origin in guess_dates #73

scottyaz · 2019-05-14T09:44:26Z

It seems like the origin for dates from Excel is dependent on the OS with origin in windows being "1899-12-30" rather than "1900-01-01". Current version of guess_dates() assumes "1900-01-01" if modern excel flag is on.

The text was updated successfully, but these errors were encountered:

zkamvar · 2019-05-14T10:34:32Z

Hi @scottyaz,

Thank you for the info! I completely forgot about that really frustrating curse, which is absolutely NOT documented in their help page on the issue: https://support.office.com/en-us/article/date-systems-in-excel-e7fe7167-48a9-4b96-bb53-5612a800b487

Can you give the output of R.version, so that I can see what version of windows you use?

R.version
#>                _                           
#> platform       x86_64-pc-linux-gnu         
#> arch           x86_64                      
#> os             linux-gnu                   
#> system         x86_64, linux-gnu           
#> status                                     
#> major          3                           
#> minor          6.0                         
#> year           2019                        
#> month          04                          
#> day            26                          
#> svn rev        76424                       
#> language       R                           
#> version.string R version 3.6.0 (2019-04-26)
#> nickname       Planting of a Tree

^{Created on 2019-05-14 by the reprex package (v0.2.1)}

scottyaz · 2019-05-14T10:40:14Z

I am not using windows but the excel file I was using was generated on a windows machine (like most that will come from MoHs). I forked the repo and if I manage to find some time, I’ll try to come up with a solution (though I can’t promise I’ll deliver).

On 14 May 2019, at 12:34, Zhian N. Kamvar wrote: Hi @scottyaz, Thank you for the info! I completely forgot about that really frustrating curse, which is absolutely NOT documented in their help page on the issue: https://support.office.com/en-us/article/date-systems-in-excel-e7fe7167-48a9-4b96-bb53-5612a800b487 Can you give the output of `R.version`, so that I can see what version of windows you use? ``` r R.version #> _ #> platform x86_64-pc-linux-gnu #> arch x86_64 #> os linux-gnu #> system x86_64, linux-gnu #> status #> major 3 #> minor 6.0 #> year 2019 #> month 04 #> day 26 #> svn rev 76424 #> language R #> version.string R version 3.6.0 (2019-04-26) #> nickname Planting of a Tree ``` Created on 2019-05-14 by the [reprex package](https://reprex.tidyverse.org) (v0.2.1) -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #73 (comment)

andrew azman

scottyaz · 2019-05-14T18:23:12Z

I wonder if there is useful meta-data in an excel file (recognising that you expect a data.frame or tidy variant, not an excel file) that can be used to figure out the OS.

xmlInternalTreeParse(unzip('my_linelist.xlsx','xl/workbook.xml')) 

## or
xmlInternalTreeParse(unzip('my_linelist.xlsx','docProps/app.xml'))

Doubt you want to go here but...

zkamvar · 2019-05-15T14:01:48Z

Hi @scottyaz, I definitely do not want to go down the route of attempting to peer into excel files themselves. I've proposed a fix (#74) by changing the modern_excel flag to excel and having three options:

(modern <- as.character(as.integer(as.Date("2019-05-15") - as.Date("1900-01-01"))))
#> [1] "43598"
(oldmac <- as.character(as.integer(as.Date("2019-05-15") - as.Date("1904-01-01"))))
#> [1] "42138"
(oldwin <- as.character(as.integer(as.Date("2019-05-15") - as.Date("1899-12-30"))))
#> [1] "43600"
guess_dates(modern)
#> [1] "2019-05-15"
guess_dates(oldmac, excel = "old-mac")
#> [1] "2019-05-15"
guess_dates(oldwin, excel = "old-win")
#> [1] "2019-05-15"

^{Created on 2019-05-15 by the reprex package (v0.2.1)}

Ultimately, it will be up to the user to know which version of excel their data was created with and include some positive checks to make sure things are working smoothly (especially since these dates can be off by only a few days).

zkamvar · 2019-05-15T14:12:00Z

Let me know if you think this will work, and I'll merge it.

scottyaz · 2019-05-15T14:17:11Z

That is totally reasonable!

zkamvar · 2019-05-15T15:19:50Z

Huh.... I think actually there are only two dates and 1900-01-01 ain't one of them 🤔

