Error in names(output) <- `*vtmp*` : 'names' attribute [1] must be the same length as the vector [0]

[vjjan91]

Hi,

I am currently running into this error using the turnover function.

spTurnover <- turnover(df = turnover_dat, time.var = "year", species.var = "species", abundance.var = "abundance",
replicate.var = "site")

Error in names(output) <- *vtmp* :
'names' attribute [1] must be the same length as the vector [0]

Link to question below:
https://stackoverflow.com/questions/73142397/error-in-namesoutput-vtmp-names-attribute-1-must-be-the-same-leng

Any help would be greatly appreciated!

[pedrosenna]

Hi,

I am currently running into this error using the turnover function.

spTurnover <- turnover(df = turnover_dat, time.var = "year", species.var = "species", abundance.var = "abundance", replicate.var = "site")

Error in names(output) <- *vtmp* : 'names' attribute [1] must be the same length as the vector [0]

Link to question below: https://stackoverflow.com/questions/73142397/error-in-namesoutput-vtmp-names-attribute-1-must-be-the-same-leng

Any help would be greatly appreciated!

Did you find any solution? I am having the same issue.

Edit:

Seems to be a formating problem of the replicate column.

[mbjones]

Hi @pedrosenna --

I am not seeing that error when I run the tests, and there is insufficient information in this ticket to replicate the problem. I suspect it is a problem with your input data not being structured as the function expects, but there is not enough info to tell. If you provide a reprex (reproducible example, see https://stackoverflow.com/a/5963610), it will likely surface the issue right away.

[crobbo27]

Hi pedrosenna and the community.

@pedrosenna did you manage to find a solution? I am experiencing the same problem. Strangely, I subset my dataset (into sediment and water samples) and the sediment samples work no problem, but the water sample subset returns this error....very strange!

R code for reference

`library(codyn)
library(readxl)
library(dplyr)
library(magrittr)
library(tidyr)

#load data
i6s_wide<-read_excel("16S_forcodyn.xlsx")
print(head(i6s_wide))

#Month Type SampleSite ASV_15 ASV_17 ASV_20 ASV_21 ASV_26 ASV_27
#MP1WJa Ja W MP1 164 345 67 0 154 102
#ASV_28 ASV_29 ASV_36 ASV_38 ASV_40 ASV_45 ASV_49 ASV_53 ASV_54
#MP1WJa 0 0 0 67 160 0 0 0 0
#ASV_57 ASV_59 ASV_63 ASV_71 ASV_77 ASV_80 ASV_81 ASV_85 ASV_86
#MP1WJa 0 0 0 85 0 0 13 0 0
#ASV_87 ASV_89 ASV_101 ASV_103 ASV_106 ASV_115 ASV_124 ASV_130
#MP1WJa 0 0 0 0 0 55 0 40
#ASV_139 ASV_152 ASV_154 ASV_155 ASV_174 ASV_178 ASV_182 ASV_191
#MP1WJa 0 0 0 89 95 0 0 0
#ASV_201 ASV_214 ASV_221 ASV_225 ASV_233 ASV_235 ASV_237 ASV_245
#MP1WJa 0 0 0 0 0 0 0 0
#ASV_249 ASV_253 ASV_256 ASV_260 ASV_265 ASV_269 ASV_271 ASV_273
#MP1WJa 0 0 0 0 0 0 17 0
#ASV_276 ASV_284 ASV_285 ASV_287 ASV_289 ASV_293 ASV_296 ASV_299
#MP1WJa 0 0 0 0 0 0 0 0
#ASV_311 ASV_323 ASV_327 ASV_330 ASV_353 ASV_356 ASV_364 ASV_371
#MP1WJa 0 0 0 43 0 0 0 0
#ASV_391 ASV_404 ASV_411 ASV_442 ASV_443 ASV_446 ASV_459 ASV_462
#MP1WJa 0 0 0 45 0 0 72 0
#ASV_463 ASV_466 ASV_490 ASV_506 ASV_508 ASV_527 ASV_530 ASV_548
#MP1WJa 0 0 0 0 0 48 0 0
#ASV_559 ASV_590 ASV_594 ASV_605 ASV_618 ASV_643 ASV_678 ASV_681
#MP1WJa 0 0 0 0 0 0 64 0
#ASV_682 ASV_688 ASV_704 ASV_711 ASV_720 ASV_727 ASV_740 ASV_743
#MP1WJa 0 0 0 0 0 0 0 0

i6s_wide <- i6s_wide %>%
tibble::column_to_rownames("Sample")

i6s_wide<-t(i6s_wide)
i6s_wide<-as.data.frame((i6s_wide))

i6s_long<-i6s_wide %>%
pivot_longer(
cols = starts_with("ASV_"),
names_to = "species",
names_prefix = "",
values_to = "abundance",
values_drop_na = TRUE
)

i6s_long$Month[i6s_long$Month=="Ja"]<-1
i6s_long$Month[i6s_long$Month=="M"]<-2
i6s_long$Month[i6s_long$Month=="Ju"]<-3
i6s_long$Month[i6s_long$Month=="S"]<-4
i6s_long$Month[i6s_long$Month=="N"]<-5

head(i6s_long)
#Month Type SampleSite species abundance
#
#1 1 W MP1 ASV_15 164
#2 1 W MP1 ASV_17 345
#3 1 W MP1 ASV_20 67
#4 1 W MP1 ASV_21 0
#5 1 W MP1 ASV_26 154
#6 1 W MP1 ASV_27 102

str(i6s_long)
i6s_long$Month<-as.numeric(i6s_long$Month)
i6s_long$abundance<-as.numeric(i6s_long$abundance)

str(i6s_long)

i6s_long_s<-subset(i6s_long, Type == "S")
head(i6s_long_s)
#A tibble: 6 × 5
#Month Type SampleSite species abundance

#1 1 S MP1 ASV_15 0
#2 1 S MP1 ASV_17 0
#3 1 S MP1 ASV_20 22
#4 1 S MP1 ASV_21 259
#5 1 S MP1 ASV_26 0
#6 1 S MP1 ASV_27 377

i6s_long_w<-subset(i6s_long, Type == "W")
head(i6s_long_w)
#A tibble: 6 × 5
#Month Type SampleSite species abundance
#
#1 1 W MP1 ASV_15 164
#2 1 W MP1 ASV_17 345
#3 1 W MP1 ASV_20 67
#4 1 W MP1 ASV_21 0
#5 1 W MP1 ASV_26 154
#6 1 W MP1 ASV_27 102

#Sediment
library(codyn)
sed_turnover <- turnover(df = i6s_long_s,
time.var = "Month",
species.var = "species",
abundance.var = "abundance",
replicate.var = "SampleSite")

#Water
wat_turnover <- turnover(df = i6s_long_w,
time.var = "Month",
species.var = "species",
abundance.var = "abundance",
replicate.var = "SampleSite")`

Error message: Error in names(output) <- *vtmp* :
'names' attribute [1] must be the same length as the vector [0]

[lagoodal]

I had this problem and appear to have solved it. The error occurs when your replicate variable only has one timestamp/year. By this I mean that your replicate.var must have at least 2 years from which can calculate the turnover. It didn't work for me until I removed replicates (in my case unique sites) that only had one year within which there was an only one observation.

[mbjones]

Glad you figured it out @lagoodal -- those types of issues are common and require tracking them down with the specific dataset you are using. I suspect the other issues in this thread are similar, but the details will vary. Providing a reprex is key to tracking these down, and the process of distilling the problem down to a reprex often reveals the issue directly.