == 0 2.4836 5.8960 0.421 0.673578
## 1986 - 1984 == 0 7.9495 9.1795 0.866 0.386486
## 1987 - 1984 == 0 8.1989 9.1795 0.893 0.371764
## 1988 - 1984 == 0 9.1546 9.1795 0.997 0.318624
## 1989 - 1984 == 0 4.7818 7.8697 0.608 0.543440
## 1990 - 1984 == 0 5.9118 7.8697 0.751 0.452524
## 1992 - 1984 == 0 11.0843 9.1795 1.208 0.227237
## 1993 - 1984 == 0 11.7584 9.1795 1.281 0.200215
## 1994 - 1984 == 0 10.7645 7.9926 1.347 0.178040
## 1995 - 1984 == 0 16.9782 7.9926 2.124 0.033649 *
## 1997 - 1984 == 0 20.8189 6.9157 3.010 0.002609 **
## 1998 - 1984 == 0 22.3153 9.4313 2.366 0.017977 *
## 2000 - 1984 == 0 26.4751 7.9926 3.312 0.000925 ***
## 2001 - 1984 == 0 27.3849 9.2708 2.954 0.003138 **
## 2002 - 1984 == 0 35.8241 7.9926 4.482 7.39e-06 ***
## 2003 - 1984 == 0 38.2061 7.9926 4.780 1.75e-06 ***
## 2004 - 1984 == 0 43.2286 9.1795 4.709 2.49e-06 ***
## 2005 - 1984 == 0 41.7714 7.9926 5.226 1.73e-07 ***
## 2006 - 1984 == 0 50.2764 9.2708 5.423 5.86e-08 ***
## 2007 - 1984 == 0 45.1582 7.9926 5.650 1.60e-08 ***
## 2010 - 1984 == 0 50.1458 7.9926 6.274 3.52e-10 ***
## 2014 - 1984 == 0 49.3730 7.3113 6.753 1.45e-11 ***
## 2015 - 1984 == 0 54.5643 7.4622 7.312 2.63e-13 ***
## 2016 - 1984 == 0 48.6540 7.4622 6.520 7.03e-11 ***
## 2017 - 1984 == 0 61.6108 7.9926 7.709 1.27e-14 ***
## 2018 - 1984 == 0 64.1910 7.4622 8.602 < 2e-16 ***
## 1986 - 1985 == 0 5.4659 9.0228 0.606 0.544656
## 1987 - 1985 == 0 5.7153 9.0228 0.633 0.526456
## 1988 - 1985 == 0 6.6710 9.0228 0.739 0.459694
## 1989 - 1985 == 0 2.2981 7.7056 0.298 0.765519
## 1990 - 1985 == 0 3.4282 7.7056 0.445 0.656396
## 1992 - 1985 == 0 8.6007 9.0228 0.953 0.340479
## 1993 - 1985 == 0 9.2748 9.0228 1.028 0.303984
## 1994 - 1985 == 0 8.2809 7.8118 1.060 0.289125
## 1995 - 1985 == 0 14.4946 7.8118 1.855 0.063529 .
## 1997 - 1985 == 0 18.3352 6.6926 2.740 0.006151 **
## 1998 - 1985 == 0 19.8317 9.2544 2.143 0.032117 *
## 2000 - 1985 == 0 23.9915 7.8118 3.071 0.002132 **
## 2001 - 1985 == 0 24.9012 9.1398 2.724 0.006440 **
## 2002 - 1985 == 0 33.3405 7.8118 4.268 1.97e-05 ***
## 2003 - 1985 == 0 35.7225 7.8118 4.573 4.81e-06 ***
## 2004 - 1985 == 0 40.7450 9.0228 4.516 6.31e-06 ***
## 2005 - 1985 == 0 39.2878 7.8118 5.029 4.92e-07 ***
## 2006 - 1985 == 0 47.7927 9.1398 5.229 1.70e-07 ***
## 2007 - 1985 == 0 42.6745 7.8118 5.463 4.69e-08 ***
## 2010 - 1985 == 0 47.6622 7.8118 6.101 1.05e-09 ***
## 2014 - 1985 == 0 46.8893 7.0976 6.606 3.94e-11 ***
## 2015 - 1985 == 0 52.0806 7.2683 7.165 7.75e-13 ***
## 2016 - 1985 == 0 46.1704 7.2683 6.352 2.12e-10 ***
## 2017 - 1985 == 0 59.1271 7.8118 7.569 3.75e-14 ***
## 2018 - 1985 == 0 61.7074 7.2683 8.490 < 2e-16 ***
## 1987 - 1986 == 0 0.2494 11.3764 0.022 0.982512
## 1988 - 1986 == 0 1.2051 11.3764 0.106 0.915638
## 1989 - 1986 == 0 -3.1677 10.3964 -0.305 0.760597
## 1990 - 1986 == 0 -2.0377 10.3964 -0.196 0.844610
## 1992 - 1986 == 0 3.1348 11.3764 0.276 0.782892
## 1993 - 1986 == 0 3.8089 11.3764 0.335 0.737774
## 1994 - 1986 == 0 2.8150 10.4417 0.270 0.787476
## 1995 - 1986 == 0 9.0287 10.4417 0.865 0.387216
## 1997 - 1986 == 0 12.8693 9.6113 1.339 0.180578
## 1998 - 1986 == 0 14.3658 11.5153 1.248 0.212201
## 2000 - 1986 == 0 18.5256 10.4417 1.774 0.076031 .
## 2001 - 1986 == 0 19.4354 11.5142 1.688 0.091422 .
## 2002 - 1986 == 0 27.8746 10.4417 2.670 0.007595 **
## 2003 - 1986 == 0 30.2566 10.4417 2.898 0.003759 **
## 2004 - 1986 == 0 35.2791 11.3764 3.101 0.001928 **
## 2005 - 1986 == 0 33.8219 10.4417 3.239 0.001199 **
## 2006 - 1986 == 0 42.3268 11.5142 3.676 0.000237 ***
## 2007 - 1986 == 0 37.2087 10.4417 3.563 0.000366 ***
## 2010 - 1986 == 0 42.1963 10.4417 4.041 5.32e-05 ***
## 2014 - 1986 == 0 41.4234 9.8926 4.187 2.82e-05 ***
## 2015 - 1986 == 0 46.6147 10.0415 4.642 3.45e-06 ***
## 2016 - 1986 == 0 40.7045 10.0415 4.054 5.04e-05 ***
## 2017 - 1986 == 0 53.6613 10.4417 5.139 2.76e-07 ***
## 2018 - 1986 == 0 56.2415 10.0415 5.601 2.13e-08 ***
## 1988 - 1987 == 0 0.9557 11.3764 0.084 0.933048
## 1989 - 1987 == 0 -3.4171 10.3964 -0.329 0.742395
## 1990 - 1987 == 0 -2.2871 10.3964 -0.220 0.825882
## 1992 - 1987 == 0 2.8854 11.3764 0.254 0.799780
## 1993 - 1987 == 0 3.5595 11.3764 0.313 0.754369
## 1994 - 1987 == 0 2.5656 10.4417 0.246 0.805909
## 1995 - 1987 == 0 8.7793 10.4417 0.841 0.400462
## 1997 - 1987 == 0 12.6200 9.6113 1.313 0.189172
## 1998 - 1987 == 0 14.1164 11.5153 1.226 0.220243
## 2000 - 1987 == 0 18.2762 10.4417 1.750 0.080064 .
## 2001 - 1987 == 0 19.1860 11.5142 1.666 0.095657 .
## 2002 - 1987 == 0 27.6252 10.4417 2.646 0.008153 **
## 2003 - 1987 == 0 30.0072 10.4417 2.874 0.004056 **
## 2004 - 1987 == 0 35.0297 11.3764 3.079 0.002076 **
## 2005 - 1987 == 0 33.5725 10.4417 3.215 0.001303 **
## 2006 - 1987 == 0 42.0775 11.5142 3.654 0.000258 ***
## 2007 - 1987 == 0 36.9593 10.4417 3.540 0.000401 ***
## 2010 - 1987 == 0 41.9469 10.4417 4.017 5.89e-05 ***
## 2014 - 1987 == 0 41.1741 9.8926 4.162 3.15e-05 ***
## 2015 - 1987 == 0 46.3654 10.0415 4.617 3.89e-06 ***
## 2016 - 1987 == 0 40.4551 10.0415 4.029 5.61e-05 ***
## 2017 - 1987 == 0 53.4119 10.4417 5.115 3.13e-07 ***
## 2018 - 1987 == 0 55.9921 10.0415 5.576 2.46e-08 ***
## 1989 - 1988 == 0 -4.3728 10.3964 -0.421 0.674038
## 1990 - 1988 == 0 -3.2428 10.3964 -0.312 0.755104
## 1992 - 1988 == 0 1.9297 11.3764 0.170 0.865308
## 1993 - 1988 == 0 2.6038 11.3764 0.229 0.818968
## 1994 - 1988 == 0 1.6099 10.4417 0.154 0.877471
## 1995 - 1988 == 0 7.8236 10.4417 0.749 0.453697
## 1997 - 1988 == 0 11.6642 9.6113 1.214 0.224903
## 1998 - 1988 == 0 13.1607 11.5153 1.143 0.253086
## 2000 - 1988 == 0 17.3205 10.4417 1.659 0.097160 .
## 2001 - 1988 == 0 18.2303 11.5142 1.583 0.113358
## 2002 - 1988 == 0 26.6695 10.4417 2.554 0.010645 *
## 2003 - 1988 == 0 29.0515 10.4417 2.782 0.005398 **
## 2004 - 1988 == 0 34.0740 11.3764 2.995 0.002743 **
## 2005 - 1988 == 0 32.6168 10.4417 3.124 0.001786 **
## 2006 - 1988 == 0 41.1217 11.5142 3.571 0.000355 ***
## 2007 - 1988 == 0 36.0036 10.4417 3.448 0.000565 ***
## 2010 - 1988 == 0 40.9912 10.4417 3.926 8.65e-05 ***
## 2014 - 1988 == 0 40.2183 9.8926 4.066 4.79e-05 ***
## 2015 - 1988 == 0 45.4096 10.0415 4.522 6.12e-06 ***
## 2016 - 1988 == 0 39.4994 10.0415 3.934 8.37e-05 ***
## 2017 - 1988 == 0 52.4561 10.4417 5.024 5.07e-07 ***
## 2018 - 1988 == 0 55.0364 10.0415 5.481 4.23e-08 ***
## 1990 - 1989 == 0 1.1301 9.2888 0.122 0.903171
## 1992 - 1989 == 0 6.3025 10.3964 0.606 0.544365
## 1993 - 1989 == 0 6.9766 10.3964 0.671 0.502181
## 1994 - 1989 == 0 5.9827 9.3646 0.639 0.522911
## 1995 - 1989 == 0 12.1964 9.3646 1.302 0.192779
## 1997 - 1989 == 0 16.0371 8.4453 1.899 0.057573 .
## 1998 - 1989 == 0 17.5336 10.5814 1.657 0.097517 .
## 2000 - 1989 == 0 21.6933 9.3646 2.317 0.020529 *
## 2001 - 1989 == 0 22.6031 10.5144 2.150 0.031577 *
## 2002 - 1989 == 0 31.0424 9.3646 3.315 0.000917 ***
## 2003 - 1989 == 0 33.4243 9.3646 3.569 0.000358 ***
## 2004 - 1989 == 0 38.4468 10.3964 3.698 0.000217 ***
## 2005 - 1989 == 0 36.9896 9.3646 3.950 7.82e-05 ***
## 2006 - 1989 == 0 45.4946 10.5144 4.327 1.51e-05 ***
## 2007 - 1989 == 0 40.3764 9.3646 4.312 1.62e-05 ***
## 2010 - 1989 == 0 45.3640 9.3646 4.844 1.27e-06 ***
## 2014 - 1989 == 0 44.5912 8.7678 5.086 3.66e-07 ***
## 2015 - 1989 == 0 49.7825 8.9162 5.583 2.36e-08 ***
## 2016 - 1989 == 0 43.8722 8.9162 4.921 8.63e-07 ***
## 2017 - 1989 == 0 56.8290 9.3646 6.068 1.29e-09 ***
## 2018 - 1989 == 0 59.4092 8.9162 6.663 2.68e-11 ***
## 1992 - 1990 == 0 5.1725 10.3964 0.498 0.618816
## 1993 - 1990 == 0 5.8466 10.3964 0.562 0.573867
## 1994 - 1990 == 0 4.8527 9.3646 0.518 0.604324
## 1995 - 1990 == 0 11.0664 9.3646 1.182 0.237314
## 1997 - 1990 == 0 14.9070 8.4453 1.765 0.077542 .
## 1998 - 1990 == 0 16.4035 10.5814 1.550 0.121090
## 2000 - 1990 == 0 20.5633 9.3646 2.196 0.028102 *
## 2001 - 1990 == 0 21.4731 10.5144 2.042 0.041127 *
## 2002 - 1990 == 0 29.9123 9.3646 3.194 0.001402 **
## 2003 - 1990 == 0 32.2943 9.3646 3.449 0.000564 ***
## 2004 - 1990 == 0 37.3168 10.3964 3.589 0.000331 ***
## 2005 - 1990 == 0 35.8596 9.3646 3.829 0.000129 ***
## 2006 - 1990 == 0 44.3645 10.5144 4.219 2.45e-05 ***
## 2007 - 1990 == 0 39.2463 9.3646 4.191 2.78e-05 ***
## 2010 - 1990 == 0 44.2340 9.3646 4.724 2.32e-06 ***
## 2014 - 1990 == 0 43.4611 8.7678 4.957 7.16e-07 ***
## 2015 - 1990 == 0 48.6524 8.9162 5.457 4.85e-08 ***
## 2016 - 1990 == 0 42.7422 8.9162 4.794 1.64e-06 ***
## 2017 - 1990 == 0 55.6989 9.3646 5.948 2.72e-09 ***
## 2018 - 1990 == 0 58.2792 8.9162 6.536 6.31e-11 ***
## 1993 - 1992 == 0 0.6741 11.3764 0.059 0.952752
## 1994 - 1992 == 0 -0.3198 10.4417 -0.031 0.975564
## 1995 - 1992 == 0 5.8939 10.4417 0.564 0.572442
## 1997 - 1992 == 0 9.7345 9.6113 1.013 0.311147
## 1998 - 1992 == 0 11.2310 11.5153 0.975 0.329407
## 2000 - 1992 == 0 15.3908 10.4417 1.474 0.140488
## 2001 - 1992 == 0 16.3006 11.5142 1.416 0.156867
## 2002 - 1992 == 0 24.7398 10.4417 2.369 0.017820 *
## 2003 - 1992 == 0 27.1218 10.4417 2.597 0.009392 **
## 2004 - 1992 == 0 32.1443 11.3764 2.826 0.004721 **
## 2005 - 1992 == 0 30.6871 10.4417 2.939 0.003294 **
## 2006 - 1992 == 0 39.1920 11.5142 3.404 0.000665 ***
## 2007 - 1992 == 0 34.0739 10.4417 3.263 0.001101 **
## 2010 - 1992 == 0 39.0615 10.4417 3.741 0.000183 ***
## 2014 - 1992 == 0 38.2886 9.8926 3.870 0.000109 ***
## 2015 - 1992 == 0 43.4799 10.0415 4.330 1.49e-05 ***
## 2016 - 1992 == 0 37.5697 10.0415 3.741 0.000183 ***
## 2017 - 1992 == 0 50.5265 10.4417 4.839 1.31e-06 ***
## 2018 - 1992 == 0 53.1067 10.0415 5.289 1.23e-07 ***
## 1994 - 1993 == 0 -0.9939 10.4417 -0.095 0.924167
## 1995 - 1993 == 0 5.2198 10.4417 0.500 0.617143
## 1997 - 1993 == 0 9.0605 9.6113 0.943 0.345841
## 1998 - 1993 == 0 10.5570 11.5153 0.917 0.359262
## 2000 - 1993 == 0 14.7167 10.4417 1.409 0.158711
## 2001 - 1993 == 0 15.6265 11.5142 1.357 0.174735
## 2002 - 1993 == 0 24.0657 10.4417 2.305 0.021179 *
## 2003 - 1993 == 0 26.4477 10.4417 2.533 0.011313 *
## 2004 - 1993 == 0 31.4702 11.3764 2.766 0.005670 **
## 2005 - 1993 == 0 30.0130 10.4417 2.874 0.004049 **
## 2006 - 1993 == 0 38.5180 11.5142 3.345 0.000822 ***
## 2007 - 1993 == 0 33.3998 10.4417 3.199 0.001381 **
## 2010 - 1993 == 0 38.3874 10.4417 3.676 0.000237 ***
## 2014 - 1993 == 0 37.6146 9.8926 3.802 0.000143 ***
## 2015 - 1993 == 0 42.8059 10.0415 4.263 2.02e-05 ***
## 2016 - 1993 == 0 36.8956 10.0415 3.674 0.000238 ***
## 2017 - 1993 == 0 49.8524 10.4417 4.774 1.80e-06 ***
## 2018 - 1993 == 0 52.4326 10.0415 5.222 1.77e-07 ***
## 1995 - 1994 == 0 6.2137 9.2888 0.669 0.503529
## 1997 - 1994 == 0 10.0544 8.3161 1.209 0.226652
## 1998 - 1994 == 0 11.5508 10.4246 1.108 0.267845
## 2000 - 1994 == 0 15.7106 9.2888 1.691 0.090771 .