Both readxl and janitor use 1899-12-30: https://github.com/tidyverse/readxl/blob/15fde898887a8941bb3839892bf30fa9866290ee/src/utils.h#L7-L40, which has to do with the leap year bug, but it's absolutely not clear to me why it need 12-30 and not 12-31 😩 I'm going to change it back to modern_excel and just change the date to 1899-12-30

scottyaz · 2019-05-24T12:45:56Z

documentation still says 1900-01-01...probably want to update.

scottyaz · 2019-05-24T12:52:48Z

Also, unless I am missing something, still doesn't work properly when the 1899 origin is being used:

old <- as.character(as.integer(as.Date("2019-05-20") - as.Date("1899-12-30"))))
[1] "43605"
guess_dates(oldwin,modern_excel = TRUE) # obviously doesn't give correct answer
[1] "2019-05-22"
guess_dates(old,modern_excel = FALSE)
[1] "43605"
Warning message:
In guess_dates(old, modern_excel = FALSE) : 
The following 1 dates were not in the correct timeframe (1969-05-24 -- 2019-05-24):

  original  |  parsed    
  --------  |  ------    
  43605     |  2023-05-21

zkamvar · 2019-05-24T13:04:52Z

Also, unless I am missing something, still doesn't work properly when the 1899 origin is being used:

This is because it's a contrived example. As I explained in #73 (comment), both readxl and janitor use this system and they both have EXTENSIVE tests. It has something to do with the leap year bug that was introduced in the 90's.

I think I have an excel file lying around somewhere that needed some of this cleaning.... let me check

scottyaz · 2019-05-24T13:06:50Z

I was trying this on real data and couldn't get the correct date and this is why I posted...See what you come up with.

zkamvar · 2019-05-24T13:07:59Z

I hate everything

zkamvar · 2019-05-24T13:08:30Z

Would you mind trying the janitor function and see if it gives you the same shitty result?

zkamvar · 2019-05-24T13:09:01Z

Also, check to make sure you have the latest version of linelist

scottyaz · 2019-05-24T13:10:57Z

Just installed from GitHub so I am pretty sure I do.

On 24 May 2019, at 15:09, Zhian N. Kamvar wrote: Also, check to make sure you have the latest version of linelist -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #73 (comment)

andrew azman

zkamvar · 2019-05-24T13:19:57Z

This is the sheet that has mixed date formats: https://github.com/everhartlab/SscPhenoProj/blob/54c8d75ddb917866e94c06f359f3bc2b61b8de7f/Analysis.R#L194-L207

zkamvar · 2019-05-24T13:48:47Z

For clarity, here is how guess_dates works on a wild excel sheet:

x <- "https://osf.io/2yfre/download"
tmp <- tempdir()
f <- file.path(tmp, "test.xlsx")
download.file(x, f)
ex <- readxl::read_excel(f)
ex
#> # A tibble: 95 x 10
#>    MCG   `AP-GenoID` InventoryID `in-JRS-collect… `AP-Continent_C…
#>    <chr> <chr>       <chr>       <chr>            <chr>           
#>  1 A     143         143         TRUE             North America_U…
#>  2 K     202         202         TRUE             North America_U…
#>  3 K     264         264         TRUE             North America_U…
#>  4 H     265         265         TRUE             North America_U…
#>  5 A     266         266         TRUE             North America_U…
#>  6 I     267         267         TRUE             North America_U…
#>  7 J     268         268         TRUE             North America_U…
#>  8 A     276         276         TRUE             North America_U…
#>  9 K     289         289         TRUE             North America_U…
#> 10 C     293A        293         FALSE            South America_A…
#> # … with 85 more rows, and 5 more variables: `JRS-Isolate #` <chr>,
#> #   `JRS-Collection Date` <chr>, `JRS-Source (Host)` <chr>,
#> #   `JRS-Geographical Location` <chr>, `JRS-Notes` <chr>
ex[["JRS-Collection Date"]]
#>  [1] "1977"     "33117"    "34516"    "34547"    "34547"    "34578"   
#>  [7] "34578"    "35309"    "1996"     "1996"     "1996"     "1996"    
#> [13] "1996"     "1996"     "36373"    "36373"    "41175"    "41175"   
#> [19] "8/1/2009" "8/1/2009" "2012"     "2014"     "2014"     "2014"    
#> [25] "2014"     "2014"     "2012"     "2012"     "2012"     "2012"    
#> [31] "2012"     "2012"     "2012"     "2012"     "2012"     "2010"    
#> [37] "2010"     "2010"     "2010"     "2010"     "2010"     "2010"    
#> [43] "2010"     "2010"     "2010"     "2009"     "2009"     "2009"    
#> [49] "2009"     "2009"     "2009"     "2009"     "2010"     "2010"    
#> [55] "2010"     "2010"     "2010"     "2010"     "NA"       "2012"    
#> [61] "2012"     "2012"     "2012"     "2012"     "2012"     "2012"    
#> [67] "2012"     "2012"     "2012"     "2012"     "2012"     "2012"    
#> [73] "2012"     "2012"     "2012"     "2012"     "2012"     "2012"    
#> [79] "2012"     "2012"     "2012"     "2012"     "2012"     "2012"    
#> [85] "2012"     "2012"     "2012"     "2012"     "2012"     "2012"    
#> [91] "2012"     "2012"     "2012"     "2012"     "2012"
linelist::guess_dates(ex[["JRS-Collection Date"]], err = 1, orders = list("Y", "mdy"))
#>  [1] "1977-01-01" "1990-09-01" "1994-07-01" "1994-08-01" "1994-08-01"
#>  [6] "1994-09-01" "1994-09-01" "1996-09-01" "1996-01-01" "1996-01-01"
#> [11] "1996-01-01" "1996-01-01" "1996-01-01" "1996-01-01" "1999-08-01"
#> [16] "1999-08-01" "2012-09-23" "2012-09-23" "2009-08-01" "2009-08-01"
#> [21] "2012-01-01" "2014-01-01" "2014-01-01" "2014-01-01" "2014-01-01"
#> [26] "2014-01-01" "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01"
#> [31] "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01"
#> [36] "2010-01-01" "2010-01-01" "2010-01-01" "2010-01-01" "2010-01-01"
#> [41] "2010-01-01" "2010-01-01" "2010-01-01" "2010-01-01" "2010-01-01"
#> [46] "2009-01-01" "2009-01-01" "2009-01-01" "2009-01-01" "2009-01-01"
#> [51] "2009-01-01" "2009-01-01" "2010-01-01" "2010-01-01" "2010-01-01"
#> [56] "2010-01-01" "2010-01-01" "2010-01-01" NA           "2012-01-01"
#> [61] "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01"
#> [66] "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01"
#> [71] "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01"
#> [76] "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01"
#> [81] "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01"
#> [86] "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01"
#> [91] "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01" "2012-01-01"

^{Created on 2019-05-24 by the reprex package (v0.3.0)}

zkamvar · 2019-05-24T13:49:20Z

If you compare this to the original sheet, you'll see that the dates have been rendered correctly: https://osf.io/2yfre/

zkamvar · 2019-05-24T13:55:41Z

Also, unless I am missing something, still doesn't work properly when the 1899 origin is being used:

old <- as.character(as.integer(as.Date("2019-05-20") - as.Date("1899-12-30"))))
[1] "43605"
guess_dates(oldwin,modern_excel = TRUE) # obviously doesn't give correct answer
[1] "2019-05-22"
guess_dates(old,modern_excel = FALSE)
[1] "43605"
Warning message:
In guess_dates(old, modern_excel = FALSE) : 
The following 1 dates were not in the correct timeframe (1969-05-24 -- 2019-05-24):

  original  |  parsed    
  --------  |  ------    
  43605     |  2023-05-21

I just noticed, the first iteration you show uses "oldwin" and not "old" as the input. When I try this, I get the following:

old <- as.character(as.integer(as.Date("2019-05-20") - as.Date("1899-12-30")))
linelist::guess_dates(old, modern_excel = TRUE)
#> [1] "2019-05-20"

^{Created on 2019-05-24 by the reprex package (v0.3.0)}

It's an understandable mistake, but please use reprex in the future when making examples.

scottyaz · 2019-05-24T13:58:24Z

Strange…. ``` R> old <- as.character(as.integer(as.Date("2019-05-20") - as.Date("1899-12-30"))) R> linelist::guess_dates(old, modern_excel = TRUE) [1] "2019-05-22" ```

On 24 May 2019, at 15:55, Zhian N. Kamvar wrote: > Also, unless I am missing something, still doesn't work properly when the 1899 origin is being used: > > ``` > old <- as.character(as.integer(as.Date("2019-05-20") - > as.Date("1899-12-30")))) > [1] "43605" > guess_dates(oldwin,modern_excel = TRUE) # obviously doesn't give > correct answer > [1] "2019-05-22" > guess_dates(old,modern_excel = FALSE) > [1] "43605" > Warning message: > In guess_dates(old, modern_excel = FALSE) : > The following 1 dates were not in the correct timeframe (1969-05-24 > -- 2019-05-24): > > original | parsed > -------- | ------ > 43605 | 2023-05-21 > ``` I just noticed, the first iteration you show uses "oldwin" and not "old" as the input. When I try this, I get the following: ``` r old <- as.character(as.integer(as.Date("2019-05-20") - as.Date("1899-12-30"))) linelist::guess_dates(old, modern_excel = TRUE) #> [1] "2019-05-20" ``` Created on 2019-05-24 by the [reprex package](https://reprex.tidyverse.org) (v0.3.0) It's an understandable mistake, but please use reprex in the future when making examples. -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #73 (comment)

andrew azman

zkamvar · 2019-05-24T14:00:34Z

Can you post the package description?

