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R Error in periodicity(x) : can not calculate periodicity of 1 observation #161

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Austik-d2d4 opened this issue Dec 15, 2016 · 9 comments
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R Error in periodicity(x) : can not calculate periodicity of 1 observation #161

Austik-d2d4 opened this issue Dec 15, 2016 · 9 comments

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@Austik-d2d4
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Austik-d2d4 commented Dec 15, 2016 •
edited by joshuaulrich
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I am working on a bit of code from my colleague but I get stuck in a specific part

library(xts)
accepted_xts <- structure(c("9d67c252-6aa4-429d-857d-6d2e4582f08c",
"9bf6a07a-abcf-41aa-a5a7-35de7e285210", "c974ac6d-758e-46bc-97b7-4e484f6ed890",
"dc47ce83-0de9-4cf7-9961-80c4f2bbe81b", "86d4a7a9-9f17-42e1-b2c3-4f7647984a55",
"d5e581eb-3d89-45b7-a918-8486632cb833", "2016-01-09", "2016-01-09",
"2016-01-09", "2016-01-09", "2016-01-09", "2016-01-09", "2016-09-04 00:00:02.1",
"2016-09-06 06:09:19.14", "2016-09-12 09:59:25.13", "2016-09-06 06:09:29.917",
"2016-09-04 00:00:25.819", "2016-09-04 00:00:20.524", NA, NA, NA, NA, NA, NA,
"1", "1", "1", "1", "1", "1", "65ae2bb4-bbff-44fa-87da-225be9c5bd55",
"65ae2bb4-bbff-44fa-87da-225be9c5bd55", "f98a8658-d1c1-46e6-8bbf-e32847663c83",
"ff98ab3a-0199-43f5-bd4e-2a5499d128ba", "ff98ab3a-0199-43f5-bd4e-2a5499d128ba",
"70e9b946-6a5f-463b-a55e-cab23f5b3b51", "f8da29ba-6f38-43b6-a4bd-52aa1f022cec",
"f8da29ba-6f38-43b6-a4bd-52aa1f022cec", "ae94e9f4-d924-43ee-afd6-f25473ec952f", 
"f8da29ba-6f38-43b6-a4bd-52aa1f022cec", "f8da29ba-6f38-43b6-a4bd-52aa1f022cec", 
"f8da29ba-6f38-43b6-a4bd-52aa1f022cec", "e4d2ff73-0d6d-4eac-bc9d-8d780e612dc0", 
"ebada61d-2cef-421d-bb43-53a3546b6c6b", "12f174c9-9952-4f89-9392-a08b46f97c8c", 
"ebada61d-2cef-421d-bb43-53a3546b6c6b", "e4d2ff73-0d6d-4eac-bc9d-8d780e612dc0", 
"e4d2ff73-0d6d-4eac-bc9d-8d780e612dc0"), .indexCLASS = "Date",
tclass = "Date", .indexTZ = "UTC", tzone = "UTC", class = c("xts", "zoo"),
index = structure(c(1452297600, 1452297600, 1452297600, 1452297600, 1452297600,
1452297600), tzone = "UTC", tclass = "Date"), .Dim = c(6L, 8L),
.Dimnames = list(NULL, c("id", "created_at", "updated_at", "deleted_at",
"status", "role_id", "user_id", "email_id")))

last1Week_accepted_xts  <- last(accepted_xts[,], "1 week")
last2weeks_accepted_xts <- last(accepted_xts[,], "2 week")
last3weeks_accepted_xts <- last(accepted_xts[,], "3 week")

I constantly get this error and I don't know how to solve it

Error in periodicity(x) : can not calculate periodicity of 1 observation
@joshuaulrich
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I cannot replicate. Please provide the output from sessionInfo().

@Austik-d2d4
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Sure thing, here we go. Thanks in advance.