## 2001 - 1994 == 0 16.6204 10.4242 1.594 0.110844
## 2002 - 1994 == 0 25.0596 9.2888 2.698 0.006979 **
## 2003 - 1994 == 0 27.4416 9.2888 2.954 0.003134 **
## 2004 - 1994 == 0 32.4641 10.4417 3.109 0.001877 **
## 2005 - 1994 == 0 31.0069 9.2888 3.338 0.000844 ***
## 2006 - 1994 == 0 39.5119 10.4242 3.790 0.000150 ***
## 2007 - 1994 == 0 34.3937 9.2888 3.703 0.000213 ***
## 2010 - 1994 == 0 39.3813 9.2888 4.240 2.24e-05 ***
## 2014 - 1994 == 0 38.6085 8.7006 4.437 9.10e-06 ***
## 2015 - 1994 == 0 43.7998 8.8366 4.957 7.17e-07 ***
## 2016 - 1994 == 0 37.8895 8.8366 4.288 1.80e-05 ***
## 2017 - 1994 == 0 50.8463 9.2888 5.474 4.40e-08 ***
## 2018 - 1994 == 0 53.4265 8.8366 6.046 1.48e-09 ***
## 1997 - 1995 == 0 3.8406 8.3161 0.462 0.644202
## 1998 - 1995 == 0 5.3371 10.4246 0.512 0.608669
## 2000 - 1995 == 0 9.4969 9.2888 1.022 0.306592
## 2001 - 1995 == 0 10.4067 10.4242 0.998 0.318124
## 2002 - 1995 == 0 18.8459 9.2888 2.029 0.042471 *
## 2003 - 1995 == 0 21.2279 9.2888 2.285 0.022295 *
## 2004 - 1995 == 0 26.2504 10.4417 2.514 0.011937 *
## 2005 - 1995 == 0 24.7932 9.2888 2.669 0.007605 **
## 2006 - 1995 == 0 33.2981 10.4242 3.194 0.001402 **
## 2007 - 1995 == 0 28.1800 9.2888 3.034 0.002415 **
## 2010 - 1995 == 0 33.1676 9.2888 3.571 0.000356 ***
## 2014 - 1995 == 0 32.3947 8.7006 3.723 0.000197 ***
## 2015 - 1995 == 0 37.5860 8.8366 4.253 2.11e-05 ***
## 2016 - 1995 == 0 31.6758 8.8366 3.585 0.000338 ***
## 2017 - 1995 == 0 44.6325 9.2888 4.805 1.55e-06 ***
## 2018 - 1995 == 0 47.2128 8.8366 5.343 9.15e-08 ***
## 1998 - 1997 == 0 1.4965 9.5337 0.157 0.875269
## 2000 - 1997 == 0 5.6563 8.3161 0.680 0.496401
## 2001 - 1997 == 0 6.5660 9.5770 0.686 0.492963
## 2002 - 1997 == 0 15.0053 8.3161 1.804 0.071173 .
## 2003 - 1997 == 0 17.3873 8.3161 2.091 0.036546 *
## 2004 - 1997 == 0 22.4098 9.6113 2.332 0.019722 *
## 2005 - 1997 == 0 20.9526 8.3161 2.520 0.011751 *
## 2006 - 1997 == 0 29.4575 9.5770 3.076 0.002099 **
## 2007 - 1997 == 0 24.3393 8.3161 2.927 0.003425 **
## 2010 - 1997 == 0 29.3270 8.3161 3.527 0.000421 ***
## 2014 - 1997 == 0 28.5541 7.6475 3.734 0.000189 ***
## 2015 - 1997 == 0 33.7454 7.8077 4.322 1.55e-05 ***
## 2016 - 1997 == 0 27.8352 7.8077 3.565 0.000364 ***
## 2017 - 1997 == 0 40.7919 8.3161 4.905 9.33e-07 ***
## 2018 - 1997 == 0 43.3721 7.8077 5.555 2.78e-08 ***
## 2000 - 1998 == 0 4.1598 10.4246 0.399 0.689867
## 2001 - 1998 == 0 5.0695 11.4676 0.442 0.658435
## 2002 - 1998 == 0 13.5088 10.4246 1.296 0.195024
## 2003 - 1998 == 0 15.8908 10.4246 1.524 0.127420
## 2004 - 1998 == 0 20.9133 11.5153 1.816 0.069352 .
## 2005 - 1998 == 0 19.4561 10.4246 1.866 0.061990 .
## 2006 - 1998 == 0 27.9610 11.4676 2.438 0.014758 *
## 2007 - 1998 == 0 22.8428 10.4246 2.191 0.028434 *
## 2010 - 1998 == 0 27.8305 10.4246 2.670 0.007592 **
## 2014 - 1998 == 0 27.0576 9.8926 2.735 0.006235 **
## 2015 - 1998 == 0 32.2489 10.0237 3.217 0.001294 **
## 2016 - 1998 == 0 26.3387 10.0237 2.628 0.008598 **
## 2017 - 1998 == 0 39.2954 10.4246 3.769 0.000164 ***
## 2018 - 1998 == 0 41.8756 10.0237 4.178 2.95e-05 ***
## 2001 - 2000 == 0 0.9098 10.4242 0.087 0.930454
## 2002 - 2000 == 0 9.3490 9.2888 1.006 0.314185
## 2003 - 2000 == 0 11.7310 9.2888 1.263 0.206621
## 2004 - 2000 == 0 16.7535 10.4417 1.604 0.108609
## 2005 - 2000 == 0 15.2963 9.2888 1.647 0.099611 .
## 2006 - 2000 == 0 23.8012 10.4242 2.283 0.022414 *
## 2007 - 2000 == 0 18.6831 9.2888 2.011 0.044289 *
## 2010 - 2000 == 0 23.6707 9.2888 2.548 0.010825 *
## 2014 - 2000 == 0 22.8978 8.7006 2.632 0.008494 **
## 2015 - 2000 == 0 28.0891 8.8366 3.179 0.001479 **
## 2016 - 2000 == 0 22.1789 8.8366 2.510 0.012077 *
## 2017 - 2000 == 0 35.1356 9.2888 3.783 0.000155 ***
## 2018 - 2000 == 0 37.7159 8.8366 4.268 1.97e-05 ***
## 2002 - 2001 == 0 8.4393 10.4242 0.810 0.418179
## 2003 - 2001 == 0 10.8212 10.4242 1.038 0.299229
## 2004 - 2001 == 0 15.8437 11.5142 1.376 0.168818
## 2005 - 2001 == 0 14.3865 10.4242 1.380 0.167552
## 2006 - 2001 == 0 22.8915 11.3764 2.012 0.044201 *
## 2007 - 2001 == 0 17.7733 10.4242 1.705 0.088193 .
## 2010 - 2001 == 0 22.7609 10.4242 2.183 0.029001 *
## 2014 - 2001 == 0 21.9881 9.9444 2.211 0.027029 *
## 2015 - 2001 == 0 27.1794 10.0233 2.712 0.006696 **
## 2016 - 2001 == 0 21.2691 10.0233 2.122 0.033840 *
## 2017 - 2001 == 0 34.2259 10.4242 3.283 0.001026 **
## 2018 - 2001 == 0 36.8061 10.0233 3.672 0.000241 ***
## 2003 - 2002 == 0 2.3820 9.2888 0.256 0.797616
## 2004 - 2002 == 0 7.4045 10.4417 0.709 0.478247
## 2005 - 2002 == 0 5.9473 9.2888 0.640 0.522002
## 2006 - 2002 == 0 14.4522 10.4242 1.386 0.165620
## 2007 - 2002 == 0 9.3340 9.2888 1.005 0.314961
## 2010 - 2002 == 0 14.3217 9.2888 1.542 0.123118
## 2014 - 2002 == 0 13.5488 8.7006 1.557 0.119414
## 2015 - 2002 == 0 18.7401 8.8366 2.121 0.033944 *
## 2016 - 2002 == 0 12.8299 8.8366 1.452 0.146529
## 2017 - 2002 == 0 25.7866 9.2888 2.776 0.005502 **
## 2018 - 2002 == 0 28.3669 8.8366 3.210 0.001327 **
## 2004 - 2003 == 0 5.0225 10.4417 0.481 0.630513
## 2005 - 2003 == 0 3.5653 9.2888 0.384 0.701105
## 2006 - 2003 == 0 12.0703 10.4242 1.158 0.246900
## 2007 - 2003 == 0 6.9521 9.2888 0.748 0.454198
## 2010 - 2003 == 0 11.9397 9.2888 1.285 0.198658
## 2014 - 2003 == 0 11.1669 8.7006 1.283 0.199329
## 2015 - 2003 == 0 16.3582 8.8366 1.851 0.064143 .
## 2016 - 2003 == 0 10.4479 8.8366 1.182 0.237069
## 2017 - 2003 == 0 23.4047 9.2888 2.520 0.011747 *
## 2018 - 2003 == 0 25.9849 8.8366 2.941 0.003276 **
## 2005 - 2004 == 0 -1.4572 10.4417 -0.140 0.889012
## 2006 - 2004 == 0 7.0478 11.5142 0.612 0.540477
## 2007 - 2004 == 0 1.9296 10.4417 0.185 0.853390
## 2010 - 2004 == 0 6.9172 10.4417 0.662 0.507676
## 2014 - 2004 == 0 6.1444 9.8926 0.621 0.534528
## 2015 - 2004 == 0 11.3357 10.0415 1.129 0.258949
## 2016 - 2004 == 0 5.4254 10.0415 0.540 0.588992
## 2017 - 2004 == 0 18.3822 10.4417 1.760 0.078330 .
## 2018 - 2004 == 0 20.9624 10.0415 2.088 0.036837 *
## 2006 - 2005 == 0 8.5049 10.4242 0.816 0.414565
## 2007 - 2005 == 0 3.3868 9.2888 0.365 0.715406
## 2010 - 2005 == 0 8.3744 9.2888 0.902 0.367293
## 2014 - 2005 == 0 7.6015 8.7006 0.874 0.382291
## 2015 - 2005 == 0 12.7928 8.8366 1.448 0.147698
## 2016 - 2005 == 0 6.8826 8.8366 0.779 0.436054
## 2017 - 2005 == 0 19.8394 9.2888 2.136 0.032693 *
## 2018 - 2005 == 0 22.4196 8.8366 2.537 0.011177 *
## 2007 - 2006 == 0 -5.1182 10.4242 -0.491 0.623432
## 2010 - 2006 == 0 -0.1306 10.4242 -0.013 0.990007
## 2014 - 2006 == 0 -0.9034 9.9444 -0.091 0.927614
## 2015 - 2006 == 0 4.2879 10.0233 0.428 0.668802
## 2016 - 2006 == 0 -1.6224 10.0233 -0.162 0.871417
## 2017 - 2006 == 0 11.3344 10.4242 1.087 0.276896
## 2018 - 2006 == 0 13.9146 10.0233 1.388 0.165068
## 2010 - 2007 == 0 4.9876 9.2888 0.537 0.591302
## 2014 - 2007 == 0 4.2148 8.7006 0.484 0.628084
## 2015 - 2007 == 0 9.4061 8.8366 1.064 0.287127
## 2016 - 2007 == 0 3.4958 8.8366 0.396 0.692394
## 2017 - 2007 == 0 16.4526 9.2888 1.771 0.076524 .
## 2018 - 2007 == 0 19.0328 8.8366 2.154 0.031251 *
## 2014 - 2010 == 0 -0.7729 8.7006 -0.089 0.929218
## 2015 - 2010 == 0 4.4185 8.8366 0.500 0.617063
## 2016 - 2010 == 0 -1.4918 8.8366 -0.169 0.865938
## 2017 - 2010 == 0 11.4650 9.2888 1.234 0.217101
## 2018 - 2010 == 0 14.0452 8.8366 1.589 0.111963
## 2015 - 2014 == 0 5.1913 8.2160 0.632 0.527483
## 2016 - 2014 == 0 -0.7189 8.2160 -0.088 0.930270
## 2017 - 2014 == 0 12.2378 8.7006 1.407 0.159559
## 2018 - 2014 == 0 14.8180 8.2160 1.804 0.071301 .
## 2016 - 2015 == 0 -5.9103 8.0444 -0.735 0.462518
## 2017 - 2015 == 0 7.0465 8.8366 0.797 0.425205
## 2018 - 2015 == 0 9.6267 8.0444 1.197 0.231422
## 2017 - 2016 == 0 12.9568 8.8366 1.466 0.142577
## 2018 - 2016 == 0 15.5370 8.0444 1.931 0.053432 .
## 2018 - 2017 == 0 2.5802 8.8366 0.292 0.770293
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)Model 2 (predicted values) plot
- Extract model 2 predicted values
# Create a new data frame for independent variables
NewData_2 <- expand.grid(Location=unique(aggr.location$Location),
Year_F=unique(aggr.location$Year_F))
pred_2 <- predict(model2 , newdata=NewData_2, level=0)
#summary(pred_2)
#length(pred_2)- Plot model predictions: Need more work to make it pretty, but not sure if it matters
# Using model data
# Effect plot
plot(emmeans(model2, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw()
# Model2_plot <- ggplot(aggr.location,
# aes(x=as.numeric(Year_F), y=Pocillopora,
# colour=Location)) +
# geom_point(aes(fill=factor(Location)),
# shape = 21, colour = "black",
# size = 2, stroke = 0.3, alpha=0.5) +
#
# scale_y_continuous("Pocillopora cover (%)",
# breaks = seq(0, 80, by=10),
# limits = c(0, 80))+
# scale_x_continuous("", limits = c(1980, 2018),
# breaks = seq(1980, 2018, by=5),
# expand = c(0.02,0.02))+
#
# geom_point(data=NewData_2,
# aes(y=predict(model2, level=0, newdata=NewData_2)),
# size=2)+
# labs(title="Model 2")#+
# #theme(axis.text.y=element_blank(), axis.title.y=element_blank())+
# #scale_fill_manual(values=my_colours) +
# #scale_colour_manual(values=my_colours)+
#
# Model2_plotAggregate data (Massives)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.mas <- aggregate(Massive ~ YEAR+Month+Site+Location,
FUN=mean,data=cover)
aggr.location.mas$Year_F<-as.factor(aggr.location.mas$YEAR)Massives model (3)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR is a continuous variable
- Location as a random factor
Model is NOT significant
# All years 1980_2018
Model3 <- lme(
Massive ~ -1 + YEAR, random = ~1|Location, data=aggr.location.mas)
summary(Model3)## Linear mixed-effects model fit by REML
## Data: aggr.location.mas
## AIC BIC logLik
## 134.7586 142.2581 -64.37931
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 0.6174295 0.4184484
##
## Fixed effects: Massive ~ -1 + YEAR
## Value Std.Error DF t-value p-value
## YEAR 0.0002705414 0.0001576658 87 1.715917 0.0897
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.4143692 -0.5243662 -0.3312173 0.3135174 3.7560655
##
## Number of Observations: 91
## Number of Groups: 4 anova(Model3) #plot(ranef(Model3)) # Symmetrical scatter effects around zero?
#plot(Model3) # plot residuals vs fitted
#resnorm1 <- resid(Model3)
#hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#coef.m1 <- as.data.frame(coef(summary(Model3))) # Coefficients of the model
#plot(Model3, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#plot(Model3, Massive ~ fitted(.), abline = c(0,1))Model 3 plot (Massives, non-significant)
Massives model 4 (+ multiple comparisons between years)
This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor
- Model is significant*
# All years 1980_2018
Model4 <- lme(
Massive ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mas)
#summary(Model4)
anova(Model4) plot(ranef(Model4)) # Symmetrical scatter effects around zero?
plot(Model4) # plot residuals vs fitted
resnorm1 <- resid(Model4)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model4))) # Coefficients of the model
plot(Model4, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model4, Massive ~ fitted(.), abline = c(0,1))
Model 4 plot (Massives, significant)
Multiple comparisons among years
Summary:
1980 is different from every year (1983-2018) -> Massive coral cover lose after 1981-82 ENSO has not recovered to pre-1982 values
1994-1997 artifact differences by incorporating Uva1m2?
- 1997 marginally diffenret from 1998 (p=0.06)
1997 different from 1999-2018 (p<0.05), except 2004-2006 -> Massive coral cover lose after 1997-98 ENSO has not recovered to pre-1997 values
m.comp_Massive <- glht(Model4, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_Massive, test = univariate())##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = Massive ~ -1 + Year_F, data = aggr.location.mas,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -1.5981735 0.4093162 -3.904 9.44e-05 ***