packageDescription("linelist")
#> Package: linelist
#> Title: Tools to Import and Tidy Case Linelist Data
#> Version: 0.0.33.9000
#> Authors@R: c(person("Thibaut", "Jombart", email =
#>        "thibautjombart@gmail.com", role = c("aut", "cre")),
#>        person("Zhian N.", "Kamvar", email = "zkamvar@gmail.com",
#>        role = c("aut")))
#> Description: A collection of wrappers for importing case linelist
#>        data from usual formats, and tools for cleaning data,
#>        detecting dates, and storing meta-information on the
#>        content of the resulting data frame.
#> Depends: R (>= 3.0.0)
#> License: MIT + file LICENSE
#> Encoding: UTF-8
#> LazyData: true
#> Suggests: outbreaks, incidence, testthat, knitr, roxygen2, covr,
#>        tibble, dplyr, magrittr
#> RoxygenNote: 6.1.1
#> Imports: lubridate, rio, epitrix, tidyselect, rlang, forcats,
#>        utils, stats, crayon
#> URL: https://github.com/reconhub/linelist
#> BugReports: https://github.com/reconhub/linelist/issues
#> VignetteBuilder: knitr
#> Roxygen: list(markdown = TRUE)
#> RemoteType: github
#> RemoteHost: api.github.com
#> RemoteRepo: linelist
#> RemoteUsername: reconhub
#> RemoteRef: master
#> RemoteSha: fda9e18b02f5853cd311ddcc513c427244b21dd7
#> GithubRepo: linelist
#> GithubUsername: reconhub
#> GithubRef: master
#> GithubSHA1: fda9e18b02f5853cd311ddcc513c427244b21dd7
#> NeedsCompilation: no
#> Packaged: 2019-05-24 13:12:12 UTC; zkamvar
#> Author: Thibaut Jombart [aut, cre], Zhian N. Kamvar [aut]
#> Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
#> Built: R 3.6.0; ; 2019-05-24 13:12:13 UTC; unix
#> 
#> -- File: /home/zkamvar/Documents/RLibrary/linelist/Meta/package.rds

