Hello,
I am stumped by a data summarising problem.
My data consists of a list (long-format) of species that have been identified from samples collected on same day. I need to calculate number of animals collected each day, and number of species collected each day, and a summary of species collected each day.
Problem: number of samples per day are variable ("labno", below), ranging from one to three. How do I count the number of samples per day to calculate these statistics?
My code is throwing an error, because 'labno" is a factor. Do I flip the data from long to wide-format? Or is there a more simple method?
Data and code below.
thanks!
df<- tibble::tribble(
~date, ~site, ~labno, ~GenusSpecies, ~Tally,
"5/27/2008", "loc-6", 109072L, "Caenis sp.", 1L,
"5/27/2008", "loc-6", 109072L, "Chironomus sp.", 1L,
"5/27/2008", "loc-6", 109071L, "Chironomus sp.", 1L,
"5/27/2008", "loc-6", 109072L, "FAMILY: COENAGRIONIDAE", 1L,
"5/27/2008", "loc-6", 109071L, "Haemonais waldvogeli", 1L,
"5/27/2008", "loc-6", 109071L, "Laevapex sp.", 1L,
"5/27/2008", "loc-6", 109070L, "Micromenetus dilatatus dilatus", 1L,
"5/27/2008", "loc-6", 109071L, "SUBFAMILY: NAIDINAE", 1L,
"5/27/2008", "loc-6", 109072L, "SUBFAMILY: NAIDINAE", 1L,
"5/27/2008", "loc-6", 109070L, "Zavreliella marmorata", 4L,
"5/27/2008", "loc-6", 109071L, "Zavreliella marmorata", 1L,
"6/2/2008", "loc-21", 109721L, "Ablabesmyia mallochi", 3L,
"6/2/2008", "loc-21", 109720L, "Ablabesmyia mallochi", 3L,
"6/2/2008", "loc-21", 109720L, "Ablabesmyia rhamphe grp.", 3L,
"6/2/2008", "loc-21", 109721L, "Ablabesmyia rhamphe grp.", 8L,
"6/2/2008", "loc-21", 109719L, "Ablabesmyia sp.", 1L,
"6/2/2008", "loc-21", 109721L, "Arrenurus sp.", 5L,
"6/2/2008", "loc-21", 109720L, "Cernotina sp.", 1L,
"6/2/2008", "loc-21", 109719L, "Cernotina sp.", 1L,
"6/2/2008", "loc-21", 109721L, "Cernotina sp.", 1L,
"6/2/2008", "loc-21", 109720L, "Chironomus sp.", 1L,
"6/2/2008", "loc-21", 109721L, "Cryptochironomus sp.", 2L,
"6/2/2008", "loc-21", 109720L, "Cryptochironomus sp.", 1L,
"6/2/2008", "loc-21", 109721L, "Dicrotendipes simpsoni", 9L,
"6/2/2008", "loc-21", 109721L, "Dicrotendipes sp.", 2L,
"6/2/2008", "loc-21", 109721L, "FAMILY: ANCYLIDAE", 1L,
"6/2/2008", "loc-21", 109720L, "FAMILY: CERATOPOGONIDAE", 1L,
"6/2/2008", "loc-21", 109719L, "FAMILY: COENAGRIONIDAE", 1L,
"6/2/2008", "loc-21", 109719L, "FAMILY: HEPTAGENIIDAE", 1L,
"6/2/2008", "loc-21", 109721L, "FAMILY: HEPTAGENIIDAE", 1L,
"6/2/2008", "loc-21", 109720L, "Glyptotendipes sp.", 1L,
"6/2/2008", "loc-21", 109720L, "Goeldichironomus sp.", 1L,
"6/2/2008", "loc-21", 109721L, "Hebetancylus excentricus", 1L,
"6/2/2008", "loc-21", 109721L, "Hyalella azteca complex", 43L,
"6/2/2008", "loc-21", 109719L, "Hyalella azteca complex", 18L,
"6/2/2008", "loc-21", 109720L, "Hyalella azteca complex", 26L,