## 1984 - 1980 == 0 -1.7094701 0.3871667 -4.415 1.01e-05 ***
## 1985 - 1980 == 0 -1.7101994 0.3823341 -4.473 7.71e-06 ***
## 1986 - 1980 == 0 -1.6838787 0.4366044 -3.857 0.000115 ***
## 1987 - 1980 == 0 -1.6132284 0.4366044 -3.695 0.000220 ***
## 1988 - 1980 == 0 -1.6504192 0.4366044 -3.780 0.000157 ***
## 1989 - 1980 == 0 -1.6877697 0.4139400 -4.077 4.56e-05 ***
## 1990 - 1980 == 0 -1.6860967 0.4139400 -4.073 4.64e-05 ***
## 1992 - 1980 == 0 -1.5619838 0.4366044 -3.578 0.000347 ***
## 1993 - 1980 == 0 -1.3728633 0.4366044 -3.144 0.001664 **
## 1994 - 1980 == 0 -1.0185485 0.4133423 -2.464 0.013733 *
## 1995 - 1980 == 0 -0.7384122 0.4133423 -1.786 0.074028 .
## 1997 - 1980 == 0 -0.8842634 0.3922385 -2.254 0.024171 *
## 1998 - 1980 == 0 -1.4503494 0.4378121 -3.313 0.000924 ***
## 2000 - 1980 == 0 -1.4376469 0.4133423 -3.478 0.000505 ***
## 2001 - 1980 == 0 -1.4959391 0.4426449 -3.380 0.000726 ***
## 2002 - 1980 == 0 -1.3981977 0.4133423 -3.383 0.000718 ***
## 2003 - 1980 == 0 -1.4121968 0.4133423 -3.417 0.000634 ***
## 2004 - 1980 == 0 -1.1033169 0.4366044 -2.527 0.011503 *
## 2005 - 1980 == 0 -1.3905410 0.4133423 -3.364 0.000768 ***
## 2006 - 1980 == 0 -1.2519926 0.4426449 -2.828 0.004678 **
## 2007 - 1980 == 0 -1.4108484 0.4133423 -3.413 0.000642 ***
## 2010 - 1980 == 0 -1.4106384 0.4133423 -3.413 0.000643 ***
## 2014 - 1980 == 0 -1.4717469 0.3986622 -3.692 0.000223 ***
## 2015 - 1980 == 0 -1.4111261 0.4042614 -3.491 0.000482 ***
## 2016 - 1980 == 0 -1.7678988 0.4042614 -4.373 1.22e-05 ***
## 2017 - 1980 == 0 -1.5708777 0.4133423 -3.800 0.000144 ***
## 2018 - 1980 == 0 -1.6858384 0.4042614 -4.170 3.04e-05 ***
## 1984 - 1983 == 0 -0.1112966 0.2571540 -0.433 0.665159
## 1985 - 1983 == 0 -0.1120259 0.2498190 -0.448 0.653844
## 1986 - 1983 == 0 -0.0857052 0.3268846 -0.262 0.793177
## 1987 - 1983 == 0 -0.0150549 0.3268846 -0.046 0.963266
## 1988 - 1983 == 0 -0.0522457 0.3268846 -0.160 0.873016
## 1989 - 1983 == 0 -0.0895961 0.2959332 -0.303 0.762074
## 1990 - 1983 == 0 -0.0879232 0.2959332 -0.297 0.766387
## 1992 - 1983 == 0 0.0361898 0.3268846 0.111 0.911845
## 1993 - 1983 == 0 0.2253103 0.3268846 0.689 0.490656
## 1994 - 1983 == 0 0.5796251 0.2950966 1.964 0.049508 *
## 1995 - 1983 == 0 0.8597614 0.2950966 2.913 0.003574 **
## 1997 - 1983 == 0 0.7139101 0.2647284 2.697 0.007002 **
## 1998 - 1983 == 0 0.1478241 0.3284959 0.450 0.652708
## 2000 - 1983 == 0 0.1605266 0.2950966 0.544 0.586455
## 2001 - 1983 == 0 0.1022344 0.3349099 0.305 0.760169
## 2002 - 1983 == 0 0.1999758 0.2950966 0.678 0.497986
## 2003 - 1983 == 0 0.1859767 0.2950966 0.630 0.528549
## 2004 - 1983 == 0 0.4948566 0.3268846 1.514 0.130062
## 2005 - 1983 == 0 0.2076325 0.2950966 0.704 0.481676
## 2006 - 1983 == 0 0.3461809 0.3349099 1.034 0.301298
## 2007 - 1983 == 0 0.1873251 0.2950966 0.635 0.525564
## 2010 - 1983 == 0 0.1875352 0.2950966 0.636 0.525100
## 2014 - 1983 == 0 0.1264266 0.2741564 0.461 0.644693
## 2015 - 1983 == 0 0.1870474 0.2822365 0.663 0.507502
## 2016 - 1983 == 0 -0.1697253 0.2822365 -0.601 0.547601
## 2017 - 1983 == 0 0.0272958 0.2950966 0.092 0.926303
## 2018 - 1983 == 0 -0.0876649 0.2822365 -0.311 0.756099
## 1985 - 1984 == 0 -0.0007293 0.1837277 -0.004 0.996833
## 1986 - 1984 == 0 0.0255914 0.2861303 0.089 0.928732
## 1987 - 1984 == 0 0.0962417 0.2861303 0.336 0.736602
## 1988 - 1984 == 0 0.0590509 0.2861303 0.206 0.836496
## 1989 - 1984 == 0 0.0217004 0.2452476 0.088 0.929492
## 1990 - 1984 == 0 0.0233734 0.2452476 0.095 0.924072
## 1992 - 1984 == 0 0.1474863 0.2861303 0.515 0.606237
## 1993 - 1984 == 0 0.3366068 0.2861303 1.176 0.239431
## 1994 - 1984 == 0 0.6909216 0.2492594 2.772 0.005573 **
## 1995 - 1984 == 0 0.9710579 0.2492594 3.896 9.79e-05 ***
## 1997 - 1984 == 0 0.8252067 0.2158794 3.823 0.000132 ***
## 1998 - 1984 == 0 0.2591207 0.2943537 0.880 0.378695
## 2000 - 1984 == 0 0.2718232 0.2492594 1.091 0.275483
## 2001 - 1984 == 0 0.2135310 0.2890637 0.739 0.460090
## 2002 - 1984 == 0 0.3112724 0.2492594 1.249 0.211742
## 2003 - 1984 == 0 0.2972733 0.2492594 1.193 0.233016
## 2004 - 1984 == 0 0.6061532 0.2861303 2.118 0.034137 *
## 2005 - 1984 == 0 0.3189291 0.2492594 1.280 0.200719
## 2006 - 1984 == 0 0.4574775 0.2890637 1.583 0.113509
## 2007 - 1984 == 0 0.2986217 0.2492594 1.198 0.230903
## 2010 - 1984 == 0 0.2988317 0.2492594 1.199 0.230575
## 2014 - 1984 == 0 0.2377232 0.2281172 1.042 0.297361
## 2015 - 1984 == 0 0.2983440 0.2338925 1.276 0.202111
## 2016 - 1984 == 0 -0.0584287 0.2338925 -0.250 0.802734
## 2017 - 1984 == 0 0.1385924 0.2492594 0.556 0.578200
## 2018 - 1984 == 0 0.0236317 0.2338925 0.101 0.919521
## 1986 - 1985 == 0 0.0263207 0.2811931 0.094 0.925424
## 1987 - 1985 == 0 0.0969710 0.2811931 0.345 0.730203
## 1988 - 1985 == 0 0.0597802 0.2811931 0.213 0.831643
## 1989 - 1985 == 0 0.0224298 0.2401068 0.093 0.925573
## 1990 - 1985 == 0 0.0241028 0.2401068 0.100 0.920040
## 1992 - 1985 == 0 0.1482157 0.2811931 0.527 0.598127
## 1993 - 1985 == 0 0.3373362 0.2811931 1.200 0.230271
## 1994 - 1985 == 0 0.6916510 0.2435680 2.840 0.004516 **
## 1995 - 1985 == 0 0.9717873 0.2435680 3.990 6.61e-05 ***
## 1997 - 1985 == 0 0.8259360 0.2088413 3.955 7.66e-05 ***
## 1998 - 1985 == 0 0.2598500 0.2887532 0.900 0.368172
## 2000 - 1985 == 0 0.2725525 0.2435680 1.119 0.263140
## 2001 - 1985 == 0 0.2142603 0.2849734 0.752 0.452135
## 2002 - 1985 == 0 0.3120018 0.2435680 1.281 0.200206
## 2003 - 1985 == 0 0.2980026 0.2435680 1.223 0.221145
## 2004 - 1985 == 0 0.6068826 0.2811931 2.158 0.030909 *
## 2005 - 1985 == 0 0.3196585 0.2435680 1.312 0.189385
## 2006 - 1985 == 0 0.4582069 0.2849734 1.608 0.107858
## 2007 - 1985 == 0 0.2993510 0.2435680 1.229 0.219063
## 2010 - 1985 == 0 0.2995611 0.2435680 1.230 0.218739
## 2014 - 1985 == 0 0.2384525 0.2213688 1.077 0.281403
## 2015 - 1985 == 0 0.2990734 0.2278174 1.313 0.189258
## 2016 - 1985 == 0 -0.0576994 0.2278174 -0.253 0.800059
## 2017 - 1985 == 0 0.1393217 0.2435680 0.572 0.567320
## 2018 - 1985 == 0 0.0243610 0.2278174 0.107 0.914843
## 1987 - 1986 == 0 0.0706503 0.3544782 0.199 0.842022
## 1988 - 1986 == 0 0.0334595 0.3544782 0.094 0.924799
## 1989 - 1986 == 0 -0.0038910 0.3239603 -0.012 0.990417
## 1990 - 1986 == 0 -0.0022180 0.3239603 -0.007 0.994537
## 1992 - 1986 == 0 0.1218949 0.3544782 0.344 0.730943
## 1993 - 1986 == 0 0.3110154 0.3544782 0.877 0.380275
## 1994 - 1986 == 0 0.6653302 0.3254251 2.044 0.040905 *
## 1995 - 1986 == 0 0.9454665 0.3254251 2.905 0.003669 **
## 1997 - 1986 == 0 0.7996153 0.2996010 2.669 0.007609 **
## 1998 - 1986 == 0 0.2335293 0.3589977 0.651 0.515367
## 2000 - 1986 == 0 0.2462318 0.3254251 0.757 0.449262
## 2001 - 1986 == 0 0.1879396 0.3589596 0.524 0.600579
## 2002 - 1986 == 0 0.2856810 0.3254251 0.878 0.380014
## 2003 - 1986 == 0 0.2716819 0.3254251 0.835 0.403801
## 2004 - 1986 == 0 0.5805618 0.3544782 1.638 0.101465
## 2005 - 1986 == 0 0.2933377 0.3254251 0.901 0.367376
## 2006 - 1986 == 0 0.4318861 0.3589596 1.203 0.228914
## 2007 - 1986 == 0 0.2730303 0.3254251 0.839 0.401472
## 2010 - 1986 == 0 0.2732403 0.3254251 0.840 0.401110
## 2014 - 1986 == 0 0.2121318 0.3082973 0.688 0.491405
## 2015 - 1986 == 0 0.2727526 0.3138103 0.869 0.384757
## 2016 - 1986 == 0 -0.0840201 0.3138103 -0.268 0.788898
## 2017 - 1986 == 0 0.1130010 0.3254251 0.347 0.728410
## 2018 - 1986 == 0 -0.0019597 0.3138103 -0.006 0.995017
## 1988 - 1987 == 0 -0.0371908 0.3544782 -0.105 0.916442
## 1989 - 1987 == 0 -0.0745412 0.3239603 -0.230 0.818019
## 1990 - 1987 == 0 -0.0728682 0.3239603 -0.225 0.822034
## 1992 - 1987 == 0 0.0512447 0.3544782 0.145 0.885055
## 1993 - 1987 == 0 0.2403652 0.3544782 0.678 0.497720
## 1994 - 1987 == 0 0.5946800 0.3254251 1.827 0.067640 .
## 1995 - 1987 == 0 0.8748163 0.3254251 2.688 0.007183 **
## 1997 - 1987 == 0 0.7289650 0.2996010 2.433 0.014969 *
## 1998 - 1987 == 0 0.1628790 0.3589977 0.454 0.650041
## 2000 - 1987 == 0 0.1755815 0.3254251 0.540 0.589511
## 2001 - 1987 == 0 0.1172893 0.3589596 0.327 0.743859
## 2002 - 1987 == 0 0.2150307 0.3254251 0.661 0.508761
## 2003 - 1987 == 0 0.2010316 0.3254251 0.618 0.536740
## 2004 - 1987 == 0 0.5099115 0.3544782 1.438 0.150297
## 2005 - 1987 == 0 0.2226874 0.3254251 0.684 0.493788
## 2006 - 1987 == 0 0.3612358 0.3589596 1.006 0.314251
## 2007 - 1987 == 0 0.2023800 0.3254251 0.622 0.534011
## 2010 - 1987 == 0 0.2025901 0.3254251 0.623 0.533587
## 2014 - 1987 == 0 0.1414815 0.3082973 0.459 0.646297
## 2015 - 1987 == 0 0.2021023 0.3138103 0.644 0.519558
## 2016 - 1987 == 0 -0.1546704 0.3138103 -0.493 0.622098
## 2017 - 1987 == 0 0.0423507 0.3254251 0.130 0.896456
## 2018 - 1987 == 0 -0.0726100 0.3138103 -0.231 0.817018
## 1989 - 1988 == 0 -0.0373504 0.3239603 -0.115 0.908213
## 1990 - 1988 == 0 -0.0356774 0.3239603 -0.110 0.912307
## 1992 - 1988 == 0 0.0884355 0.3544782 0.249 0.802989
## 1993 - 1988 == 0 0.2775560 0.3544782 0.783 0.433628
## 1994 - 1988 == 0 0.6318708 0.3254251 1.942 0.052176 .
