How to calculate Shannon diversity by factor levels in r

Asked Mar 22 '22 at 11:12

Active Mar 24 '22 at 10:34

Viewed 168 times

I am a newbie with R. I have a large dataset (66M obs) with pixel temperature data of 4 water bodies (REF,LMB, OTH, FP) at hourly time steps (6am,7am,8am...), with several NA values illustrating blank pixels. I want to calculate a proxy for temperature heterogeneity/diversity for each water body at each time, by using Shannon Diversity or other similar indexes. I have so far managed to calculate basic stats using an available online source, but not sure how to apply more specific diversity indexes.

My data looks like: First column Temp, second Time, third water

My code:

DF<-read.csv("DF_total.csv",stringsAsFactors = T)

levels(DF$water)

[1]"OTH" "LMB" "REF" "FP"

levels(DF$time) NULL

source("group_by_summary_stats.R")[**]

summary<-group_by_summary_stats(DF, Temp ,water ,time)

[**]source found online

edited Mar 24 '22 at 10:34

asked Mar 22 '22 at 11:12

RCM

Refer on how to ask reproducible example https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example – Nad Pat Mar 22 '22 at 12:38
Please provide enough code so others can better understand or reproduce the problem. – Community Mar 22 '22 at 12:44
Done, see edited version, thanks! – RCM Mar 22 '22 at 22:32

How to calculate Shannon diversity by factor levels in r

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