Add visualization images to readme.md

[vijaybarve]

It will be useful to have some interesting visualizations added to the readme.md file to give some idea to users what to expect from each function.

[siddhantdubey]

Distriplan Plot:

DistriPlot Tomato

India Plot Size: 0.1 indiaplotsize0 1

India Plot Size: 1

[khknopp]

Hello! Here are all pictures for all of the functions: bdcalendarheat: bdcomplete: chronohorogram: distrigraph: mapgrid: taxotree: tempolar:

[khknopp]

Distriplan Plot:

DistriPlot Tomato

India Plot Size: 0.1 indiaplotsize0 1

India Plot Size: 1

Hi! I suppose you had a problem with the Collection Date column from rinat. If so, do you need a tip? @siddhantdubey

[siddhantdubey]

@khknopp Yes, the tip would be much appreciated!

[khknopp]

So, as you know, the column Collection Date is not available. However, you can solve this by renaming that column and then plotting all the necessary graphs. To rename the column you can, for example, export the table to csv, change the column name in a code editor and then read and use that imported table from csv. write.csv() and read.csv()

[siddhantdubey]

MapGrid Size 1 in America for Icterus:

MapGrid Size 0.1 in America for Icterus:

Icterus Daily:

Icterus Weekly:

Icterus Monthly:

Chronohorogram:

Completeness Map:

CalendarHeat Map:

DistriGraph Tomato:

DistriGraph White:

CollectionEfforts:

require("bdvis")
require("rgbif")

spiders = occ_search(scientificName="Icterus", limit=10000)
spiders = format_bdvis(spiders$data, "rgbif")
mapgrid(spiders, ptype="species", region=c("America"))
mapgrid(spiders,ptype="records",region=c("America"),gridscale=0.1) 
tempolar(spiders, color="green", title="Daily", plottype="r", timescale="d")
tempolar(spiders, color="blue", title="Weekly", plottype="p", timescale="w") 
tempolar(spiders, color="red", title="Monthly", plottype="r", timescale="m")
chronohorogram(spiders)
comp=bdcomplete(spiders,recs=5)
mapgrid(comp, ptype="complete", region=c("America"))
bdcalendarheat(spiders) 
distrigraph(spiders,ptype="cell",col="tomato") 
distrigraph(spiders,ptype="species",ylab="Species") 
distrigraph(spiders,ptype="efforts",col="red") 

[siddhantdubey]

With Everything Fixed:

Accumulation of Species Data Over Time:

Oriole Distribution in the Americas:

Calendar Heat Map:

Chronhorogram:

Completeness vs Species:

Daily Records:

Distribution Records per Species:

Distribution Tomato Records per Cell:

Icterus Complete Map:

Monthly Record:

Weekly Records:

require("bdvis")
require("rgbif")

orioles = occ_search(scientificName="Icterus", limit=50000)
orioles = format_bdvis(orioles$data, "rgbif")
mapgrid(orioles, ptype="species", title="Distribution of Oriole Sightings in the Americas", region=c("USA", "Mexico", "Argentina", "Chile", "Bolivia", "Venezuela", "Brazil", "Peru", "Colombia", "Ecuador", "Uruguay", "Paraguay", "Guyana", "Suriname", "French Guiana", "Aruba"))
tempolar(orioles, color="green", title="Daily Record Collection", plottype="r", timescale="d")
tempolar(orioles, color="blue", title="Weekly Record Collection", plottype="p", timescale="w") 
tempolar(orioles, color="red", title="Monthly Record Collection", plottype="r", timescale="m")
chronohorogram(orioles, title="Chronohorogram of Oriole Sightings")
comp=bdcomplete(orioles,recs=5)
mapgrid(comp, ptype="complete", title="Complete Map Orioles", region=c("USA", "Mexico", "Argentina", "Chile", "Bolivia", "Venezuela", "Brazil", "Peru", "Colombia", "Ecuador", "Uruguay", "Paraguay", "Guyana", "Suriname", "French Guiana", "Aruba"))
bdcalendarheat(orioles, title="Calendar Heat Map of Oriole Sightings") 
distrigraph(orioles,ptype="cell",col="tomato") 
distrigraph(orioles,ptype="species",ylab="Species") 
distrigraph(orioles,ptype="effortspecies",col="red",cumulative=T,type="l")

