aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorKen Kellner <ken@kenkellner.com>2017-11-17 19:40:15 (GMT)
committerKen Kellner <ken@kenkellner.com>2017-11-17 19:40:15 (GMT)
commit7c2f2ad171fb86b4216158be63be9ae356ec1dcf (patch)
tree17f359669f9d553c1993f600e2b550cce891a1af
parent28fd1eb65e706db522698923f298cd7fa65d4839 (diff)
Combine output tables into single pdf
-rw-r--r--supplements/appendixS2.Rmd243
1 files changed, 243 insertions, 0 deletions
diff --git a/supplements/appendixS2.Rmd b/supplements/appendixS2.Rmd
new file mode 100644
index 0000000..c663d06
--- /dev/null
+++ b/supplements/appendixS2.Rmd
@@ -0,0 +1,243 @@
+---
+title: "Appendix S2"
+output: pdf_document
+---
+
+Supplemental information for:
+
+Kellner, K. F., Duchamp, J. E., & Swihart R. K. Niche breadth and vertebrate sensitivity to habitat modification: signals from multiple taxa across replicated landscapes. Diversity & Distributions.
+
+```{r, echo=FALSE, warning=FALSE, message=FALSE}
+setwd('..')
+source('.Rprofile')
+```
+
+# Species Index
+
+**Table S2.2**. Mammal species included in analyses and matching index values.
+
+```{r,echo=F}
+mam.sp <- read.csv('lvl1/mam_species.csv',header=T)
+names(mam.sp) <- c('Index','Code','Species Name')
+knitr::kable(mam.sp)
+```
+
+**Table S2.3**. Bat species included in analyses and matching index values.
+
+```{r,echo=F}
+bats.sp <- read.csv('lvl1/bat_species.csv',header=T)
+names(bats.sp) <- c('Index','Code','Species Name')
+knitr::kable(bats.sp)
+```
+
+\pagebreak
+
+**Table S2.4**. Bird species included in analyses and matching index values.
+
+```{r,echo=F}
+bird.sp <- read.csv('lvl1/bird_species.csv',header=T)
+names(bird.sp) <- c('Index','Code','Species Name')
+knitr::kable(bird.sp)
+```
+
+\pagebreak
+
+**Table S2.5**. Aquatic turtle species included in analyses and matching index values.
+
+```{r,echo=F}
+turtle.sp <- read.csv('lvl1/turtle_species.csv',header=T)
+names(turtle.sp) <- c('Index','Code','Species Name')
+knitr::kable(turtle.sp)
+```
+
+# Level-1 Analysis Output (Individual Plot Scale)
+
+**Table S2.6**. Output from multi-species plot-level occupancy model for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl1/mam_lvl1.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.7**. Output from multi-species plot-level occupancy model for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl1/bat_lvl1.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.8**. Output from multi-species plot-level occupancy model for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl1/bird_lvl1.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.9**. Output from multi-species plot-level occupancy model for aquatic turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl1/turtle_lvl1.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+# Level-2 Analysis Output (Landscape Scale)
+
+## Small Mammals
+
+**Table S2.10**. Output from model NN (no imperfect detection, no phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/mam_NN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.11**. Output from model IN (imperfect detection, no phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/mam_IN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.12**. Output from model NP (no imperfect detection, phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/mam_NP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.13**. Output from model IP (imperfect detection, phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/mam_IP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+## Bats
+
+**Table S2.14**. Output from model NN (no imperfect detection, no phylogenetic relationships) for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bat_NN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.15**. Output from model IN (imperfect detection, no phylogenetic relationships) for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bat_IN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.16**. Output from model NP (no imperfect detection, phylogenetic relationships) for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bat_NP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.17**. Output from model IP (imperfect detection, phylogenetic relationships) for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bat_IP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+## Birds
+
+**Table S2.18**. Output from model NN (no imperfect detection, no phylogenetic relationships) for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bird_NN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.19**. Output from model IN (imperfect detection, no phylogenetic relationships) for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bird_IN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.20**. Output from model NP (no imperfect detection, phylogenetic relationships) for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bird_NP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.21**. Output from model IP (imperfect detection, phylogenetic relationships) for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bird_IP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+## Aquatic Turtles
+
+**Table S2.22**. Output from model NN (no imperfect detection, no phylogenetic relationships) for turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/turtle_NN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.23**. Output from model IN (imperfect detection, no phylogenetic relationships) for turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/turtle_IN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.24**. Output from model NP (no imperfect detection, phylogenetic relationships) for turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/turtle_NP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.25**. Output from model IP (imperfect detection, phylogenetic relationships) for turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/turtle_IP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```