## 1995 - 1988 == 0 0.9120071 0.3254251 2.803 0.005071 **
## 1997 - 1988 == 0 0.7661558 0.2996010 2.557 0.010550 *
## 1998 - 1988 == 0 0.2000698 0.3589977 0.557 0.577322
## 2000 - 1988 == 0 0.2127723 0.3254251 0.654 0.513222
## 2001 - 1988 == 0 0.1544801 0.3589596 0.430 0.666937
## 2002 - 1988 == 0 0.2522215 0.3254251 0.775 0.438309
## 2003 - 1988 == 0 0.2382224 0.3254251 0.732 0.464148
## 2004 - 1988 == 0 0.5471023 0.3544782 1.543 0.122733
## 2005 - 1988 == 0 0.2598783 0.3254251 0.799 0.424533
## 2006 - 1988 == 0 0.3984266 0.3589596 1.110 0.267021
## 2007 - 1988 == 0 0.2395708 0.3254251 0.736 0.461622
## 2010 - 1988 == 0 0.2397809 0.3254251 0.737 0.461230
## 2014 - 1988 == 0 0.1786723 0.3082973 0.580 0.562221
## 2015 - 1988 == 0 0.2392931 0.3138103 0.763 0.445737
## 2016 - 1988 == 0 -0.1174796 0.3138103 -0.374 0.708133
## 2017 - 1988 == 0 0.0795415 0.3254251 0.244 0.806903
## 2018 - 1988 == 0 -0.0354192 0.3138103 -0.113 0.910135
## 1990 - 1989 == 0 0.0016730 0.2894303 0.006 0.995388
## 1992 - 1989 == 0 0.1257859 0.3239603 0.388 0.697812
## 1993 - 1989 == 0 0.3149064 0.3239603 0.972 0.331024
## 1994 - 1989 == 0 0.6692212 0.2918955 2.293 0.021867 *
## 1995 - 1989 == 0 0.9493575 0.2918955 3.252 0.001144 **
## 1997 - 1989 == 0 0.8035062 0.2633420 3.051 0.002279 **
## 1998 - 1989 == 0 0.2374202 0.3299965 0.719 0.471856
## 2000 - 1989 == 0 0.2501227 0.2918955 0.857 0.391505
## 2001 - 1989 == 0 0.1918306 0.3277847 0.585 0.558391
## 2002 - 1989 == 0 0.2895720 0.2918955 0.992 0.321178
## 2003 - 1989 == 0 0.2755728 0.2918955 0.944 0.345129
## 2004 - 1989 == 0 0.5844528 0.3239603 1.804 0.071218 .
## 2005 - 1989 == 0 0.2972287 0.2918955 1.018 0.308549
## 2006 - 1989 == 0 0.4357771 0.3277847 1.329 0.183696
## 2007 - 1989 == 0 0.2769212 0.2918955 0.949 0.342773
## 2010 - 1989 == 0 0.2771313 0.2918955 0.949 0.342407
## 2014 - 1989 == 0 0.2160227 0.2733205 0.790 0.429315
## 2015 - 1989 == 0 0.2766436 0.2788879 0.992 0.321221
## 2016 - 1989 == 0 -0.0801292 0.2788879 -0.287 0.773870
## 2017 - 1989 == 0 0.1168919 0.2918955 0.400 0.688819
## 2018 - 1989 == 0 0.0019312 0.2788879 0.007 0.994475
## 1992 - 1990 == 0 0.1241129 0.3239603 0.383 0.701637
## 1993 - 1990 == 0 0.3132334 0.3239603 0.967 0.333600
## 1994 - 1990 == 0 0.6675482 0.2918955 2.287 0.022199 *
## 1995 - 1990 == 0 0.9476845 0.2918955 3.247 0.001168 **
## 1997 - 1990 == 0 0.8018332 0.2633420 3.045 0.002328 **
## 1998 - 1990 == 0 0.2357472 0.3299965 0.714 0.474984
## 2000 - 1990 == 0 0.2484498 0.2918955 0.851 0.394681
## 2001 - 1990 == 0 0.1901576 0.3277847 0.580 0.561827
## 2002 - 1990 == 0 0.2878990 0.2918955 0.986 0.323982
## 2003 - 1990 == 0 0.2738998 0.2918955 0.938 0.348065
## 2004 - 1990 == 0 0.5827798 0.3239603 1.799 0.072031 .
## 2005 - 1990 == 0 0.2955557 0.2918955 1.013 0.311280
## 2006 - 1990 == 0 0.4341041 0.3277847 1.324 0.185384
## 2007 - 1990 == 0 0.2752483 0.2918955 0.943 0.345697
## 2010 - 1990 == 0 0.2754583 0.2918955 0.944 0.345329
## 2014 - 1990 == 0 0.2143497 0.2733205 0.784 0.432898
## 2015 - 1990 == 0 0.2749706 0.2788879 0.986 0.324156
## 2016 - 1990 == 0 -0.0818021 0.2788879 -0.293 0.769281
## 2017 - 1990 == 0 0.1152189 0.2918955 0.395 0.693045
## 2018 - 1990 == 0 0.0002582 0.2788879 0.001 0.999261
## 1993 - 1992 == 0 0.1891205 0.3544782 0.534 0.593675
## 1994 - 1992 == 0 0.5434353 0.3254251 1.670 0.094934 .
## 1995 - 1992 == 0 0.8235716 0.3254251 2.531 0.011382 *
## 1997 - 1992 == 0 0.6777203 0.2996010 2.262 0.023693 *
## 1998 - 1992 == 0 0.1116343 0.3589977 0.311 0.755830
## 2000 - 1992 == 0 0.1243368 0.3254251 0.382 0.702406
## 2001 - 1992 == 0 0.0660447 0.3589596 0.184 0.854022
## 2002 - 1992 == 0 0.1637861 0.3254251 0.503 0.614754
## 2003 - 1992 == 0 0.1497869 0.3254251 0.460 0.645315
## 2004 - 1992 == 0 0.4586669 0.3544782 1.294 0.195693
## 2005 - 1992 == 0 0.1714428 0.3254251 0.527 0.598314
## 2006 - 1992 == 0 0.3099912 0.3589596 0.864 0.387817
## 2007 - 1992 == 0 0.1511353 0.3254251 0.464 0.642344
## 2010 - 1992 == 0 0.1513454 0.3254251 0.465 0.641881
## 2014 - 1992 == 0 0.0902368 0.3082973 0.293 0.769756
## 2015 - 1992 == 0 0.1508577 0.3138103 0.481 0.630709
## 2016 - 1992 == 0 -0.2059151 0.3138103 -0.656 0.511710
## 2017 - 1992 == 0 -0.0088940 0.3254251 -0.027 0.978196
## 2018 - 1992 == 0 -0.1238547 0.3138103 -0.395 0.693079
## 1994 - 1993 == 0 0.3543148 0.3254251 1.089 0.276253
## 1995 - 1993 == 0 0.6344511 0.3254251 1.950 0.051223 .
## 1997 - 1993 == 0 0.4885998 0.2996010 1.631 0.102925
## 1998 - 1993 == 0 -0.0774862 0.3589977 -0.216 0.829112
## 2000 - 1993 == 0 -0.0647837 0.3254251 -0.199 0.842205
## 2001 - 1993 == 0 -0.1230758 0.3589596 -0.343 0.731698
## 2002 - 1993 == 0 -0.0253344 0.3254251 -0.078 0.937947
## 2003 - 1993 == 0 -0.0393336 0.3254251 -0.121 0.903795
## 2004 - 1993 == 0 0.2695464 0.3544782 0.760 0.447014
## 2005 - 1993 == 0 -0.0176777 0.3254251 -0.054 0.956679
## 2006 - 1993 == 0 0.1208707 0.3589596 0.337 0.736324
## 2007 - 1993 == 0 -0.0379852 0.3254251 -0.117 0.907078
## 2010 - 1993 == 0 -0.0377751 0.3254251 -0.116 0.907590
## 2014 - 1993 == 0 -0.0988837 0.3082973 -0.321 0.748406
## 2015 - 1993 == 0 -0.0382628 0.3138103 -0.122 0.902955
## 2016 - 1993 == 0 -0.3950356 0.3138103 -1.259 0.208090
## 2017 - 1993 == 0 -0.1980145 0.3254251 -0.608 0.542870
## 2018 - 1993 == 0 -0.3129752 0.3138103 -0.997 0.318600
## 1995 - 1994 == 0 0.2801363 0.2894303 0.968 0.333100
## 1997 - 1994 == 0 0.1342850 0.2591329 0.518 0.604312
## 1998 - 1994 == 0 -0.4318010 0.3248838 -1.329 0.183817
## 2000 - 1994 == 0 -0.4190984 0.2894303 -1.448 0.147614
## 2001 - 1994 == 0 -0.4773906 0.3248698 -1.469 0.141702
## 2002 - 1994 == 0 -0.3796492 0.2894303 -1.312 0.189617
## 2003 - 1994 == 0 -0.3936484 0.2894303 -1.360 0.173805
## 2004 - 1994 == 0 -0.0847684 0.3254251 -0.260 0.794490
## 2005 - 1994 == 0 -0.3719925 0.2894303 -1.285 0.198702
## 2006 - 1994 == 0 -0.2334441 0.3248698 -0.719 0.472401
## 2007 - 1994 == 0 -0.3922999 0.2894303 -1.355 0.175283
## 2010 - 1994 == 0 -0.3920899 0.2894303 -1.355 0.175515
## 2014 - 1994 == 0 -0.4531985 0.2711192 -1.672 0.094606 .
## 2015 - 1994 == 0 -0.3925776 0.2763065 -1.421 0.155374
## 2016 - 1994 == 0 -0.7493503 0.2763065 -2.712 0.006687 **
## 2017 - 1994 == 0 -0.5523293 0.2894303 -1.908 0.056348 .
## 2018 - 1994 == 0 -0.6672900 0.2763065 -2.415 0.015734 *
## 1997 - 1995 == 0 -0.1458513 0.2591329 -0.563 0.573541
## 1998 - 1995 == 0 -0.7119373 0.3248838 -2.191 0.028426 *
## 2000 - 1995 == 0 -0.6992348 0.2894303 -2.416 0.015696 *
## 2001 - 1995 == 0 -0.7575269 0.3248698 -2.332 0.019712 *
## 2002 - 1995 == 0 -0.6597855 0.2894303 -2.280 0.022631 *
## 2003 - 1995 == 0 -0.6737847 0.2894303 -2.328 0.019914 *
## 2004 - 1995 == 0 -0.3649047 0.3254251 -1.121 0.262153
## 2005 - 1995 == 0 -0.6521288 0.2894303 -2.253 0.024250 *
## 2006 - 1995 == 0 -0.5135804 0.3248698 -1.581 0.113905
## 2007 - 1995 == 0 -0.6724363 0.2894303 -2.323 0.020162 *
## 2010 - 1995 == 0 -0.6722262 0.2894303 -2.323 0.020201 *
## 2014 - 1995 == 0 -0.7333348 0.2711192 -2.705 0.006834 **
## 2015 - 1995 == 0 -0.6727139 0.2763065 -2.435 0.014906 *
## 2016 - 1995 == 0 -1.0294867 0.2763065 -3.726 0.000195 ***
## 2017 - 1995 == 0 -0.8324656 0.2894303 -2.876 0.004025 **
## 2018 - 1995 == 0 -0.9474263 0.2763065 -3.429 0.000606 ***
## 1998 - 1997 == 0 -0.5660860 0.2970854 -1.905 0.056720 .
## 2000 - 1997 == 0 -0.5533835 0.2591329 -2.136 0.032719 *
## 2001 - 1997 == 0 -0.6116757 0.2985142 -2.049 0.040456 *
## 2002 - 1997 == 0 -0.5139342 0.2591329 -1.983 0.047336 *
## 2003 - 1997 == 0 -0.5279334 0.2591329 -2.037 0.041619 *
## 2004 - 1997 == 0 -0.2190535 0.2996010 -0.731 0.464687
## 2005 - 1997 == 0 -0.5062775 0.2591329 -1.954 0.050732 .
## 2006 - 1997 == 0 -0.3677291 0.2985142 -1.232 0.218000
## 2007 - 1997 == 0 -0.5265850 0.2591329 -2.032 0.042143 *
## 2010 - 1997 == 0 -0.5263749 0.2591329 -2.031 0.042225 *
## 2014 - 1997 == 0 -0.5874835 0.2383074 -2.465 0.013692 *
## 2015 - 1997 == 0 -0.5268627 0.2443875 -2.156 0.031095 *
## 2016 - 1997 == 0 -0.8836354 0.2443875 -3.616 0.000300 ***
## 2017 - 1997 == 0 -0.6866143 0.2591329 -2.650 0.008057 **
## 2018 - 1997 == 0 -0.8015750 0.2443875 -3.280 0.001038 **
## 2000 - 1998 == 0 0.0127025 0.3248838 0.039 0.968812
## 2001 - 1998 == 0 -0.0455897 0.3574857 -0.128 0.898522
## 2002 - 1998 == 0 0.0521518 0.3248838 0.161 0.872468
## 2003 - 1998 == 0 0.0381526 0.3248838 0.117 0.906516
## 2004 - 1998 == 0 0.3470325 0.3589977 0.967 0.333709
## 2005 - 1998 == 0 0.0598085 0.3248838 0.184 0.853941
## 2006 - 1998 == 0 0.1983568 0.3574857 0.555 0.578986
## 2007 - 1998 == 0 0.0395010 0.3248838 0.122 0.903228
## 2010 - 1998 == 0 0.0397111 0.3248838 0.122 0.902716
## 2014 - 1998 == 0 -0.0213975 0.3082973 -0.069 0.944667
## 2015 - 1998 == 0 0.0392233 0.3132490 0.125 0.900354
## 2016 - 1998 == 0 -0.3175494 0.3132490 -1.014 0.310712
## 2017 - 1998 == 0 -0.1205283 0.3248838 -0.371 0.710646
## 2018 - 1998 == 0 -0.2354890 0.3132490 -0.752 0.452194
## 2001 - 2000 == 0 -0.0582922 0.3248698 -0.179 0.857598
## 2002 - 2000 == 0 0.0394492 0.2894303 0.136 0.891584
## 2003 - 2000 == 0 0.0254501 0.2894303 0.088 0.929931
## 2004 - 2000 == 0 0.3343300 0.3254251 1.027 0.304249
## 2005 - 2000 == 0 0.0471059 0.2894303 0.163 0.870712
## 2006 - 2000 == 0 0.1856543 0.3248698 0.571 0.567679
## 2007 - 2000 == 0 0.0267985 0.2894303 0.093 0.926229
## 2010 - 2000 == 0 0.0270086 0.2894303 0.093 0.925652
## 2014 - 2000 == 0 -0.0341000 0.2711192 -0.126 0.899910
## 2015 - 2000 == 0 0.0265208 0.2763065 0.096 0.923534
## 2016 - 2000 == 0 -0.3302519 0.2763065 -1.195 0.231994
## 2017 - 2000 == 0 -0.1332308 