Introduction

This is a re-creation of the elevational graph of species published in “Distributional Patterns of Amphibians and Reptiles in Ghandruk, Annapurna Conservation Area, Nepal” using the same dataset.

Note that I did not create the graph for the article. However, I did create the map for the article and the authors acknowledged my contribution in their acknowledgement section.

Importing the dataset

setwd("D:/Rfiles/Chart_Bivek/ElevationGraph") # Setting the working directory

library(readxl)

if (!require (tidyverse)) {install.packages ("tidyverse")}
if (!require (DT)) {install.packages ("DT")}
library(tidyverse)
library(plotly)
library(scales)
library(DT)
dataset <- read_excel("Bivek_Data.xlsx")

Viewing the dataset

Lets view the raw dataset what it looks like.

datatable(dataset, colnames = c('ID' = 1))

This is a sparse matrix and the table is in a wide format. We need to pivot it into a long format.

Let’s use Gather and summarize functions in R.

a <-dataset %>% 
  gather(key = Species, value, `Duttaphrynus melanostictus`: `Oligodon erythrogaster`)


b <- a %>%
  mutate (SpeciesNo = ifelse(a$value > 0, 1, 0))

head(b)
## # A tibble: 6 x 4
##     Ele Species                    value SpeciesNo
##   <dbl> <chr>                      <dbl>     <dbl>
## 1  1080 Duttaphrynus melanostictus     0         0
## 2  1064 Duttaphrynus melanostictus     0         0
## 3  1060 Duttaphrynus melanostictus     0         0
## 4  1080 Duttaphrynus melanostictus     0         0
## 5  1064 Duttaphrynus melanostictus     0         0
## 6  1060 Duttaphrynus melanostictus     0         0
c <- na_if(b, 0) %>% 
  drop_na()

head(c)
## # A tibble: 6 x 4
##     Ele Species                    value SpeciesNo
##   <dbl> <chr>                      <dbl>     <dbl>
## 1  2003 Duttaphrynus melanostictus     1         1
## 2  1911 Duttaphrynus melanostictus     4         1
## 3  1811 Duttaphrynus melanostictus     2         1
## 4  1759 Duttaphrynus melanostictus    10         1
## 5  1646 Duttaphrynus melanostictus     1         1
## 6  1507 Duttaphrynus melanostictus     2         1
d <- c %>% group_by(Species) %>% 
  summarize (Max = max(Ele), Min = min(Ele))

Viewing the dataset again

Lets view the dataset after converting it into a long format.

datatable(d, colnames = c('ID' = 1))

Max/min column refers to the maximum/minimum elevation each species was found. Range of each species is the difference between its maximum and minimum elevation it was found.

Plotting

ggplot(c, aes(Ele, Species, group = Species)) + 
  geom_line(size = 2) +
  labs(x="Elevation", y=NULL, title=" Elevational ranges of herpetofaunal species")+
  scale_x_continuous(breaks = seq(0, 3500, 100))+
  theme_bw()

As it can be seen that there are few species that are found in only one elevation, but are not plotted in the map. We will increase their ranges by 10 meter elevation.

e <- d %>% 
  mutate (range = Max-Min) %>% 
  mutate ( MaxAdded = case_when 
                (range == 0 ~ (Max +10),
                TRUE ~ Max))

head(e)
## # A tibble: 6 x 5
##   Species                      Max   Min range MaxAdded
##   <chr>                      <dbl> <dbl> <dbl>    <dbl>
## 1 Amolops formosus            1745  1745     0     1755
## 2 Amolops marmoratus          1195  1195     0     1205
## 3 Asymblepharus sikimmensis   2425  1975   450     2425
## 4 Calotes versicolor          2019  2000    19     2019
## 5 Duttaphrynus himalayanus    2331  1947   384     2331
## 6 Duttaphrynus melanostictus  2254  1142  1112     2254
f <- e %>% select (Species, MaxAdded, Min) %>% 
  gather(MinMax, value, MaxAdded:Min)

head(f)
## # A tibble: 6 x 3
##   Species                    MinMax   value
##   <chr>                      <chr>    <dbl>
## 1 Amolops formosus           MaxAdded  1755
## 2 Amolops marmoratus         MaxAdded  1205
## 3 Asymblepharus sikimmensis  MaxAdded  2425
## 4 Calotes versicolor         MaxAdded  2019
## 5 Duttaphrynus himalayanus   MaxAdded  2331
## 6 Duttaphrynus melanostictus MaxAdded  2254

Plotting the final graph

p <- ggplot(f, aes(value, Species, group = Species)) + 
  geom_line(size = 1.5) +
  labs(x="Elevation", y=NULL, title=" Elevational ranges of herpetofaunal species")+
  scale_x_continuous(breaks = seq(0, 3500, 100))+
  theme_bw()+
  theme( axis.text.y = element_text(face = 'italic')) # To make species name italic

# View(f)
  
ggplotly(p)

You can hover your mouse cursor on the lower or upper end of the line of the graph to view lower or upper elevation of each herpetofaunal species.

Thanks,
Rajesh Sigdel

Bibilography

Gautam, B., Chalise, M., Thapa, K., & Bhattarai, S. (2020).Distributional Patterns of Amphibians and Reptiles in Ghandruk. Annapurna Conservation Area, Nepal. IRCF Reptiles and Amphibians, 27, 48-49.