[ZeroDawn0D]

BioDiversity Data from https://www.inaturalist.org/projects/flora-of-japan

[ZeroDawn0D]

Updated Graphs

[Rishi0812]

Hello Sir @vijaybarve Here are the Plottings on The topic: Spiders Of the World

Program Script: Program Code.txt

[Rishi0812]

Hello Sir @vijaybarve Here are the Plottings on The topic: Spiders Of Minnesota:

Here is the Program Script: SoM Program Code.txt

[arthtyagi]

These are the visualizations I got : MapGrid Distribution Records Mapgrid with GridScale=0.1 taxotree(inat)

[arthtyagi]

I used this https://www.inaturalist.org/projects/arthropods-on-snow dataset for generating these. Distribution Per Cell : Distribution per species : Map Grid for Arthropods on Snow :

[ghost]

Visualisation for bdvis.zip

[transparentChange]

https://github.com/transparentPresence/bdvis_samples

[adtserapio]

Hello Sir @vijaybarve, could you please advise?

After running

require("bdvis")
require("rgbif")

kangaroos<-occ_search(scientificName="Macropus", limit=1000)
kangaroos<-format_bdvis(kangaroos$data, "rgbif")

kangaroos<-gettaxo(kangaroos)
taxotree(kangaroos) 

such as

Error: duplicate column name: Kingdom

I tried fixing duplicate Genus column errors which I remedied by deleting the duplicate ones with NA values. I get this error instead:

Error in do.call("format", args.legend) : second argument must be a list

[hxxr]

require(bdvis)
require(rgbif)
data <- occ_search(scientificName="Acer", limit=20000)
data <- format_bdvis(data$data, "rgbif")
mapgrid(data, ptype="species", title="Maple Trees in the World")
chronohorogram(data, title="Chronohorogram of Maple Tree Observations")
bdcalendarheat(data, title="Maple Tree Observations")
tempolar(data, title="Maple Tree Observations by Day", plottype="r", timescale="d")
tempolar(data, title="Maple Tree Observations by Week", plottype="r", timescale="w")
tempolar(data, title="Maple Tree Observations by Month", plottype="r", timescale="m")
distrigraph(data, ptype="cell")
distrigraph(data, ptype="species")
distrigraph(data, ptype="efforts")

[pratishrai]

library(bdvis)
library(rinat)
mammals <- read.csv("calafornia_mammals.csv", header = TRUE, sep = ',')
colnames(mammals)[24] <- "Latitude"
colnames(mammals)[25] <- "Longitude"
colnames(mammals)[4] <- "Date_collected"
colnames(mammals)[35] <- "Scientific_name"
mammals$Scientific_name <- as.character(mammals$Scientific_name)
mammals <- format_bdvis(mammals, source = "rinat")
bdcalendarheat(mammals, title = "Calendar Heat Map of Mammals")
bdcomplete(mammals)
chronohorogram(mammals)
distrigraph(mammals,ptype="cell",col="tomato")
distrigraph(mammals,ptype="species",ylab="Species", col="red")
distrigraph(mammals,ptype="efforts",col="blue")
distrigraph(mammals,ptype="efforts",col="red",type="s")
tempolar(mammals, color="green", title="Daily Record Collection", plottype="r", timescale="d")
tempolar(mammals, color="skyblue", title="Weekly Record Collection", plottype="p", timescale="w")
tempolar(mammals, color="yellow", title="Monthly Record Collection", plottype="r", timescale="m")
bdcomplete(mammals)
mapgrid(mammals,ptype="species", region="USA", title = "Mammals in California")
mapgrid(mammals,ptype="records", region="USA", title = "Mammals in California")
mapgrid(mammals,ptype="presence", region="USA", title = "Mammals in California")
mammals_mapgrid = bdcomplete(mammals, recs = 5)
mapgrid(mammals_mapgrid, ptype="complete", region="USA", title = "Mammals in California")

I have used the "california-mammals" dataset from (https://www.inaturalist.org/projects/california-mammals) for the above visualizations.