"6/2/2008", "loc-21", 109721L, "Kiefferulus sp.", 2L,
"6/2/2008", "loc-21", 109721L, "Labrundinia sp.", 1L,
"6/2/2008", "loc-21", 109719L, "Maccaffertium sp.", 5L,
"6/2/2008", "loc-21", 109721L, "Nilothauma sp.", 1L,
"6/2/2008", "loc-21", 109720L, "Nilothauma sp.", 1L,
"6/2/2008", "loc-21", 109720L, "Oecetis cinerascens", 1L,
"6/2/2008", "loc-21", 109719L, "Oecetis cinerascens", 1L,
"6/2/2008", "loc-21", 109721L, "Oecetis sp.", 1L,
"6/2/2008", "loc-21", 109721L, "ORDER: ACARIFORMES", 1L,
"6/2/2008", "loc-21", 109721L, "Paralauterborniella nigrohalteralis", 2L,
"6/2/2008", "loc-21", 109720L, "Paralauterborniella nigrohalteralis", 1L,
"6/2/2008", "loc-21", 109721L, "Paranyctiophylax sp.", 9L,
"6/2/2008", "loc-21", 109720L, "Paranyctiophylax sp.", 15L,
"6/2/2008", "loc-21", 109719L, "Paranyctiophylax sp.", 8L,
"6/2/2008", "loc-21", 109721L, "Pentaneura inconspicua", 1L,
"6/2/2008", "loc-21", 109721L, "Polypedilum fallax grp.", 17L,
"6/2/2008", "loc-21", 109720L, "Polypedilum fallax grp.", 4L,
"6/2/2008", "loc-21", 109719L, "Polypedilum scalaenum grp.", 3L,
"6/2/2008", "loc-21", 109720L, "Polypedilum scalaenum grp.", 16L,
"6/2/2008", "loc-21", 109721L, "Polypedilum scalaenum grp.", 32L,
"6/2/2008", "loc-21", 109721L, "Polypedilum sp.", 2L,
"6/2/2008", "loc-21", 109721L, "Procladius sp.", 1L,
"6/2/2008", "loc-21", 109720L, "Slavina appendiculata", 2L,
"6/2/2008", "loc-21", 109720L, "Stenacron sp.", 2L,
"6/2/2008", "loc-21", 109719L, "Stenochironomus sp.", 7L,
"6/2/2008", "loc-21", 109720L, "Stenochironomus sp.", 30L,
"6/2/2008", "loc-21", 109721L, "SUBFAMILY: CHIRONOMINAE", 5L,
"6/2/2008", "loc-21", 109720L, "SUBFAMILY: CHIRONOMINAE", 3L,
"6/2/2008", "loc-21", 109719L, "SUBFAMILY: CHIRONOMINAE", 1L,
"6/2/2008", "loc-21", 109720L, "SUBFAMILY: NAIDINAE", 1L,
"6/2/2008", "loc-21", 109720L, "Tanytarsus sp.", 3L,
"6/2/2008", "loc-21", 109719L, "Tanytarsus sp.", 1L,
"6/2/2008", "loc-21", 109721L, "Tanytarsus sp.", 5L,
"6/2/2008", "loc-21", 109719L, "Tanytarsus sp. A", 2L,
"6/2/2008", "loc-21", 109720L, "Tanytarsus sp. A", 20L,
"6/2/2008", "loc-21", 109720L, "Tanytarsus sp. C", 3L,
"6/2/2008", "loc-21", 109720L, "Tanytarsus sp. L", 1L,
"6/2/2008", "loc-21", 109720L, "Tribelos sp.", 1L,
"6/2/2008", "loc-21", 109719L, "Tribelos sp.", 1L
)
df$date <- as.Date(macros$date, format = "%m/%d/%Y")
#> Error in as.Date(macros$date, format = "%m/%d/%Y"): object 'macros' not found
df$site <- as.factor(df$site)
df$labno <- as.factor(df$labno)
df$GenusSpecies <-as.factor(df$GenusSpecies)
output <- df %>%
group_by(site, date, labno) %>%
# group_by(site, date, labno, GenusSpecies) %>%
summarise(counts = sum(Tally),
reps = count(labno),
means = counts/reps)
#> Error in df %>% group_by(site, date, labno) %>% summarise(counts = sum(Tally), : could not find function "%>%"
Created on 2023-03-29 by the reprex package (v2.0.1)