> sessionInfo(NULL)
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] lubridate_1.6.0      devtools_1.12.0      shiny_0.14.2         ISOweek_0.6-2        rpivotTable_0.1.5.20
 [6] RPostgreSQL_0.4-1    DBI_0.5-13           googleVis_0.6.1      reshape_0.8.6        xts_0.9-7           
[11] zoo_1.7-13           data.table_1.10.0    stringr_1.1.0        dplyr_0.5.0          ggplot2_2.2.0       
[16] knitr_1.15.1         flexdashboard_0.3   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8.2    git2r_0.16.0     plyr_1.8.4       RPostgres_0.1-2  tools_3.3.2      digest_0.6.10   
 [7] jsonlite_1.1     evaluate_0.10    memoise_1.0.0    tibble_1.2       gtable_0.2.0     lattice_0.20-34 
[13] curl_2.3         httr_1.2.1       withr_1.0.2      htmlwidgets_0.8  rprojroot_1.1    grid_3.3.2      
[19] R6_2.2.0         rmarkdown_1.2    magrittr_1.5     backports_1.0.4  scales_0.4.1     codetools_0.2-15
[25] htmltools_0.3.5  assertthat_0.1   xtable_1.8-2     mime_0.5         colorspace_1.3-1 httpuv_1.3.3    
[31] stringi_1.1.2    lazyeval_0.2.0   munsell_0.4.3

@joshuaulrich
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I still can't replicate, even with data.table and dplyr loaded. Can you run the code below in a R session with zero non-base packages loaded (other than xts and zoo)?

library(xts)
accepted_xts <- structure(c("9d67c252-6aa4-429d-857d-6d2e4582f08c",
"9bf6a07a-abcf-41aa-a5a7-35de7e285210", "c974ac6d-758e-46bc-97b7-4e484f6ed890",
"dc47ce83-0de9-4cf7-9961-80c4f2bbe81b", "86d4a7a9-9f17-42e1-b2c3-4f7647984a55",
"d5e581eb-3d89-45b7-a918-8486632cb833", "2016-01-09", "2016-01-09",
"2016-01-09", "2016-01-09", "2016-01-09", "2016-01-09", "2016-09-04 00:00:02.1",
"2016-09-06 06:09:19.14", "2016-09-12 09:59:25.13", "2016-09-06 06:09:29.917",
"2016-09-04 00:00:25.819", "2016-09-04 00:00:20.524", NA, NA, NA, NA, NA, NA,
"1", "1", "1", "1", "1", "1", "65ae2bb4-bbff-44fa-87da-225be9c5bd55",
"65ae2bb4-bbff-44fa-87da-225be9c5bd55", "f98a8658-d1c1-46e6-8bbf-e32847663c83",
"ff98ab3a-0199-43f5-bd4e-2a5499d128ba", "ff98ab3a-0199-43f5-bd4e-2a5499d128ba",
"70e9b946-6a5f-463b-a55e-cab23f5b3b51", "f8da29ba-6f38-43b6-a4bd-52aa1f022cec",
"f8da29ba-6f38-43b6-a4bd-52aa1f022cec", "ae94e9f4-d924-43ee-afd6-f25473ec952f", 
"f8da29ba-6f38-43b6-a4bd-52aa1f022cec", "f8da29ba-6f38-43b6-a4bd-52aa1f022cec", 
"f8da29ba-6f38-43b6-a4bd-52aa1f022cec", "e4d2ff73-0d6d-4eac-bc9d-8d780e612dc0", 
"ebada61d-2cef-421d-bb43-53a3546b6c6b", "12f174c9-9952-4f89-9392-a08b46f97c8c", 
"ebada61d-2cef-421d-bb43-53a3546b6c6b", "e4d2ff73-0d6d-4eac-bc9d-8d780e612dc0", 
"e4d2ff73-0d6d-4eac-bc9d-8d780e612dc0"), .indexCLASS = "Date",
tclass = "Date", .indexTZ = "UTC", tzone = "UTC", class = c("xts", "zoo"),
index = structure(c(1452297600, 1452297600, 1452297600, 1452297600, 1452297600,
1452297600), tzone = "UTC", tclass = "Date"), .Dim = c(6L, 8L),
.Dimnames = list(NULL, c("id", "created_at", "updated_at", "deleted_at",
"status", "role_id", "user_id", "email_id")))

last1Week_accepted_xts  <- last(accepted_xts[,], "1 week")
last2weeks_accepted_xts <- last(accepted_xts[,], "2 week")
last3weeks_accepted_xts <- last(accepted_xts[,], "3 week")
traceback()
sessionInfo()

@Austik-d2d4
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I cannot run the code if I detach RPostgreSQL because the data is retrieved from a DB.
Checking the dataset I noticed that there are NA. Look here and the head is different from the tail.

