Hi everyone,
I am trying to rename a column, however, this is not working and returning an error. Please could you help.
# install and load packages
#Import packages
pacman::p_load(
rio, # for importing data
here, # for locating files
skimr, # for reviewing the data
janitor, # for data cleaning
lubridate, # for date cleaning
epikit, # creating age categories
officer, # border lines
gtsummary, # creating tables
RColorBrewer, # for colour palettes
viridis, # for more colour palettes
apyramid, # for age/sex pyramids
tsibble, # for epiweeks and other time series analyses
scales, # percents in tables
datapasta, #to make a sample data
reprex, #reproduce your data
flextable, # for making pretty tables
gghighlight, # highlighting plot parts
ggExtra, # special plotting functions
tidyverse) # for data management and visualization
# import data
linelist <- data.frame(
stringsAsFactors = FALSE,
pid = c("c126657fb2326383",
"6989fe7ae7f4fc48",
"822024a12816255c",
"431166f74563284f",
"e81e2899487af357",
"634a52b08becb88a",
"39b30e1ae306bb10",
"72614d37b9f022fb",
"bd5bdfae67977791",
"ec30121d62d794f4"),
report_dt = c("2021-06-23",
"2020-10-03",
"2021-01-07","2020-12-29",
"2021-01-22",
"2020-11-02",
"2020-12-14","2021-01-25",
"2020-08-11",
"2021-03-13"),
case_age = c(39,38,16,31,
82,27,42,26,31,
17),
case_gender = c("Female",
"Female","Male",
"Female","Female",
"Female","Female",
"Female","Male","Female"),
case_race = c("OTHER",
"BLACK",NA,"BLACK",
"WHITE","WHITE",
"WHITE","WHITE","BLACK",
"WHITE"),
case_eth = c("HISPANIC/LATINO",
"NON-HISPANIC/LATINO",NA,
"NON-HISPANIC/LATINO",
"NON-HISPANIC/LATINO",
"HISPANIC/LATINO",
"NON-HISPANIC/LATINO",
"NON-HISPANIC/LATINO",
"NON-HISPANIC/LATINO",
"NON-HISPANIC/LATINO"),
city = c("Atlanta",
"Atlanta","Atlanta",
"Alpharetta",
"Atlanta","Duluth",
"College Park","Atlanta",
"Roswell","Atlanta"),
case_zip = c(30314,30354,
30309,30009,30331,
30097,30349,30310,
30076,30349),
contact_id = c("Yes-Symptomatic",NA,
"Yes-Symptomatic",
"Yes-Symptomatic",NA,
"Yes-Symptomatic",NA,
"Yes-Symptomatic",NA,
"Yes-Symptomatic"),
sym_startdt = c("2021-06-16",
"2020-09-29",
"2021-01-03","2020-12-25",
NA,"2020-10-28",
NA,"2021-01-17",NA,
"2021-03-08"),
sym_fever = c("Yes",NA,"No",
"Yes",NA,"Yes",
NA,"No",NA,"No"),
sym_subjfever = c("No",NA,"No",
"No",NA,"Yes",NA,
"No",NA,"No"),
sym_myalgia = c("Yes",NA,"No",
"Yes",NA,"Yes",
NA,"Yes",NA,"Yes"),
sym_losstastesmell = c("Yes",NA,
"Yes","Yes",NA,"Yes",
NA,"Yes",NA,
"Yes"),
sym_sorethroat = c("Yes",NA,"No",
"Yes",NA,"Yes",
NA,"No",NA,"Yes"),
sym_cough = c("Yes",NA,
"Yes","No",NA,"No",
NA,"No",NA,"Yes"),
sym_headache = c("Yes",NA,
"Yes","Yes",NA,"Yes",
NA,"No",NA,"Yes"),
sym_resolved = c("No, still symptomatic",NA,
"Yes, date unknown",
"No, still symptomatic",
NA,
"Yes, date specified below",NA,
"Yes, date specified below",NA,
"No, still symptomatic"),
sym_resolveddt = c(NA,NA,NA,NA,
NA,"2020-11-06",
NA,"2021-01-27",NA,
NA),
contact_household = c("No",NA,"Yes",
"Yes",NA,"Yes",
NA,"Yes",NA,"Yes"),
hospitalized = c("No",NA,"No",
"No",NA,"No",NA,
"No",NA,"No"),
hosp_admidt = c(NA,NA,NA,NA,
NA,NA,NA,NA,NA,
NA),
hosp_dischdt = c(NA,NA,NA,NA,
NA,NA,NA,NA,NA,
NA),
died = c("No",NA,"No",
"No",NA,"No",NA,
"No",NA,"No"),
died_covid = c("No",NA,"No",
"No",NA,"No",NA,
NA,NA,"No"),
died_dt = c(NA,NA,NA,NA,
NA,NA,NA,NA,NA,
NA),
confirmed_case = c("Yes","Yes",
"Yes","Yes","Yes",
"Yes","Yes","Yes",
"Yes","Yes"),
covid_dx = c("Confirmed",
"Confirmed",
"Confirmed","Confirmed",
"Confirmed",
"Confirmed","Confirmed",
"Confirmed","Confirmed",
"Confirmed"),
pos_sampledt = c("2021-06-20",
"2020-09-29",
"2021-01-04","2020-12-25",
"2021-01-19",
"2020-10-30",
"2020-12-10","2021-01-22",
"2020-12-25",
"2021-03-09"),
latitude_jitt = c(33.77532872,
33.67956413,
33.74224015,33.99779446,
33.87027514,
33.81472975,34.00576392,
33.83798863,33.6479832,
34.10367749),
longitude_jitt = c(-84.49943201,
-84.59542137,
-84.40567851,-84.34865274,
-84.3818667,
-84.40830841,-84.30134341,
-84.37291059,
-84.49215805,
-84.2999521)
)#Error in trying to rename casegender
clean_linelist <-linelist %>%
mutate(case_age=as.numeric(case_age),
report_dt=ymd(report_dt),
died_dt=ymd(died_dt),
sym_resolveddt=ymd(sym_resolveddt),
hosp_admidt=ydm(hosp_admidt),
hosp_dischdt=ydm(hosp_dischdt),
pos_sampledt=ydm(pos_sampledt)) %>%
filter(report_dt>=params$data_date) %>%
mutate(age_group=age_categories(case_age,lower = 0,upper=100,by=10),
case_gender=na_if(case_gender, "Unknown")) %>%
rename(report_date=report_dt,
system_start_date=sym_startdt,
death_date=died_dt,
age=case_age,
gender=casegender,
)
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `pos_sampledt = ydm(pos_sampledt)`.