0.2894303 -0.460 0.645286
## 2018 - 2000 == 0 -0.2481915 0.2763065 -0.898 0.369054
## 2002 - 2001 == 0 0.0977414 0.3248698 0.301 0.763519
## 2003 - 2001 == 0 0.0837423 0.3248698 0.258 0.796583
## 2004 - 2001 == 0 0.3926222 0.3589596 1.094 0.274052
## 2005 - 2001 == 0 0.1053981 0.3248698 0.324 0.745611
## 2006 - 2001 == 0 0.2439465 0.3544782 0.688 0.491336
## 2007 - 2001 == 0 0.0850907 0.3248698 0.262 0.793381
## 2010 - 2001 == 0 0.0853007 0.3248698 0.263 0.792883
## 2014 - 2001 == 0 0.0241922 0.3100067 0.078 0.937798
## 2015 - 2001 == 0 0.0848130 0.3132344 0.271 0.786572
## 2016 - 2001 == 0 -0.2719597 0.3132344 -0.868 0.385268
## 2017 - 2001 == 0 -0.0749386 0.3248698 -0.231 0.817569
## 2018 - 2001 == 0 -0.1898993 0.3132344 -0.606 0.544347
## 2003 - 2002 == 0 -0.0139992 0.2894303 -0.048 0.961423
## 2004 - 2002 == 0 0.2948808 0.3254251 0.906 0.364862
## 2005 - 2002 == 0 0.0076567 0.2894303 0.026 0.978895
## 2006 - 2002 == 0 0.1462051 0.3248698 0.450 0.652680
## 2007 - 2002 == 0 -0.0126507 0.2894303 -0.044 0.965136
## 2010 - 2002 == 0 -0.0124407 0.2894303 -0.043 0.965715
## 2014 - 2002 == 0 -0.0735493 0.2711192 -0.271 0.786176
## 2015 - 2002 == 0 -0.0129284 0.2763065 -0.047 0.962681
## 2016 - 2002 == 0 -0.3697011 0.2763065 -1.338 0.180893
## 2017 - 2002 == 0 -0.1726801 0.2894303 -0.597 0.550761
## 2018 - 2002 == 0 -0.2876407 0.2763065 -1.041 0.297866
## 2004 - 2003 == 0 0.3088800 0.3254251 0.949 0.342540
## 2005 - 2003 == 0 0.0216559 0.2894303 0.075 0.940356
## 2006 - 2003 == 0 0.1602043 0.3248698 0.493 0.621918
## 2007 - 2003 == 0 0.0013484 0.2894303 0.005 0.996283
## 2010 - 2003 == 0 0.0015585 0.2894303 0.005 0.995704
## 2014 - 2003 == 0 -0.0595501 0.2711192 -0.220 0.826147
## 2015 - 2003 == 0 0.0010708 0.2763065 0.004 0.996908
## 2016 - 2003 == 0 -0.3557020 0.2763065 -1.287 0.197974
## 2017 - 2003 == 0 -0.1586809 0.2894303 -0.548 0.583518
## 2018 - 2003 == 0 -0.2736416 0.2763065 -0.990 0.322001
## 2005 - 2004 == 0 -0.2872241 0.3254251 -0.883 0.377446
## 2006 - 2004 == 0 -0.1486757 0.3589596 -0.414 0.678739
## 2007 - 2004 == 0 -0.3075315 0.3254251 -0.945 0.344651
## 2010 - 2004 == 0 -0.3073215 0.3254251 -0.944 0.344981
## 2014 - 2004 == 0 -0.3684301 0.3082973 -1.195 0.232068
## 2015 - 2004 == 0 -0.3078092 0.3138103 -0.981 0.326654
## 2016 - 2004 == 0 -0.6645819 0.3138103 -2.118 0.034194 *
## 2017 - 2004 == 0 -0.4675608 0.3254251 -1.437 0.150783
## 2018 - 2004 == 0 -0.5825215 0.3138103 -1.856 0.063413 .
## 2006 - 2005 == 0 0.1385484 0.3248698 0.426 0.669763
## 2007 - 2005 == 0 -0.0203074 0.2894303 -0.070 0.944064
## 2010 - 2005 == 0 -0.0200974 0.2894303 -0.069 0.944641
## 2014 - 2005 == 0 -0.0812060 0.2711192 -0.300 0.764542
## 2015 - 2005 == 0 -0.0205851 0.2763065 -0.075 0.940612
## 2016 - 2005 == 0 -0.3773578 0.2763065 -1.366 0.172026
## 2017 - 2005 == 0 -0.1803368 0.2894303 -0.623 0.533235
## 2018 - 2005 == 0 -0.2952974 0.2763065 -1.069 0.285191
## 2007 - 2006 == 0 -0.1588558 0.3248698 -0.489 0.624854
## 2010 - 2006 == 0 -0.1586458 0.3248698 -0.488 0.625312
## 2014 - 2006 == 0 -0.2197544 0.3100067 -0.709 0.478405
## 2015 - 2006 == 0 -0.1591335 0.3132344 -0.508 0.611430
## 2016 - 2006 == 0 -0.5159062 0.3132344 -1.647 0.099552 .
## 2017 - 2006 == 0 -0.3188851 0.3248698 -0.982 0.326308
## 2018 - 2006 == 0 -0.4338458 0.3132344 -1.385 0.166037
## 2010 - 2007 == 0 0.0002101 0.2894303 0.001 0.999421
## 2014 - 2007 == 0 -0.0608985 0.2711192 -0.225 0.822276
## 2015 - 2007 == 0 -0.0002777 0.2763065 -0.001 0.999198
## 2016 - 2007 == 0 -0.3570504 0.2763065 -1.292 0.196279
## 2017 - 2007 == 0 -0.1600293 0.2894303 -0.553 0.580324
## 2018 - 2007 == 0 -0.2749900 0.2763065 -0.995 0.319622
## 2014 - 2010 == 0 -0.0611086 0.2711192 -0.225 0.821673
## 2015 - 2010 == 0 -0.0004877 0.2763065 -0.002 0.998592
## 2016 - 2010 == 0 -0.3572605 0.2763065 -1.293 0.196016
## 2017 - 2010 == 0 -0.1602394 0.2894303 -0.554 0.579827
## 2018 - 2010 == 0 -0.2752001 0.2763065 -0.996 0.319252
## 2015 - 2014 == 0 0.0606209 0.2570624 0.236 0.813571
## 2016 - 2014 == 0 -0.2961519 0.2570624 -1.152 0.249296
## 2017 - 2014 == 0 -0.0991308 0.2711192 -0.366 0.714637
## 2018 - 2014 == 0 -0.2140915 0.2570624 -0.833 0.404936
## 2016 - 2015 == 0 -0.3567727 0.2506540 -1.423 0.154630
## 2017 - 2015 == 0 -0.1597516 0.2763065 -0.578 0.563151
## 2018 - 2015 == 0 -0.2747123 0.2506540 -1.096 0.273086
## 2017 - 2016 == 0 0.1970211 0.2763065 0.713 0.475813
## 2018 - 2016 == 0 0.0820604 0.2506540 0.327 0.743377
## 2018 - 2017 == 0 -0.1149607 0.2763065 -0.416 0.677365
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)Aggregate data (Millepora)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.mill <- aggregate(Millepora ~ YEAR+Month+Site+Location,
FUN=mean,data=cover)
aggr.location.mill$Year_F<-as.factor(aggr.location.mill$YEAR)Millepora model (5)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR is continuous
- Location as a random factor
Model is NOT signif.
# All years 1980_2018
Model5 <- lme(
Millepora ~ -1 + YEAR, random = ~1|Location, data=aggr.location.mill)
summary(Model5)## Linear mixed-effects model fit by REML
## Data: aggr.location.mill
## AIC BIC logLik
## 400.2517 407.7511 -197.1258
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 0.7592385 1.897247
##
## Fixed effects: Millepora ~ -1 + YEAR
## Value Std.Error DF t-value p-value
## YEAR 0.0002333967 0.0002282586 87 1.02251 0.3094
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -0.73481541 -0.06467798 -0.06098742 -0.03398906 6.83286726
##
## Number of Observations: 91
## Number of Groups: 4 anova(Model5) #plot(ranef(Model5)) # Symmetrical scatter effects around zero?
#plot(Model5) # plot residuals vs fitted
#resnorm1 <- resid(Model5)
#hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#coef.m1 <- as.data.frame(coef(summary(Model5))) # Coefficients of the model
#plot(Model5, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#plot(Model5, Millepora ~ fitted(.), abline = c(0,1))Millepora model 6 (multiple comparisons between years)
This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor
# All years 1980_2018
Model6 <- lme(
Millepora ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mill)
#summary(Model6)
anova(Model6) #plot(ranef(Model6)) # Symmetrical scatter effects around zero?
#plot(Model6) # plot residuals vs fitted
#resnorm1 <- resid(Model6)
#hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#coef.m1 <- as.data.frame(coef(summary(Model6))) # Coefficients of the model
#plot(Model6, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#plot(Model6, Millepora ~ fitted(.), abline = c(0,1))
#m.comp_Massive <- glht(Model6, linfct = mcp(Year_F = "Tukey"))
#summary(m.comp_Massive, test = univariate())Millepora plots (non-significant models)
Aggregate data (Scleractinian)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.scl <- aggregate(All_Corals ~ YEAR+Month+Site+Location,
FUN=mean,data=cover)
aggr.location.scl$Year_F<-as.factor(aggr.location.scl$YEAR)All scleractinians (model 7)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR as a continuous variable
- Location as a random factor
Model is signif.
# All years 1980_2018
Model7 <- lme(
All_Corals ~ -1 + YEAR, random = ~1|Location, data=aggr.location.scl)
summary(Model7)## Linear mixed-effects model fit by REML
## Data: aggr.location.scl
## AIC BIC logLik
## 848.9995 856.5321 -421.4998
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 18.70805 21.39092
##
## Fixed effects: All_Corals ~ -1 + YEAR
## Value Std.Error DF t-value p-value
## YEAR 0.01618138 0.00495211 88 3.267573 0.0015
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.1559272 -0.7964812 -0.2348954 0.4544262 2.4369400
##
## Number of Observations: 92
## Number of Groups: 4 anova(Model7) plot(ranef(Model7)) # Symmetrical scatter effects around zero?
plot(Model7) # plot residuals vs fitted
resnorm1 <- resid(Model7)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model7))) # Coefficients of the model
plot(Model7, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model7, All_Corals ~ fitted(.), abline = c(0,1))
Model 7 plot
Scleractinian_plot <- ggplot(aggr.location.scl,
aes(x=YEAR, y=All_Corals)) +
#geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
#stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(colour=Location))+
geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
geom_smooth(span = 0.3, se=T, colour="darkgray")+
scale_y_continuous("Coral cover (%)", limits = c(-0.5, 80), expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1979, 2019, by=2), expand = c(0,0))+
annotate("rect", xmin = 1982, xmax = 1983,
ymin = 0, ymax = 80, alpha = .2, fill="red")+
annotate("rect", xmin = 1997, xmax = 1998,
ymin = 0, ymax = 80, alpha = .2, fill="red")+
annotate("rect", xmin = 2015, xmax = 2016,
ymin = 0, ymax = 80, alpha = .2, fill="red")
Scleractinian_plot + theme(legend.position = c(0.25, 0.8))
Scleractinians model 8 (multiple comparisons between years)
This model includes data from Chiriqui
- Aggregated by location
- Year as a factor
- Location as a random factor
# All years 1980_2018
Model8 <- lme(
All_Corals ~ -1 + Year_F, random = ~1|Location, data=aggr.location.scl)
#summary(Model8)
anova(Model8) plot(ranef(Model8)) # Symmetrical scatter effects around zero?