> head(accepted_xts)
           id                                     created_at   updated_at                deleted_at status
2016-01-09 "9d67c252-6aa4-429d-857d-6d2e4582f08c" "2016-01-09" "2016-09-04 00:00:02.1"   NA         "1"   
2016-01-09 "9bf6a07a-abcf-41aa-a5a7-35de7e285210" "2016-01-09" "2016-09-06 06:09:19.14"  NA         "1"   
2016-01-09 "c974ac6d-758e-46bc-97b7-4e484f6ed890" "2016-01-09" "2016-09-12 09:59:25.13"  NA         "1"   
2016-01-09 "dc47ce83-0de9-4cf7-9961-80c4f2bbe81b" "2016-01-09" "2016-09-06 06:09:29.917" NA         "1"   
2016-01-09 "86d4a7a9-9f17-42e1-b2c3-4f7647984a55" "2016-01-09" "2016-09-04 00:00:25.819" NA         "1"   
2016-01-09 "d5e581eb-3d89-45b7-a918-8486632cb833" "2016-01-09" "2016-09-04 00:00:20.524" NA         "1"   
           role_id                                user_id                               
2016-01-09 "65ae2bb4-bbff-44fa-87da-225be9c5bd55" "f8da29ba-6f38-43b6-a4bd-52aa1f022cec"
2016-01-09 "65ae2bb4-bbff-44fa-87da-225be9c5bd55" "f8da29ba-6f38-43b6-a4bd-52aa1f022cec"
2016-01-09 "f98a8658-d1c1-46e6-8bbf-e32847663c83" "ae94e9f4-d924-43ee-afd6-f25473ec952f"
2016-01-09 "ff98ab3a-0199-43f5-bd4e-2a5499d128ba" "f8da29ba-6f38-43b6-a4bd-52aa1f022cec"
2016-01-09 "ff98ab3a-0199-43f5-bd4e-2a5499d128ba" "f8da29ba-6f38-43b6-a4bd-52aa1f022cec"
2016-01-09 "70e9b946-6a5f-463b-a55e-cab23f5b3b51" "f8da29ba-6f38-43b6-a4bd-52aa1f022cec"
           email_id                               group_id                              
2016-01-09 "e4d2ff73-0d6d-4eac-bc9d-8d780e612dc0" "3ff59ec0-aabf-4a23-9eac-ca1d0a60c685"
2016-01-09 "ebada61d-2cef-421d-bb43-53a3546b6c6b" "3ff59ec0-aabf-4a23-9eac-ca1d0a60c685"
2016-01-09 "12f174c9-9952-4f89-9392-a08b46f97c8c" "a1643f20-e5cb-4499-a3d3-a85f334a4133"
2016-01-09 "ebada61d-2cef-421d-bb43-53a3546b6c6b" "e096c24a-dd27-4cb3-81b7-0138c86610d2"
2016-01-09 "e4d2ff73-0d6d-4eac-bc9d-8d780e612dc0" "e096c24a-dd27-4cb3-81b7-0138c86610d2"
2016-01-09 "e4d2ff73-0d6d-4eac-bc9d-8d780e612dc0" "bc3d5df7-8a78-4bae-9dd2-
f20171fcba80"

