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Boulangeat Isabelle
IFD_shrubSPOM
Commits
34b85f25
Commit
34b85f25
authored
Jan 29, 2020
by
Boulangeat Isabelle
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rebuild main analysis output document
parent
a040a2b7
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Main_analyse.Rmd
Main_analyse.Rmd
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Main_analyse.html
Main_analyse.html
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Main_analyse_files/figure-html/lambda, fig-TRUE-1.png
Main_analyse_files/figure-html/lambda, fig-TRUE-1.png
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Main_analyse_files/figure-html/lambda, fig-TRUE-2.png
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Main_analyse_files/figure-html/lambda, fig-TRUE-3.png
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Main_analyse_files/figure-html/lambda_sign-1.png
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Main_analyse_files/figure-html/plot_coeffs-1.png
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Main_analyse_files/figure-html/plot_coeffs-2.png
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README.md
README.md
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Main_analyse.Rmd
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...
@@ -3,9 +3,9 @@ title: "Main_analyse.Rmd"
...
@@ -3,9 +3,9 @@ title: "Main_analyse.Rmd"
author: "Isabelle Boulangeat"
author: "Isabelle Boulangeat"
date: "23/01/2020"
date: "23/01/2020"
output:
output:
md_document:
variant: markdown_github
html_document:
html_document:
keep_md: yes
variant: markdown_github
editor_options:
editor_options:
chunk_output_type: console
chunk_output_type: console
always_allow_html: true
always_allow_html: true
...
@@ -97,7 +97,7 @@ res.tab.eval = as.data.frame(do.call(rbind, lapply(eval.models, function(x)unlis
...
@@ -97,7 +97,7 @@ res.tab.eval = as.data.frame(do.call(rbind, lapply(eval.models, function(x)unlis
res.tab.vars = as.data.frame(do.call(rbind, lapply(eval.models, function(x)unlist(x[5:6]))))
res.tab.vars = as.data.frame(do.call(rbind, lapply(eval.models, function(x)unlist(x[5:6]))))
kable(res.tab.eval, caption = "model evaluation", digits = 2) %>% kable_styling(bootstrap_options = c("striped", "hover", "responsive"), full_width=FALSE)
kable(res.tab.eval, caption = "model evaluation", digits = 2) %>% kable_styling(bootstrap_options = c("striped", "hover", "responsive"), full_width=FALSE)
kable(res.tab.vars, caption = "selected variables")%>% kable_styling(bootstrap_options = c("striped", "hover", "responsive"), font_size = 10)
#
kable(res.tab.vars, caption = "selected variables")%>% kable_styling(bootstrap_options = c("striped", "hover", "responsive"), font_size = 10)
```
```
N.B. Some models do not fit well. The variables explain more or less depending on species but also on processes (extinction and colonisation).
N.B. Some models do not fit well. The variables explain more or less depending on species but also on processes (extinction and colonisation).
...
@@ -133,7 +133,7 @@ data.frame(unclass(table(coeffs.all$var, coeffs.all$process))) %>%
...
@@ -133,7 +133,7 @@ data.frame(unclass(table(coeffs.all$var, coeffs.all$process))) %>%
kable_styling("striped")
kable_styling("striped")
```
```
## Variable
s
effect coefficients
## Variable effect coefficients
This gives a summary of selected variables with significant impact on colonisation or extinction and their estimated coefficients.
This gives a summary of selected variables with significant impact on colonisation or extinction and their estimated coefficients.
...
@@ -153,18 +153,15 @@ coeffs.all[which(coeffs.all$process == "extinction" & coeffs.all$Pr...z..<0.1),]
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@@ -153,18 +153,15 @@ coeffs.all[which(coeffs.all$process == "extinction" & coeffs.all$Pr...z..<0.1),]
## Lambda (1-ext/colo)
## Lambda (1-ext/colo)
An overview of the performance of populations by site of by species
An overview of the performance of populations by site of by species
```{r lambda, fig-TRUE, fig.width=10}
```{r lambda, fig-TRUE, fig.width=10
, warning=FALSE, fig.height=7
}
all.sites = unique(DATA$cover[,c("SemiUniquePLOT", "YEAR", "SUBSITE", "SoilMoist", "TotalCover")])
all.sites = unique(DATA$cover[,c("SemiUniquePLOT", "YEAR", "SUBSITE", "SoilMoist", "TotalCover")])
pDATA = proj.dat.shape(all.sites, DATA$climato)
pDATA = proj.dat.shape(all.sites, DATA$climato)
str(pDATA)
summary(pDATA)
selectVars = c("snowDays", "GSL", "GST", "SoilMoist", "TotalCover")
selectVars = c("snowDays", "GSL", "GST", "SoilMoist", "TotalCover")
pDATA.all = na.omit(pDATA[,c(selectVars,"SemiUniquePLOT", "YEAR", "SUBSITE") ])
pDATA.all = na.omit(pDATA[,c(selectVars,"SemiUniquePLOT", "YEAR", "SUBSITE") ])
pred.all = lapply(spDATA.fit, predictions, pred.data = pDATA.all, selectVars=selectVars)
pred.all = lapply(spDATA.fit, predictions, pred.data = pDATA.all, selectVars=selectVars)
pred.tab = lapply(pred.all, function(x)data.frame(sp = x$sp, lambda = x$lambda, YEAR = x$YEAR, SUBSITE = x$SUBSITE))
pred.tab = lapply(pred.all, function(x)data.frame(sp = x$sp, lambda = x$lambda, YEAR = x$YEAR, SUBSITE = x$SUBSITE))
pred.all.together = do.call(rbind, pred.tab)
pred.all.together = do.call(rbind, pred.tab)
head(pred.all.together)
pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
ggplot(aes(YEAR, lambda)) +
ggplot(aes(YEAR, lambda)) +
...
@@ -180,7 +177,7 @@ pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
...
@@ -180,7 +177,7 @@ pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
ggplot(aes(SITE, lambda, sp)) +
ggplot(aes(SITE, lambda, sp)) +
theme(axis.text.x = element_text(angle=90, hjust=1)) +
theme(axis.text.x = element_text(angle=90, hjust=1)) +
geom_boxplot() + geom_hline(yintercept = 0) +
geom_boxplot() + geom_hline(yintercept = 0) +
facet_wrap( ~ sp,scales = "free_x", ncol =
4
)
facet_wrap( ~ sp,scales = "free_x", ncol =
7
)
pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
ggplot(aes(SITE, lambda, sp)) +
ggplot(aes(SITE, lambda, sp)) +
...
@@ -190,7 +187,7 @@ pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
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@@ -190,7 +187,7 @@ pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
```
```
Simplified version focusing only on the sign of lambda
Simplified version focusing only on the sign of lambda
```{r lambda_sign, fig=TRUE, fig.width=10}
```{r lambda_sign, fig=TRUE, fig.width=10
, warning=FALSE
}
pred.all.together$lambdaSign = ifelse(pred.all.together$lambda>0, "+", "-")
pred.all.together$lambdaSign = ifelse(pred.all.together$lambda>0, "+", "-")
pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
pred.all.together[-which(pred.all.together$sp == "Rubus chamaemorus"), ] %>%
...
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