plot(Model8) # plot residuals vs fitted
resnorm1 <- resid(Model8)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model8))) # Coefficients of the model
plot(Model8, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model8, All_Corals ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm_scle<-emmeans(Model8, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups_Scle<-cld(Year_F.emm_scle, by=NULL) # compact-letter display
year_groups_Scle# Effect plot
plot(emmeans(Model8, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw()
Model 8 plot
Multiple comparisons among years
Summary:
Pretty much same as only Pocillopora …
- 1980 is different from 1983-2001 -> Coral cover lose after 1981-82 ENSO
- “Recovery” by 2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
- 1997 not different from 1998, 2000, 2001, 2003
2015 not different from 2016, 2017, 2018
m.comp_Massive <- glht(Model8, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_Massive, test = univariate())##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = All_Corals ~ -1 + Year_F, data = aggr.location.scl,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -28.45888 10.78117 -2.640 0.008298 **
## 1984 - 1980 == 0 -52.47809 9.43883 -5.560 2.70e-08 ***
## 1985 - 1980 == 0 -49.99844 9.27770 -5.389 7.08e-08 ***
## 1986 - 1980 == 0 -44.51400 11.69793 -3.805 0.000142 ***
## 1987 - 1980 == 0 -44.19400 11.69793 -3.778 0.000158 ***
## 1988 - 1980 == 0 -43.27550 11.69793 -3.699 0.000216 ***
## 1989 - 1980 == 0 -47.68204 10.69013 -4.460 8.18e-06 ***
## 1990 - 1980 == 0 -46.54804 10.69013 -4.354 1.33e-05 ***
## 1992 - 1980 == 0 -41.25900 11.69793 -3.527 0.000420 ***
## 1993 - 1980 == 0 -40.39450 11.69793 -3.453 0.000554 ***
## 1994 - 1980 == 0 -40.03083 10.73663 -3.728 0.000193 ***
## 1995 - 1980 == 0 -31.12910 10.73663 -2.899 0.003740 **
## 1997 - 1980 == 0 -28.57674 9.88271 -2.892 0.003833 **
## 1998 - 1980 == 0 -30.69387 11.84045 -2.592 0.009534 **
## 2000 - 1980 == 0 -26.25950 10.73663 -2.446 0.014454 *
## 2001 - 1980 == 0 -25.65722 11.83931 -2.167 0.030226 *
## 2002 - 1980 == 0 -16.86980 10.73663 -1.571 0.116127
## 2003 - 1980 == 0 -14.50159 10.73663 -1.351 0.176803
## 2004 - 1980 == 0 -8.65600 11.69793 -0.740 0.459324
## 2005 - 1980 == 0 -10.91668 10.73663 -1.017 0.309263
## 2006 - 1980 == 0 -2.52131 11.83931 -0.213 0.831358
## 2007 - 1980 == 0 -7.54983 10.73663 -0.703 0.481941
## 2010 - 1980 == 0 -2.56207 10.73663 -0.239 0.811393
## 2014 - 1980 == 0 -3.26856 10.17201 -0.321 0.747962
## 2015 - 1980 == 0 1.86811 10.32385 0.181 0.856406
## 2016 - 1980 == 0 -4.40114 10.32385 -0.426 0.669883
## 2017 - 1980 == 0 8.74250 10.73663 0.814 0.415491
## 2018 - 1980 == 0 11.21983 10.32385 1.087 0.277131
## 1984 - 1983 == 0 -24.01921 8.46317 -2.838 0.004539 **
## 1985 - 1983 == 0 -21.53956 8.22600 -2.618 0.008832 **
## 1986 - 1983 == 0 -16.05512 10.78117 -1.489 0.136440
## 1987 - 1983 == 0 -15.73512 10.78117 -1.460 0.144428
## 1988 - 1983 == 0 -14.81662 10.78117 -1.374 0.169347
## 1989 - 1983 == 0 -19.22316 9.75383 -1.971 0.048743 *
## 1990 - 1983 == 0 -18.08916 9.75383 -1.855 0.063658 .
## 1992 - 1983 == 0 -12.80012 10.78117 -1.187 0.235123
## 1993 - 1983 == 0 -11.93562 10.78117 -1.107 0.268259
## 1994 - 1983 == 0 -11.57195 9.72880 -1.189 0.234261
## 1995 - 1983 == 0 -2.67023 9.72880 -0.274 0.783726
## 1997 - 1983 == 0 -0.11786 8.72691 -0.014 0.989225
## 1998 - 1983 == 0 -2.23499 10.83339 -0.206 0.836552
## 2000 - 1983 == 0 2.19938 9.72880 0.226 0.821148
## 2001 - 1983 == 0 2.80166 11.03330 0.254 0.799551
## 2002 - 1983 == 0 11.58908 9.72880 1.191 0.233570
## 2003 - 1983 == 0 13.95729 9.72880 1.435 0.151391
## 2004 - 1983 == 0 19.80288 10.78117 1.837 0.066239 .
## 2005 - 1983 == 0 17.54220 9.72880 1.803 0.071369 .
## 2006 - 1983 == 0 25.93757 11.03330 2.351 0.018731 *
## 2007 - 1983 == 0 20.90905 9.72880 2.149 0.031619 *
## 2010 - 1983 == 0 25.89680 9.72880 2.662 0.007771 **
## 2014 - 1983 == 0 25.19032 9.04151 2.786 0.005335 **
## 2015 - 1983 == 0 30.32699 9.27125 3.271 0.001071 **
## 2016 - 1983 == 0 24.05774 9.27125 2.595 0.009463 **
## 2017 - 1983 == 0 37.20138 9.72880 3.824 0.000131 ***
## 2018 - 1983 == 0 39.67871 9.27125 4.280 1.87e-05 ***
## 1985 - 1984 == 0 2.47965 6.06259 0.409 0.682533
## 1986 - 1984 == 0 7.96409 9.43883 0.844 0.398805
## 1987 - 1984 == 0 8.28409 9.43883 0.878 0.380128
## 1988 - 1984 == 0 9.20259 9.43883 0.975 0.329575
## 1989 - 1984 == 0 4.79605 8.09208 0.593 0.553393
## 1990 - 1984 == 0 5.93005 8.09208 0.733 0.463668
## 1992 - 1984 == 0 11.21909 9.43883 1.189 0.234593
## 1993 - 1984 == 0 12.08359 9.43883 1.280 0.200475
## 1994 - 1984 == 0 12.44726 8.21816 1.515 0.129873
## 1995 - 1984 == 0 21.34898 8.21816 2.598 0.009383 **
## 1997 - 1984 == 0 23.90135 7.11067 3.361 0.000776 ***
## 1998 - 1984 == 0 21.78422 9.69723 2.246 0.024676 *
## 2000 - 1984 == 0 26.21859 8.21816 3.190 0.001421 **
## 2001 - 1984 == 0 26.82087 9.53246 2.814 0.004898 **
## 2002 - 1984 == 0 35.60829 8.21816 4.333 1.47e-05 ***
## 2003 - 1984 == 0 37.97650 8.21816 4.621 3.82e-06 ***
## 2004 - 1984 == 0 43.82209 9.43883 4.643 3.44e-06 ***
## 2005 - 1984 == 0 41.56141 8.21816 5.057 4.25e-07 ***
## 2006 - 1984 == 0 49.95678 9.53246 5.241 1.60e-07 ***
## 2007 - 1984 == 0 44.92826 8.21816 5.467 4.58e-08 ***
## 2010 - 1984 == 0 49.91601 8.21816 6.074 1.25e-09 ***
## 2014 - 1984 == 0 49.20953 7.51764 6.546 5.91e-11 ***
## 2015 - 1984 == 0 54.34620 7.67103 7.085 1.39e-12 ***
## 2016 - 1984 == 0 48.07695 7.67103 6.267 3.67e-10 ***
## 2017 - 1984 == 0 61.22059 8.21816 7.449 9.37e-14 ***
## 2018 - 1984 == 0 63.69792 7.67103 8.304 < 2e-16 ***
## 1986 - 1985 == 0 5.48444 9.27770 0.591 0.554425
## 1987 - 1985 == 0 5.80444 9.27770 0.626 0.531556
## 1988 - 1985 == 0 6.72294 9.27770 0.725 0.468677
## 1989 - 1985 == 0 2.31640 7.92339 0.292 0.770020
## 1990 - 1985 == 0 3.45040 7.92339 0.435 0.663222
## 1992 - 1985 == 0 8.73944 9.27770 0.942 0.346201
## 1993 - 1985 == 0 9.60394 9.27770 1.035 0.300593
## 1994 - 1985 == 0 9.96760 8.03234 1.241 0.214630
## 1995 - 1985 == 0 18.86933 8.03234 2.349 0.018815 *
## 1997 - 1985 == 0 21.42170 6.88133 3.113 0.001852 **
## 1998 - 1985 == 0 19.30457 9.51544 2.029 0.042482 *
## 2000 - 1985 == 0 23.73894 8.03234 2.955 0.003122 **
## 2001 - 1985 == 0 24.34122 9.39774 2.590 0.009594 **
## 2002 - 1985 == 0 33.12863 8.03234 4.124 3.72e-05 ***
## 2003 - 1985 == 0 35.49685 8.03234 4.419 9.90e-06 ***
## 2004 - 1985 == 0 41.34244 9.27770 4.456 8.35e-06 ***
## 2005 - 1985 == 0 39.08176 8.03234 4.866 1.14e-06 ***
## 2006 - 1985 == 0 47.47713 9.39774 5.052 4.37e-07 ***
## 2007 - 1985 == 0 42.44860 8.03234 5.285 1.26e-07 ***
## 2010 - 1985 == 0 47.43636 8.03234 5.906 3.51e-09 ***
## 2014 - 1985 == 0 46.72988 7.29798 6.403 1.52e-10 ***
## 2015 - 1985 == 0 51.86655 7.47161 6.942 3.87e-12 ***
## 2016 - 1985 == 0 45.59730 7.47161 6.103 1.04e-09 ***
## 2017 - 1985 == 0 58.74094 8.03234 7.313 2.61e-13 ***
## 2018 - 1985 == 0 61.21827 7.47161 8.193 2.22e-16 ***
## 1987 - 1986 == 0 0.32000 11.69793 0.027 0.978176
## 1988 - 1986 == 0 1.23850 11.69793 0.106 0.915683
## 1989 - 1986 == 0 -3.16804 10.69013 -0.296 0.766961
## 1990 - 1986 == 0 -2.03404 10.69013 -0.190 0.849095
## 1992 - 1986 == 0 3.25500 11.69793 0.278 0.780817
## 1993 - 1986 == 0 4.11950 11.69793 0.352 0.724721
## 1994 - 1986 == 0 4.48317 10.73663 0.418 0.676270
## 1995 - 1986 == 0 13.38490 10.73663 1.247 0.212523
## 1997 - 1986 == 0 15.93726 9.88271 1.613 0.106822
## 1998 - 1986 == 0 13.82013 11.84045 1.167 0.243131
## 2000 - 1986 == 0 18.25450 10.73663 1.700 0.089092 .
## 2001 - 1986 == 0 18.85678 11.83931 1.593 0.111222
## 2002 - 1986 == 0 27.64420 10.73663 2.575 0.010031 *
## 2003 - 1986 == 0 30.01241 10.73663 2.795 0.005185 **
## 2004 - 1986 == 0 35.85800 11.69793 3.065 0.002174 **
## 2005 - 1986 == 0 33.59732 10.73663 3.129 0.001753 **
## 2006 - 1986 == 0 41.99269 11.83931 3.547 0.000390 ***
## 2007 - 1986 == 0 36.96417 10.73663 3.443 0.000576 ***
## 2010 - 1986 == 0 41.95193 10.73663 3.907 9.33e-05 ***
## 2014 - 1986 == 0 41.24544 10.17201 4.055 5.02e-05 ***
## 2015 - 1986 == 0 46.38211 10.32385 4.493 7.03e-06 ***
## 2016 - 1986 == 0 40.11286 10.32385 3.885 0.000102 ***
## 2017 - 1986 == 0 53.25650 10.73663 4.960 7.04e-07 ***
## 2018 - 1986 == 0 55.73383 10.32385 5.399 6.72e-08 ***
## 1988 - 1987 == 0 0.91850 11.69793 0.079 0.937416
## 1989 - 1987 == 0 -3.48804 10.69013 -0.326 0.744208
## 1990 - 1987 == 0 -2.35404 10.69013 -0.220 0.825710
## 1992 - 1987 == 0 2.93500 11.69793 0.251 0.801892
## 1993 - 1987 == 0 3.79950 11.69793 0.325 0.745332
## 1994 - 1987 == 0 4.16317 10.73663 0.388 0.698198
## 1995 - 1987 == 0 13.06490 10.73663 1.217 0.223660
## 1997 - 1987 == 0 15.61726 9.88271 1.580 0.114047
## 1998 - 1987 == 0 13.50013 11.84045 1.140 0.254215
## 2000 - 1987 == 0 17.93450 10.73663 1.670 0.094840 .
## 2001 - 1987 == 0 18.53678 11.83931 1.566 0.117419
## 2002 - 1987 == 0 27.32420 10.73663 2.545 0.010929 *
## 2003 - 1987 == 0 29.69241 10.73663 2.766 0.005683 **
## 2004 - 1987 == 0 35.53800 11.69793 3.038 0.002382 **
## 2005 - 1987 == 0 33.27732 10.73663 3.099 0.001939 **
## 2006 - 1987 == 0 41.67269 11.83931 3.520 0.000432 ***
## 2007 - 1987 == 0 36.64417 10.73663 3.413 0.000643 ***
## 2010 - 1987 == 0 41.63193 10.73663 3.878 0.000106 ***
## 2014 - 1987 == 0 40.92544 10.17201 4.023 5.74e-05 ***
## 2015 - 1987 == 0 46.06211 10.32385 4.462 8.13e-06 ***
## 2016 - 1987 == 0 39.79286 10.32385 3.854 0.000116 ***
## 2017 - 1987 == 0 52.93650 10.73663 4.930 8.20e-07 ***
## 2018 - 1987 == 0 55.41383 10.32385 5.368 7.98e-08 ***
## 1989 - 1988 == 0 -4.40654 10.69013 -0.412 0.680188
## 1990 - 1988 == 0 -3.27254 10.69013 -0.306 0.759508
## 1992 - 1988 == 0 2.01650 11.69793 0.172 0.863138
## 1993 - 1988 == 0 2.88100 11.69793 0.246 0.805463
## 1994 - 1988 == 0 3.24467 10.73663 0.302 0.762495
## 1995 - 1988 == 0 12.14640 10.73663 1.131 0.257927
## 1997 - 1988 == 0 14.69876 9.88271 1.487 0.136930
## 1998 - 1988 == 0 12.58163 11.84045 1.063 0.287965
## 2000 - 1988 == 0 17.01600 10.73663 1.585 0.112999
## 2001 - 1988 == 0 17.61828 11.83931 1.488 0.136720
## 2002 - 1988 == 0 26.40570 10.73663 2.459 0.013917 *
## 2003 - 1988 == 0 28.77391 10.73663 2.680 0.007363 **
## 2004 - 1988 == 0 34.61950 11.69793 2.959 0.003082 **
## 2005 - 1988 == 0 32.35882 10.73663 3.014 0.002579 **
## 2006 - 1988 == 0 40.75419 11.83931 3.442 0.000577 ***
## 2007 - 1988 == 0 35.72567 10.73663 3.327 0.000876 ***
## 2010 - 1988 == 0 40.71343 10.73663 3.792 0.000149 ***
## 2014 - 1988 == 0 40.00694 10.17201 3.933 8.39e-05 ***
## 2015 - 1988 == 0 45.14361 10.32385 4.373 1.23e-05 ***
## 2016 - 1988 == 0 38.87436 10.32385 3.765 0.000166 ***
## 2017 - 1988 == 0 52.01800 10.73663 4.845 1.27e-06 ***
## 2018 - 1988 == 0 54.49533 10.32385 5.279 1.30e-07 ***
## 1990 - 1989 == 0 1.13400 9.55132 0.119 0.905492
## 1992 - 1989 == 0 6.42304 10.69013 0.601 0.547948
## 1993 - 1989 == 0 7.28754 10.69013 0.682 0.495424
## 1994 - 1989 == 0 7.65121 9.62905 0.795 0.426848
## 1995 - 1989 == 0 16.55294 9.62905 1.719 0.085603 .