^{Created on 2019-05-24 by the reprex package (v0.3.0)}

scottyaz · 2019-05-24T14:06:54Z

``` R> packageDescription("linelist") Package: linelist Title: Tools to Import and Tidy Case Linelist Data Version: 0.0.33.9000 Authors@R: c(person("Thibaut", "Jombart", email = "thibautjombart@gmail.com", role = c("aut", "cre")), person("Zhian N.", "Kamvar", email = "zkamvar@gmail.com", role = c("aut"))) Description: A collection of wrappers for importing case linelist data from usual formats, and tools for cleaning data, detecting dates, and storing meta-information on the content of the resulting data frame. Depends: R (>= 3.0.0) License: MIT + file LICENSE Encoding: UTF-8 LazyData: true Suggests: outbreaks, incidence, testthat, knitr, roxygen2, covr, tibble, dplyr, magrittr RoxygenNote: 6.1.1 Imports: lubridate, rio, epitrix, tidyselect, rlang, forcats, utils, stats, crayon URL: https://github.com/reconhub/linelist BugReports: https://github.com/reconhub/linelist/issues VignetteBuilder: knitr Roxygen: list(markdown = TRUE) RemoteType: github RemoteHost: api.github.com RemoteRepo: linelist RemoteUsername: reconhub RemoteRef: master RemoteSha: fda9e18 GithubRepo: linelist GithubUsername: reconhub GithubRef: master GithubSHA1: fda9e18 NeedsCompilation: no Packaged: 2019-05-24 14:04:18 UTC; andrewa Author: Thibaut Jombart [aut, cre], Zhian N. Kamvar [aut] Maintainer: Thibaut Jombart <thibautjombart@gmail.com> Built: R 3.5.2; ; 2019-05-24 14:04:18 UTC; unix

-- File: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/linelist/Meta/package.rds ``` I wonder if it is something about dependency versions? ``` R> sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.3 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib 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] linelist_0.0.33.9000 stringr_1.4.0 aweek_0.2.0 tidyr_0.8.3 [5] here_0.1 dplyr_0.8.0.1 readr_1.3.1 readxl_1.3.1 [9] pacman_0.5.1 loaded via a namespace (and not attached): [1] tidyselect_0.2.5 remotes_2.0.2 purrr_0.3.1 haven_2.1.0 usethis_1.4.0 [6] yaml_2.2.0 utf8_1.1.4 rlang_0.3.1 pkgbuild_1.0.2 pillar_1.3.1 [11] foreign_0.8-71 glue_1.3.0 withr_2.1.2 sessioninfo_1.1.1 cellranger_1.1.0 [16] zip_2.0.1 devtools_2.0.1 memoise_1.1.0 rio_0.5.16 forcats_0.4.0 [21] callr_3.1.1 ps_1.3.0 curl_3.3 fansi_0.4.0 Rcpp_1.0.0 [26] backports_1.1.3 desc_1.2.0 pkgload_1.0.2 fs_1.2.6 hms_0.4.2 [31] digest_0.6.18 stringi_1.3.1 openxlsx_4.1.0 processx_3.2.1 rprojroot_1.3-2 [36] cli_1.0.1 tools_3.5.2 magrittr_1.5 tibble_2.0.1 crayon_1.3.4 [41] pkgconfig_2.0.2 data.table_1.12.0 prettyunits_1.0.2 lubridate_1.7.4 assertthat_0.2.0 [46] rstudioapi_0.9.0 R6_2.4.0 compiler_3.5.2 git2r_0.24.0 ```

On 24 May 2019, at 16:00, Zhian N. Kamvar wrote: Can you post the package description? ``` r packageDescription("linelist") #> Package: linelist #> Title: Tools to Import and Tidy Case Linelist Data #> Version: 0.0.33.9000 #> ***@***.***: c(person("Thibaut", "Jombart", email = #> ***@***.***", role = c("aut", "cre")), #> person("Zhian N.", "Kamvar", email = ***@***.***", #> role = c("aut"))) #> Description: A collection of wrappers for importing case linelist #> data from usual formats, and tools for cleaning data, #> detecting dates, and storing meta-information on the #> content of the resulting data frame. #> Depends: R (>= 3.0.0) #> License: MIT + file LICENSE #> Encoding: UTF-8 #> LazyData: true #> Suggests: outbreaks, incidence, testthat, knitr, roxygen2, covr, #> tibble, dplyr, magrittr #> RoxygenNote: 6.1.1 #> Imports: lubridate, rio, epitrix, tidyselect, rlang, forcats, #> utils, stats, crayon #> URL: https://github.com/reconhub/linelist #> BugReports: https://github.com/reconhub/linelist/issues #> VignetteBuilder: knitr #> Roxygen: list(markdown = TRUE) #> RemoteType: github #> RemoteHost: api.github.com #> RemoteRepo: linelist #> RemoteUsername: reconhub #> RemoteRef: master #> RemoteSha: fda9e18 #> GithubRepo: linelist #> GithubUsername: reconhub #> GithubRef: master #> GithubSHA1: fda9e18 #> NeedsCompilation: no #> Packaged: 2019-05-24 13:12:12 UTC; zkamvar #> Author: Thibaut Jombart [aut, cre], Zhian N. Kamvar [aut] #> Maintainer: Thibaut Jombart ***@***.***> #> Built: R 3.6.0; ; 2019-05-24 13:12:13 UTC; unix #> #> -- File: /home/zkamvar/Documents/RLibrary/linelist/Meta/package.rds ``` Created on 2019-05-24 by the [reprex package](https://reprex.tidyverse.org) (v0.3.0) -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #73 (comment)

andrew azman

zkamvar · 2019-05-24T14:12:52Z

The only think I can think of why there would be a discrepancy is that you may have an unclean R session. Can you restart R and try again?

scottyaz · 2019-05-24T17:13:23Z

arggggg. i'll shut up now.

zkamvar self-assigned this May 14, 2019

zkamvar added the bug Something isn't working label May 14, 2019

zkamvar added a commit that referenced this issue May 15, 2019

change excel argument to address #73

f5b775c

zkamvar mentioned this issue May 15, 2019

Speedup guess dates #74

Merged

zkamvar closed this as completed in 00f0e3d May 15, 2019

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origin in guess_dates #73

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