#> Caused by warning:
#> ! 7 failed to parse.
#> Error in `filter()`:
#> ℹ In argument: `report_dt >= params$data_date`.
#> Caused by error:
#> ! object 'params' not found
Created on 2024-03-08 with reprex v2.1.0
Session info
sessionInfo()
#> R version 4.3.2 (2023-10-31 ucrt)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 19045)
#>
#> Matrix products: default
#>
#>
#> locale:
#> [1] LC_COLLATE=English_United Kingdom.utf8
#> [2] LC_CTYPE=English_United Kingdom.utf8
#> [3] LC_MONETARY=English_United Kingdom.utf8
#> [4] LC_NUMERIC=C
#> [5] LC_TIME=English_United Kingdom.utf8
#>
#> time zone: Europe/London
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
#> [5] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0
#> [9] ggExtra_0.10.1 gghighlight_0.4.1 ggplot2_3.4.4 flextable_0.9.4
#> [13] reprex_2.1.0 datapasta_3.1.0 scales_1.3.0 tsibble_1.1.4
#> [17] apyramid_0.1.3 viridis_0.6.5 viridisLite_0.4.2 RColorBrewer_1.1-3
#> [21] gtsummary_1.7.2 officer_0.6.4 epikit_0.1.6 lubridate_1.9.3
#> [25] janitor_2.2.0 skimr_2.1.5 here_1.0.1 rio_1.0.1
#>
#> loaded via a namespace (and not attached):
#> [1] tidyselect_1.2.0 fastmap_1.1.1 fontquiver_0.2.1
#> [4] pacman_0.5.1 promises_1.2.1 broom.helpers_1.14.0
#> [7] digest_0.6.34 mime_0.12 timechange_0.3.0
#> [10] lifecycle_1.0.4 sf_1.0-15 ellipsis_0.3.2
#> [13] gfonts_0.2.0 magrittr_2.0.3 compiler_4.3.2
#> [16] rlang_1.1.3 tools_4.3.2 utf8_1.2.4
#> [19] yaml_2.3.8 gt_0.10.1 data.table_1.15.0
#> [22] knitr_1.45 askpass_1.2.0 classInt_0.4-10
#> [25] curl_5.2.0 xml2_1.3.6 repr_1.1.6
#> [28] KernSmooth_2.23-22 miniUI_0.1.1.1 httpcode_0.3.0
#> [31] withr_3.0.0 grid_4.3.2 fansi_1.0.6
#> [34] gdtools_0.3.5 xtable_1.8-4 e1071_1.7-14
#> [37] colorspace_2.1-0 crul_1.4.0 cli_3.6.2
#> [40] anytime_0.3.9 crayon_1.5.2 rmarkdown_2.25
#> [43] ragg_1.2.7 generics_0.1.3 rstudioapi_0.15.0
#> [46] tzdb_0.4.0 DBI_1.2.1 proxy_0.4-27
#> [49] base64enc_0.1-3 vctrs_0.6.5 jsonlite_1.8.8
#> [52] fontBitstreamVera_0.1.1 hms_1.1.3 systemfonts_1.0.5
#> [55] units_0.8-5 glue_1.7.0 stringi_1.8.3
#> [58] gtable_0.3.4 later_1.3.2 munsell_0.5.0
#> [61] pillar_1.9.0 htmltools_0.5.7 openssl_2.1.1
#> [64] R6_2.5.1 textshaping_0.3.7 rprojroot_2.0.4
#> [67] shiny_1.8.0 evaluate_0.23 snakecase_0.11.1
#> [70] httpuv_1.6.14 fontLiberation_0.1.0 class_7.3-22
#> [73] Rcpp_1.0.12 zip_2.3.1 uuid_1.2-0
#> [76] gridExtra_2.3 xfun_0.41 fs_1.6.3
#> [79] pkgconfig_2.0.3