## 1997 - 1989 == 0 19.10530 8.68365 2.200 0.027796 *
## 1998 - 1989 == 0 16.98817 10.88006 1.561 0.118428
## 2000 - 1989 == 0 21.42254 9.62905 2.225 0.026096 *
## 2001 - 1989 == 0 22.02482 10.81123 2.037 0.041628 *
## 2002 - 1989 == 0 30.81224 9.62905 3.200 0.001375 **
## 2003 - 1989 == 0 33.18045 9.62905 3.446 0.000569 ***
## 2004 - 1989 == 0 39.02604 10.69013 3.651 0.000262 ***
## 2005 - 1989 == 0 36.76536 9.62905 3.818 0.000134 ***
## 2006 - 1989 == 0 45.16073 10.81123 4.177 2.95e-05 ***
## 2007 - 1989 == 0 40.13221 9.62905 4.168 3.08e-05 ***
## 2010 - 1989 == 0 45.11997 9.62905 4.686 2.79e-06 ***
## 2014 - 1989 == 0 44.41349 9.01544 4.926 8.38e-07 ***
## 2015 - 1989 == 0 49.55015 9.16653 5.406 6.46e-08 ***
## 2016 - 1989 == 0 43.28090 9.16653 4.722 2.34e-06 ***
## 2017 - 1989 == 0 56.42454 9.62905 5.860 4.63e-09 ***
## 2018 - 1989 == 0 58.90187 9.16653 6.426 1.31e-10 ***
## 1992 - 1990 == 0 5.28904 10.69013 0.495 0.620770
## 1993 - 1990 == 0 6.15354 10.69013 0.576 0.564867
## 1994 - 1990 == 0 6.51721 9.62905 0.677 0.498515
## 1995 - 1990 == 0 15.41894 9.62905 1.601 0.109312
## 1997 - 1990 == 0 17.97130 8.68365 2.070 0.038494 *
## 1998 - 1990 == 0 15.85417 10.88006 1.457 0.145068
## 2000 - 1990 == 0 20.28854 9.62905 2.107 0.035116 *
## 2001 - 1990 == 0 20.89082 10.81123 1.932 0.053319 .
## 2002 - 1990 == 0 29.67824 9.62905 3.082 0.002055 **
## 2003 - 1990 == 0 32.04645 9.62905 3.328 0.000874 ***
## 2004 - 1990 == 0 37.89204 10.69013 3.545 0.000393 ***
## 2005 - 1990 == 0 35.63136 9.62905 3.700 0.000215 ***
## 2006 - 1990 == 0 44.02673 10.81123 4.072 4.65e-05 ***
## 2007 - 1990 == 0 38.99821 9.62905 4.050 5.12e-05 ***
## 2010 - 1990 == 0 43.98597 9.62905 4.568 4.92e-06 ***
## 2014 - 1990 == 0 43.27949 9.01544 4.801 1.58e-06 ***
## 2015 - 1990 == 0 48.41615 9.16653 5.282 1.28e-07 ***
## 2016 - 1990 == 0 42.14690 9.16653 4.598 4.27e-06 ***
## 2017 - 1990 == 0 55.29054 9.62905 5.742 9.35e-09 ***
## 2018 - 1990 == 0 57.76787 9.16653 6.302 2.94e-10 ***
## 1993 - 1992 == 0 0.86450 11.69793 0.074 0.941088
## 1994 - 1992 == 0 1.22817 10.73663 0.114 0.908928
## 1995 - 1992 == 0 10.12990 10.73663 0.943 0.345431
## 1997 - 1992 == 0 12.68226 9.88271 1.283 0.199395
## 1998 - 1992 == 0 10.56513 11.84045 0.892 0.372237
## 2000 - 1992 == 0 14.99950 10.73663 1.397 0.162402
## 2001 - 1992 == 0 15.60178 11.83931 1.318 0.187572
## 2002 - 1992 == 0 24.38920 10.73663 2.272 0.023111 *
## 2003 - 1992 == 0 26.75741 10.73663 2.492 0.012697 *
## 2004 - 1992 == 0 32.60300 11.69793 2.787 0.005319 **
## 2005 - 1992 == 0 30.34232 10.73663 2.826 0.004713 **
## 2006 - 1992 == 0 38.73769 11.83931 3.272 0.001068 **
## 2007 - 1992 == 0 33.70917 10.73663 3.140 0.001692 **
## 2010 - 1992 == 0 38.69693 10.73663 3.604 0.000313 ***
## 2014 - 1992 == 0 37.99044 10.17201 3.735 0.000188 ***
## 2015 - 1992 == 0 43.12711 10.32385 4.177 2.95e-05 ***
## 2016 - 1992 == 0 36.85786 10.32385 3.570 0.000357 ***
## 2017 - 1992 == 0 50.00150 10.73663 4.657 3.21e-06 ***
## 2018 - 1992 == 0 52.47883 10.32385 5.083 3.71e-07 ***
## 1994 - 1993 == 0 0.36367 10.73663 0.034 0.972979
## 1995 - 1993 == 0 9.26540 10.73663 0.863 0.388154
## 1997 - 1993 == 0 11.81776 9.88271 1.196 0.231774
## 1998 - 1993 == 0 9.70063 11.84045 0.819 0.412627
## 2000 - 1993 == 0 14.13500 10.73663 1.317 0.187999
## 2001 - 1993 == 0 14.73728 11.83931 1.245 0.213214
## 2002 - 1993 == 0 23.52470 10.73663 2.191 0.028447 *
## 2003 - 1993 == 0 25.89291 10.73663 2.412 0.015881 *
## 2004 - 1993 == 0 31.73850 11.69793 2.713 0.006664 **
## 2005 - 1993 == 0 29.47782 10.73663 2.746 0.006041 **
## 2006 - 1993 == 0 37.87319 11.83931 3.199 0.001379 **
## 2007 - 1993 == 0 32.84467 10.73663 3.059 0.002220 **
## 2010 - 1993 == 0 37.83243 10.73663 3.524 0.000426 ***
## 2014 - 1993 == 0 37.12594 10.17201 3.650 0.000262 ***
## 2015 - 1993 == 0 42.26261 10.32385 4.094 4.25e-05 ***
## 2016 - 1993 == 0 35.99336 10.32385 3.486 0.000490 ***
## 2017 - 1993 == 0 49.13700 10.73663 4.577 4.73e-06 ***
## 2018 - 1993 == 0 51.61433 10.32385 5.000 5.75e-07 ***
## 1995 - 1994 == 0 8.90173 9.55132 0.932 0.351342
## 1997 - 1994 == 0 11.45409 8.55105 1.339 0.180409
## 1998 - 1994 == 0 9.33696 10.71909 0.871 0.383722
## 2000 - 1994 == 0 13.77133 9.55132 1.442 0.149352
## 2001 - 1994 == 0 14.37361 10.71868 1.341 0.179924
## 2002 - 1994 == 0 23.16103 9.55132 2.425 0.015312 *
## 2003 - 1994 == 0 25.52924 9.55132 2.673 0.007521 **
## 2004 - 1994 == 0 31.37483 10.73663 2.922 0.003475 **
## 2005 - 1994 == 0 29.11415 9.55132 3.048 0.002302 **
## 2006 - 1994 == 0 37.50952 10.71868 3.499 0.000466 ***
## 2007 - 1994 == 0 32.48100 9.55132 3.401 0.000672 ***
## 2010 - 1994 == 0 37.46876 9.55132 3.923 8.75e-05 ***
## 2014 - 1994 == 0 36.76228 8.94640 4.109 3.97e-05 ***
## 2015 - 1994 == 0 41.89894 9.08483 4.612 3.99e-06 ***
## 2016 - 1994 == 0 35.62969 9.08483 3.922 8.79e-05 ***
## 2017 - 1994 == 0 48.77333 9.55132 5.106 3.28e-07 ***
## 2018 - 1994 == 0 51.25066 9.08483 5.641 1.69e-08 ***
## 1997 - 1995 == 0 2.55237 8.55105 0.298 0.765332
## 1998 - 1995 == 0 0.43524 10.71909 0.041 0.967612
## 2000 - 1995 == 0 4.86961 9.55132 0.510 0.610166
## 2001 - 1995 == 0 5.47189 10.71868 0.511 0.609701
## 2002 - 1995 == 0 14.25930 9.55132 1.493 0.135459
## 2003 - 1995 == 0 16.62752 9.55132 1.741 0.081708 .
## 2004 - 1995 == 0 22.47310 10.73663 2.093 0.036338 *
## 2005 - 1995 == 0 20.21242 9.55132 2.116 0.034328 *
## 2006 - 1995 == 0 28.60780 10.71868 2.669 0.007608 **
## 2007 - 1995 == 0 23.57927 9.55132 2.469 0.013561 *
## 2010 - 1995 == 0 28.56703 9.55132 2.991 0.002782 **
## 2014 - 1995 == 0 27.86055 8.94640 3.114 0.001845 **
## 2015 - 1995 == 0 32.99722 9.08483 3.632 0.000281 ***
## 2016 - 1995 == 0 26.72797 9.08483 2.942 0.003261 **
## 2017 - 1995 == 0 39.87161 9.55132 4.174 2.99e-05 ***
## 2018 - 1995 == 0 42.34894 9.08483 4.661 3.14e-06 ***
## 1998 - 1997 == 0 -2.11713 9.80307 -0.216 0.829014
## 2000 - 1997 == 0 2.31724 8.55105 0.271 0.786400
## 2001 - 1997 == 0 2.91952 9.84756 0.296 0.766870
## 2002 - 1997 == 0 11.70694 8.55105 1.369 0.170979
## 2003 - 1997 == 0 14.07515 8.55105 1.646 0.099761 .
## 2004 - 1997 == 0 19.92074 9.88271 2.016 0.043830 *
## 2005 - 1997 == 0 17.66006 8.55105 2.065 0.038899 *
## 2006 - 1997 == 0 26.05543 9.84756 2.646 0.008148 **
## 2007 - 1997 == 0 21.02691 8.55105 2.459 0.013933 *
## 2010 - 1997 == 0 26.01466 8.55105 3.042 0.002348 **
## 2014 - 1997 == 0 25.30818 7.86352 3.218 0.001289 **
## 2015 - 1997 == 0 30.44485 8.02664 3.793 0.000149 ***
## 2016 - 1997 == 0 24.17560 8.02664 3.012 0.002596 **
## 2017 - 1997 == 0 37.31924 8.55105 4.364 1.28e-05 ***
## 2018 - 1997 == 0 39.79657 8.02664 4.958 7.12e-07 ***
## 2000 - 1998 == 0 4.43437 10.71909 0.414 0.679102
## 2001 - 1998 == 0 5.03665 11.79155 0.427 0.669277
## 2002 - 1998 == 0 13.82407 10.71909 1.290 0.197166
## 2003 - 1998 == 0 16.19228 10.71909 1.511 0.130890
## 2004 - 1998 == 0 22.03787 11.84045 1.861 0.062711 .
## 2005 - 1998 == 0 19.77719 10.71909 1.845 0.065031 .
## 2006 - 1998 == 0 28.17256 11.79155 2.389 0.016884 *
## 2007 - 1998 == 0 23.14404 10.71909 2.159 0.030839 *
## 2010 - 1998 == 0 28.13179 10.71909 2.624 0.008679 **
## 2014 - 1998 == 0 27.42531 10.17201 2.696 0.007015 **
## 2015 - 1998 == 0 32.56198 10.30561 3.160 0.001580 **
## 2016 - 1998 == 0 26.29273 10.30561 2.551 0.010732 *
## 2017 - 1998 == 0 39.43637 10.71909 3.679 0.000234 ***
## 2018 - 1998 == 0 41.91370 10.30561 4.067 4.76e-05 ***
## 2001 - 2000 == 0 0.60228 10.71868 0.056 0.955191
## 2002 - 2000 == 0 9.38970 9.55132 0.983 0.325569
## 2003 - 2000 == 0 11.75791 9.55132 1.231 0.218314
## 2004 - 2000 == 0 17.60350 10.73663 1.640 0.101094
## 2005 - 2000 == 0 15.34282 9.55132 1.606 0.108196
## 2006 - 2000 == 0 23.73819 10.71868 2.215 0.026784 *
## 2007 - 2000 == 0 18.70967 9.55132 1.959 0.050129 .
## 2010 - 2000 == 0 23.69742 9.55132 2.481 0.013099 *
## 2014 - 2000 == 0 22.99094 8.94640 2.570 0.010174 *
## 2015 - 2000 == 0 28.12761 9.08483 3.096 0.001961 **
## 2016 - 2000 == 0 21.85836 9.08483 2.406 0.016127 *
## 2017 - 2000 == 0 35.00200 9.55132 3.665 0.000248 ***
## 2018 - 2000 == 0 37.47933 9.08483 4.125 3.70e-05 ***
## 2002 - 2001 == 0 8.78742 10.71868 0.820 0.412317
## 2003 - 2001 == 0 11.15563 10.71868 1.041 0.297984
## 2004 - 2001 == 0 17.00122 11.83931 1.436 0.151003
## 2005 - 2001 == 0 14.74054 10.71868 1.375 0.169063
## 2006 - 2001 == 0 23.13591 11.69793 1.978 0.047954 *
## 2007 - 2001 == 0 18.10739 10.71868 1.689 0.091156 .
## 2010 - 2001 == 0 23.09514 10.71868 2.155 0.031188 *
## 2014 - 2001 == 0 22.38866 10.22526 2.190 0.028557 *
## 2015 - 2001 == 0 27.52533 10.30517 2.671 0.007562 **
## 2016 - 2001 == 0 21.25608 10.30517 2.063 0.039145 *
## 2017 - 2001 == 0 34.39972 10.71868 3.209 0.001330 **
## 2018 - 2001 == 0 36.87705 10.30517 3.578 0.000346 ***
## 2003 - 2002 == 0 2.36821 9.55132 0.248 0.804176
## 2004 - 2002 == 0 8.21380 10.73663 0.765 0.444256
## 2005 - 2002 == 0 5.95312 9.55132 0.623 0.533102
## 2006 - 2002 == 0 14.34849 10.71868 1.339 0.180687
## 2007 - 2002 == 0 9.31997 9.55132 0.976 0.329174
## 2010 - 2002 == 0 14.30773 9.55132 1.498 0.134137
## 2014 - 2002 == 0 13.60125 8.94640 1.520 0.128435
## 2015 - 2002 == 0 18.73791 9.08483 2.063 0.039155 *
## 2016 - 2002 == 0 12.46866 9.08483 1.372 0.169917
## 2017 - 2002 == 0 25.61230 9.55132 2.682 0.007328 **
## 2018 - 2002 == 0 28.08963 9.08483 3.092 0.001989 **
## 2004 - 2003 == 0 5.84559 10.73663 0.544 0.586130
## 2005 - 2003 == 0 3.58491 9.55132 0.375 0.707414
## 2006 - 2003 == 0 11.98028 10.71868 1.118 0.263694
## 2007 - 2003 == 0 6.95176 9.55132 0.728 0.466716
## 2010 - 2003 == 0 11.93952 9.55132 1.250 0.211285
## 2014 - 2003 == 0 11.23303 8.94640 1.256 0.209264
## 2015 - 2003 == 0 16.36970 9.08483 1.802 0.071566 .
## 2016 - 2003 == 0 10.10045 9.08483 1.112 0.266227
## 2017 - 2003 == 0 23.24409 9.55132 2.434 0.014949 *
## 2018 - 2003 == 0 25.72142 9.08483 2.831 0.004637 **
## 2005 - 2004 == 0 -2.26068 10.73663 -0.211 0.833232
## 2006 - 2004 == 0 6.13469 11.83931 0.518 0.604345
## 2007 - 2004 == 0 1.10617 10.73663 0.103 0.917941
## 2010 - 2004 == 0 6.09393 10.73663 0.568 0.570318
## 2014 - 2004 == 0 5.38744 10.17201 0.530 0.596366
## 2015 - 2004 == 0 10.52411 10.32385 1.019 0.308014
## 2016 - 2004 == 0 4.25486 10.32385 0.412 0.680237
## 2017 - 2004 == 0 17.39850 10.73663 1.620 0.105129
## 2018 - 2004 == 0 19.87583 10.32385 1.925 0.054200 .
## 2006 - 2005 == 0 8.39537 10.71868 0.783 0.433482
## 2007 - 2005 == 0 3.36685 9.55132 0.353 0.724463
## 2010 - 2005 == 0 8.35461 9.55132 0.875 0.381733
## 2014 - 2005 == 0 7.64812 8.94640 0.855 0.392616
## 2015 - 2005 == 0 12.78479 9.08483 1.407 0.159348
## 2016 - 2005 == 0 6.51554 9.08483 0.717 0.473258
## 2017 - 2005 == 0 19.65918 9.55132 2.058 0.039564 *
## 2018 - 2005 == 0 22.13651 9.08483 2.437 0.014824 *
## 2007 - 2006 == 0 -5.02852 10.71868 -0.469 0.638972
## 2010 - 2006 == 0 -0.04077 10.71868 -0.004 0.996965
## 2014 - 2006 == 0 -0.74725 10.22526 -0.073 0.941744
## 2015 - 2006 == 0 4.38942 10.30517 0.426 0.670149
## 2016 - 2006 == 0 -1.87983 10.30517 -0.182 0.855256
## 2017 - 2006 == 0 11.26381 10.71868 1.051 0.293324
## 2018 - 2006 == 0 13.74114 10.30517 1.333 0.182393
## 2010 - 2007 == 0 4.98776 9.55132 0.522 0.601527
## 2014 - 2007 == 0 4.28128 8.94640 0.479 0.632261
## 2015 - 2007 == 0 9.41794 9.08483 1.037 0.299891
## 2016 - 2007 == 0 3.14869 9.08483 0.347 0.728901
## 2017 - 2007 == 0 16.29233 9.55132 1.706 0.088051 .
## 2018 - 2007 == 0 18.76966 9.08483 2.066 0.038824 *
## 2014 - 2010 == 0 -0.70648 8.94640 -0.079 0.937058
## 2015 - 2010 == 0 4.43019 9.08483 0.488 0.625800
## 2016 - 2010 == 0 -1.83906 9.08483 -0.202 0.839579
## 2017 - 2010 == 0 11.30458 9.55132 1.184 0.236586
## 2018 - 2010 == 0 13.78190 9.08483 1.517 0.129261
## 2015 - 2014 == 0 5.13667 8.44657 0.608 0.543097
## 2016 - 2014 == 0 -1.13258 8.44657 -0.134 0.893333
## 2017 - 2014 == 0 12.01106 8.94640 1.343 0.179415
## 2018 - 2014 == 0 14.48839 8.44657 1.715 0.086291 .
## 2016 - 2015 == 0 -6.26925 8.27168 -0.758 0.448501
## 2017 - 2015 == 0 6.87439 9.08483 0.757 0.449236
## 2018 - 2015 == 0 9.35172 8.27168 1.131 0.258236
## 2017 - 2016 == 0 13.14364 9.08483 1.447 0.147962
## 2018 - 2016 == 0 15.62097 8.27168 1.888 0.058961 .
## 2018 - 2017 == 0 2.47733 9.08483 0.273 0.785093
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)Aggregated categories? Plot algae as well?
