zkamvar
commented
5 years ago That is most certainly and without a doubt a bug! I will get to this as soon as I get back from holiday.
Sent from my iPhone
On Apr 19, 2019, at 10:16, Alex Spina notifications@github.com wrote:
hey - @epiamsterdam trying to run cholera template on data from mozambique. Runs in to this error:
linelist_cleaned$epiweek <- aweek::date2week(linelist_cleaned$date_of_onset, week_start = "Monday", floor_day = TRUE, factor = TRUE) Error in charToDate(x) : character string is not in a standard unambiguous format
It is a date and seems normal, but has NAs:
class(linelist_cleaned$date_of_onset) [1] "Date" head(linelist_cleaned$date_of_onset, 20) [1] "2019-04-08" "2019-04-08" "2019-04-08" "2019-04-09" "2019-04-03" "2019-04-03" "2019-04-04" "2019-04-04" [9] "2019-04-04" "2019-04-04" NA NA NA "2019-04-09" "2019-04-09" "2019-04-08" [17] NA NA NA NA
The NAs seem to be recognised normally though:
table(is.na(linelist_cleaned$date_of_onset)) FALSE TRUE 2903 1408
If you run date2week, without factor = TRUE, it works, but produces funky looking NAs
aweek::date2week(linelist_cleaned$date_of_onset, week_start = "Monday", floor_day = TRUE )
[1] "2019-W15" "2019-W15" "2019-W15" "2019-W15" "2019-W14" "2019-W14" "2019-W14" [8] "2019-W14" "2019-W14" "2019-W14" " NA-WNA-NA" " NA-WNA-NA" " NA-WNA-NA" "2019-W15" [15] "2019-W15" "2019-W15" " NA-WNA-NA" " NA-WNA-NA" " NA-WNA-NA" " NA-WNA-NA" " NA-WNA-NA" Not sure where to go from here.... session info below just incase
sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] bindrcpp_0.2.2 ggspatial_1.0.3 sf_0.7-2 epitools_0.5-10 aweek_0.2.0 [6] incidence_1.7.0 sitrep_0.1.0 summarytools_0.8.7 ggplot2_3.1.0 dplyr_0.7.8 [11] knitr_1.20
loaded via a namespace (and not attached): [1] Rcpp_1.0.0 lubridate_1.7.4 lattice_0.20-35 tidyr_0.8.3 class_7.3-14 [6] assertthat_0.2.0 digest_0.6.18 utf8_1.1.4 R6_2.4.0 cellranger_1.1.0 [11] plyr_1.8.4 survey_3.33-2 e1071_1.6-8 srvyr_0.3.3 pillar_1.3.1 [16] rlang_0.3.1 lazyeval_0.2.1 curl_3.2 readxl_1.1.0 rstudioapi_0.8 [21] data.table_1.11.2 Matrix_1.2-14 splines_3.5.0 stringr_1.4.0 foreign_0.8-70 [26] pander_0.6.1 ISOweek_0.6-2 RCurl_1.95-4.10 munsell_0.5.0 compiler_3.5.0 [31] pkgconfig_2.0.2 htmltools_0.3.6 tidyselect_0.2.5 tibble_2.0.1 rio_0.5.10 [36] codetools_0.2-15 matrixStats_0.54.0 fansi_0.4.0 crayon_1.3.4 withr_2.1.2 [41] bitops_1.0-6 grid_3.5.0 spData_0.2.8.3 lwgeom_0.1-5 gtable_0.2.0 [46] DBI_1.0.0 magrittr_1.5 units_0.6-2 scales_1.0.0 cli_1.0.1 [51] stringi_1.3.1 pryr_0.1.4 rapportools_1.0 cowplot_0.9.2 openxlsx_4.0.17 [56] tools_3.5.0 forcats_0.3.0 epitrix_0.2.1 glue_1.3.0 purrr_0.3.2 [61] survival_2.42-3 yaml_2.2.0 colorspace_1.4-0 classInt_0.2-3 bindr_0.1.1 [66] haven_1.1.1
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aspina7
hey - @epiamsterdam trying to run cholera template on data from mozambique. Runs in to this error, which seems to be beacuse of trying to make factor levels??
It is a date and seems normal, but has NAs:
The NAs seem to be recognised normally though:
If you run date2week, without factor = TRUE, it works, but produces funky looking NAs
Not sure where to go from here.... session info below just incase