> tail(accepted_xts)
     id                                     created_at updated_at                   deleted_at status
<NA> "a89412aa-c6f7-4f2a-9abb-94e6081d66e9" NA         "2016-12-14 13:45:10.601569" NA         "1"   
<NA> "cce0548d-50af-4916-a95e-318ec91c9c84" NA         "2016-12-14 14:03:43.924224" NA         "1"   
<NA> "6b7b11bd-1bcf-4734-8aa1-7585e4a34888" NA         "2016-12-14 14:28:40.324394" NA         "1"   
<NA> "c02e75a8-b3bb-4ff1-be5d-aaec5d82f865" NA         "2016-12-15 09:25:48.833265" NA         "1"   
<NA> "46112cd2-a9cb-4691-bff2-73603c8d4207" NA         "2016-12-15 11:57:30.263413" NA         "1"   
<NA> "7e3143cf-3bd7-49a7-9cc5-7d744eb4ba2f" NA         "2016-12-15 15:19:14.226456" NA         "1"   
     role_id                                user_id                                email_id                              
<NA> "2cdd0a5b-4745-4886-ae1c-dfd71f94a08a" "7aad1b26-b1df-414c-9815-7e07eecb8d70" "7c129191-efa8-4a5e-af0c-fedbdf2f7833"
<NA> "2cdd0a5b-4745-4886-ae1c-dfd71f94a08a" "9276480d-d933-4a87-89a4-cc1dfce2b1fa" "0ab1731d-58ea-4eac-8980-7fe6e62456cf"
<NA> "8145e21b-138b-4d97-b2d2-5933ddeb8e99" "8dce3723-1d3d-4b48-aea8-25014e10f48f" "5ffb7a74-1b65-4956-a2a1-d8a0fdb32439"
<NA> "9a842798-dad1-4601-b2b9-a4ee327362da" "f8da29ba-6f38-43b6-a4bd-52aa1f022cec" "e6bf117d-cb7f-4536-ad42-8124ebd1f94c"
<NA> "e648a2d7-7fe5-4a43-89a8-858a94f560d4" "353f60e8-7a79-452a-bbb4-54f4f1e5ccaa" "b2e4861a-b174-4d23-a1ad-ac4c197b9359"
<NA> "9a842798-dad1-4601-b2b9-a4ee327362da" "8dce3723-1d3d-4b48-aea8-25014e10f48f" "4870c4e2-cdc6-4689-8a37-73c0605fabba"
     group_id                              
<NA> "321fbf6a-1df5-4f81-a475-57cc20abd1e6"
<NA> "321fbf6a-1df5-4f81-a475-57cc20abd1e6"
<NA> "32c0d250-5900-453d-acd0-863ec82b8ad4"
<NA> "a4b6c13f-1759-48c0-aca2-c40cffb8d06f"
<NA> "2b6b20f1-81c7-4379-801e-0f114b51be3a"
<NA> "a4b6c13f-1759-48c0-aca2-c40cffb8d06f"

@DarrenCook
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DarrenCook commented Dec 15, 2016 •
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(BTW, this might've been more appropriate on StackOverflow?)

I just tested this in a fresh R session and get a different message:

> last1Week_accepted_xts   <-  last(accepted_xts[,],"1 week")
> last2weeks_accepted_xts  <-  last(accepted_xts[,],"2 week")
Warning message:
In last.xts(accepted_xts[, ], "2 week") :
  requested length is greater than original
> last3weeks_accepted_xts  <-  last(accepted_xts[,],"3 week")
Warning message:
In last.xts(accepted_xts[, ], "3 week") :
  requested length is greater than original

(However, it is just a warning, and I do get the expected data in there.)

I removed the redundant [,] and it is the same. And "week" and "weeks" give same results.

R 3.2.5, xts_0.9.874, zoo_1.7-12. env is en_GB.UTF-8.

I also did this test:

> endpoints(accepted_xts,on="weeks")
[1] 0 6
> endpoints(accepted_xts,on="weeks",k=1)
[1] 0 6
> endpoints(accepted_xts,on="weeks",k=2)
[1] 0 6
> endpoints(accepted_xts,on="weeks",k=3)
[1] 0 6

However, looking at xts:::last.xts, it is not using the k argument. (Why?)

@joshuaulrich
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@alex929 the NA in the index are likely the cause of the error.

R> last(.xts(1:10, c(1:7,NA,NA,NA)), 'second')
Error in periodicity(x) : can not calculate periodicity of 1 observation

You need to determine why they are there. What command do you use to create the accepted_xts object? Are you calling the xts() constructor, or are you calling as.xts on an object?

@DarrenCook I noticed that warning too. It's not clear to me what the logic that causes it is doing. I'd have to spend some time looking at it before I would be comfortable making any changes. And since it's just a warning and the returned data are correct, fixing it is not a high priority for me.

@Austik-d2d4
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Austik-d2d4 commented Dec 15, 2016 •
edited
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@joshuaulrich I used xts() constructor as you can see in the bit of code.

library(xts)
idx <- invitations_accepted$created_at
accepted_xts <- xts(invitations_accepted, order.by= idx)

last1Week_accepted_xts <- last(accepted_xts[,], "1 week") 
last2weeks_accepted_xts<- last(accepted_xts[,], "2 week") 
last3weeks_accepted_xts<- last(accepted_xts[,], "3 week")

@DarrenCook I think that it worked because in the minimal dataset you used there were no NA, if you try the same with the head() and tail() I have added I think you should get the same error as me.

@joshuaulrich
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@alex929, then I assume there are NA in invitations_accepted$created_at. The index should not have NA. I'll look into adding a check for that in the xts() constructor.

@joshuaulrich
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Closing, since this issue is now covered by the fixes in #173 and #174.

@joshuaulrich joshuaulrich mentioned this issue Mar 21, 2018
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@DarrenCook @joshuaulrich @Austik-d2d4