Only plots, not stats
Explore 4x5
Data4_5<-subset(cover, Location=="4x5")
Explore Uva chains
Data_Chain_Uva<-subset(cover, Location=="UvRf-Chains")By transect
Mean Chains
Uva_1m2
Data_Uva12<-subset(cover, Location=="Uva_1m2")By transect
Mean 1m2
SECAS-Chains
# Data_Chain_SECAS<-subset(cover, Location=="Secas_Chains")By transect
# Plot_Secas <- ggplot(Data_Chain_SECAS, aes(x=Date)) +
#
# geom_line(aes(y=(Millepora)), colour="yellow4") +
# geom_point(aes(y=(Millepora)), colour="yellow4", shape=1) +
#
# geom_line(aes(y=(Pocillopora+Massive)), colour="brown2") +
# geom_point(aes(y=(Pocillopora+Massive)), colour="brown2", shape=3) +
#
# geom_line(aes(y=Pocillopora), colour="orange4") +
# geom_point(aes(y=Pocillopora), colour="orange4", shape=1) +
#
#
# #geom_line(aes(y=(100-Substrate)), colour="black") +
# geom_line(aes(y=(100-Algae)), colour="green4") +
# geom_point(aes(y=(100-Algae)), colour="green4", shape=1) +
#
# #geom_line(aes(y=(100-Substrate-Algae)), colour="black") +
#
# scale_y_continuous("Cover (%)",
# limits = c(-2, 101), breaks = seq(0, 100, by=20), expand = c(0,0))+
#
# scale_x_date("", date_breaks = "2 years",
# date_labels = "%Y"
# #limits = c(1979, 2019),
# #expand = c(0,0)
# )+
# annotate("rect", xmin = as.Date("1983-01-01"),
# xmax = as.Date("1983-12-31"),
# ymin = 0, ymax = 100, alpha = .2, fill="gray")+
# annotate("rect", xmin = as.Date("1997-06-01"),
# xmax = as.Date("1998-08-15"),
# ymin = 0, ymax = 100, alpha = .2, fill="gray")+
# annotate("rect", xmin = as.Date("2015-05-15"),
# xmax = as.Date("2016-04-15"),
# ymin = 0, ymax = 100, alpha = .2, fill="gray")
# Plot_Secas+facet_wrap(~Transect)Mean Secas Chains
# Plot_SecasChains2 <- ggplot(Data_Chain_SECAS, aes(x=Date)) +
# stat_summary(aes(y=Millepora),
# fun.y=mean, geom="line", colour="yellow4")+ # Millepora alone
# stat_summary(aes(y=(Massive+Pocillopora)),
# fun.y=mean, geom="line", colour="brown2")+ # Massive + Pocillopora
# stat_summary(aes(y=(Pocillopora)),
# fun.y=mean, geom="line", colour="orange4")+ # Pocillopora alone
# stat_summary(aes(y=100-Algae),
# fun.y=mean, geom="line", colour="green4")+
#
# stat_summary(aes(y=Millepora),
# fun.data="mean_cl_boot",geom = "errorbar", colour="yellow4")+
# stat_summary(aes(y=(Massive+Pocillopora)),
# fun.data="mean_cl_boot",geom = "errorbar", colour="brown2")+
# stat_summary(aes(y=(Pocillopora)),
# fun.data="mean_cl_boot",geom = "errorbar", colour="orange4")+
# stat_summary(aes(y=(y=100-Algae)),
# fun.data="mean_cl_boot",geom = "errorbar", colour="green4")+
#
# scale_y_continuous("Coral (%)",
# limits = c(-2, 101),
# breaks = seq(0, 100, by=20), expand = c(0,0),
# sec.axis = sec_axis(~ .-100, name="Algae (%)"))+
# scale_x_date("", date_breaks = "2 years",
# date_labels = "%Y")+
#
# annotate("rect", xmin = as.Date("1983-01-01"),
# xmax = as.Date("1983-12-31"),
# ymin = 0, ymax = 100, alpha = .2, fill="gray")+
# annotate("rect", xmin = as.Date("1997-06-01"),
# xmax = as.Date("1998-08-15"),
# ymin = 0, ymax = 100, alpha = .2, fill="gray")+
# annotate("rect", xmin = as.Date("2015-05-15"),
# xmax = as.Date("2016-04-15"),
# ymin = 0, ymax = 100, alpha = .2, fill="gray")+
# ggtitle("Secas Island (Chains)")
# Plot_SecasChains2Canal de afuera
Data_CanalAfuera<-subset(cover, Location=="Canal de Afuera Reef")By transect
Canal de Afuera
Mean (stacked) coral cover by dataset
- Millepora data is not stacked (values correspond to real Millepora cover)
- Pocillopora data is not stacked (values correspond to real Pocillopora cover)
- Massive data IS stacked (values correspond to Pocillopora + Massive cover = Scleractinia cover)
- Alga values are inverse (secondary y-axes in the right)
Cover<-grid.arrange(Plot_45 , Plot_Uva1m2, Plot_UvaChains,
Plot_Canal2, ncol=2)
Issues
- Uva 4x5 suggests no coral loss in 1997-1998, but there is not data until 2002. There could have been coral cover loss and recovery by 2002
- 2 data points in Secas Islands are very weird:
- 1980 has a crazy increase in Massives
- 2005 has a crazy increase in Pocilllopora
Stats Pocillopora repeated measurements per transect?
# library(betareg)
# library(plyr)
# library(lmtest)
# library(glmmTMB)
# library(boot)
# library(emmeans)
# library(brms)
# library(mvtnorm)
# library(rstan)# plot(Pocillopora ~ YEAR, cover)
#
# aggr.location$Pocillopora_T<-aggr.location$Pocillopora/100
#
# transform01 <- function(x) {
# (x * (length(x) - 1) + 0.5) / (length(x))
# }
#
# aggr.location$Pocillopora.scaled <- transform01(aggr.location$Pocillopora_T)
#
#
# bm2 <- betareg(Pocillopora.scaled ~ Year_F, data = aggr.location)
# bmnull <- betareg(Pocillopora.scaled ~1, data = aggr.location)
# lm1 <- lm(Pocillopora.scaled ~ Year_F, data= aggr.location)
#
# summary(bm2)
# plot(resid(bm2) ~ fitted(bm2))
#
# lrtest(bm2, bmnull)
#
# AIC(lm1, bm2, bmnull)
#
# dbeta2 <- function(X, mu, phi, ...) {
# dbeta(X, shape1 = mu * phi, shape2 = (1 - mu) * phi, ...)
# }
#
# rbeta2 <- function(N, mu, phi, ...) {
# rbeta(N, shape1 = mu * phi, shape2 = (1 - mu) * phi, ...)
# }# extract coefficients of beta regression model
# coefs.bm2 <- coef(bm2)
# create vector spanning the transformed 0-1 interval
# n.bm2 <- length(fitted(bm2))
# x.range <- seq(0.5/n.bm2 , 1-0.5/n.bm2 , length.out = 200)
# x.range.bt <- (x.range*n.bm2 - 0.5)/(n.bm2-1)
# 1980
# plot(x.range.bt, dbeta2(x.range, inv.logit(coefs.bm2["(Intercept)"]), coefs.bm2["(phi)"]),
# type = "l", lty = 2, lwd = 2,
# ylab = "Probability density", xlab = "Proportion cover",
# ylim=c(0, 20)
# )
# # 1983
# lines(x.range.bt, dbeta2(x.range, inv.logit(coefs.bm2["(Intercept)"] + coefs.bm2[2]), coefs.bm2["(phi)"]),lwd = 2, col = "red")
#
# # 1997
# lines(x.range.bt, dbeta2(x.range, inv.logit(coefs.bm2["(Intercept)"] + coefs.bm2[14]), coefs.bm2["(phi)"]), col = "blue", lwd = 2)
#
# # 1998
# lines(x.range.bt, dbeta2(x.range, inv.logit(coefs.bm2["(Intercept)"] + coefs.bm2[15]), coefs.bm2["(phi)"]), col = "purple", lwd = 2)
#
# # 2015
# lines(x.range.bt, dbeta2(x.range, inv.logit(coefs.bm2["(Intercept)"] + coefs.bm2[26]), coefs.bm2["(phi)"]), col = "green", lwd = 2)
#
# # 1998
# lines(x.range.bt, dbeta2(x.range, inv.logit(coefs.bm2["(Intercept)"] + coefs.bm2[27]), coefs.bm2["(phi)"]), col = "yellow", lwd = 2)
#
# rug(aggr.location$Pocillopora[aggr.location$Year_F=="1980"], lwd=1.5,pos=10)
# rug(aggr.location$Pocillopora[aggr.location$Year_F=="1983"], col="red", pos=9.75, side = 3,lwd=1.5)
# rug(aggr.location$Pocillopora[aggr.location$Year_F=="1997"], col="blue", pos = 9.5, side = 3, lwd=1.5)
# rug(aggr.location$Pocillopora[aggr.location$Year_F=="1998"], pos=9.25, col="purple", side = 3, lwd=1.5)
#
# rug(aggr.location$Pocillopora[aggr.location$Year_F=="2015"], pos=9.00, col="green", side = 3, lwd=1.5)
#
# rug(aggr.location$Pocillopora[aggr.location$Year_F=="2016"], pos=8.75, col="yellow", side = 3, lwd=1.5)
#
# legend("topright", lwd = 2, lty = c(2, 1, 1, 1), col = c("black", "red", "blue", "purple", "green", "yellow"), legend = c("1980", "1983", "1997", "1998", "2015", "2016"), bty = "n")
#
# ```
#
#
# ```{r}
# bm3 <- betareg(Pocillopora.scaled ~ Year_F | Year_F, data = aggr.location)
#
# summary(bm3)
#
# lrtest(bm2, bm3)
# lrtest(bmnull, bm2, bm3)
#
# par(mfrow = c(2, 1), oma = c(0, 0, 0, 0), mar = c(4, 4, 0.2, 0.2))
# plot(residuals(bm2) ~ fitted(bm2))
# plot(residuals(bm3) ~ fitted(bm3))
#
# test(pairs(emmeans(bm3, ~Year_F, mode = "link")))# # plot distributions
# muphi.bm3 <- unique(data.frame(
# mu = fitted(bm3),
# phi = predict(bm3, type = "precision"),
# treatment = aggr.location$Year_F
# ))
#
#
#
# # plot(x.range.bt , dbeta2(x.range, muphi.bm3[1, 1], muphi.bm3[1, 2]),
# # type="l",
# # xlab = "Proportion cover", ylab = "Probability density",
# # lty = 2, lwd = 2)
# #
# # for (i in 2:4) {
# # lines(x.range.bt, dbeta2(x.range, muphi.bm3[i, 1], muphi.bm3[i, 2]), col = c("black", "blue", "red", "green")[i], lty = 1, lwd = 2)
# # }
# # legend("topright", lwd = 2, lty = c(2, 1, 1, 1), col = c("black", "blue", "green", "red"), legend = c("Control", "0.33", "0.66", "Removal"), bty = "n")Packages used
# Creates bibliography
# knitr::write_bib(c(.packages()), "packages.bib")Auguie, Baptiste. 2017. GridExtra: Miscellaneous Functions for “Grid” Graphics. https://CRAN.R-project.org/package=gridExtra.
Genz, Alan, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, and Torsten Hothorn. 2019. Mvtnorm: Multivariate Normal and T Distributions. https://CRAN.R-project.org/package=mvtnorm.
Hothorn, Torsten. 2019. TH.data: TH’s Data Archive. https://CRAN.R-project.org/package=TH.data.
Hothorn, Torsten, Frank Bretz, and Peter Westfall. 2019. Multcomp: Simultaneous Inference in General Parametric Models. https://CRAN.R-project.org/package=multcomp.
Pinheiro, José, Douglas Bates, and R-core. 2019. Nlme: Linear and Nonlinear Mixed Effects Models. https://CRAN.R-project.org/package=nlme.
R Core Team. 2020. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Ripley, Brian. 2019. MASS: Support Functions and Datasets for Venables and Ripley’s Mass. https://CRAN.R-project.org/package=MASS.
Therneau, Terry M. 2019. Survival: Survival Analysis. https://CRAN.R-project.org/package=survival.
Wickham, Hadley. 2018. Scales: Scale Functions for Visualization. https://CRAN.R-project.org/package=scales.
Wickham, Hadley, Winston Chang, Lionel Henry, Thomas Lin Pedersen, Kohske Takahashi, Claus Wilke, Kara Woo, and Hiroaki Yutani. 2019. Ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. https://CRAN.R-project.org/package=ggplot2.
Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller. 2019. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.