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seabbs avatar seabbs commented on July 19, 2024 1

Hi Sarah,

Sorry your having issues here. I just tried your example and this is what I see:

> library(covidregionaldata)
> get_regional_data("india")
# A tibble: 10,336 x 13
   date       state iso_3166_2 cases_new cases_total deaths_new deaths_total recovered_new recovered_total hosp_new hosp_total tested_new
   <date>     <chr> <chr>          <dbl>       <dbl>      <dbl>        <dbl>         <dbl>           <dbl>    <int>      <int>      <int>
 1 2020-03-14 Anda… IN-AN              0           0          0            0             0               0       NA         NA         NA
 2 2020-03-14 Andh… IN-AP              1           1          0            0             0               0       NA         NA         NA
 3 2020-03-14 Arun… IN-AR              0           0          0            0             0               0       NA         NA         NA
 4 2020-03-14 Assam IN-AS              0           0          0            0             0               0       NA         NA         NA
 5 2020-03-14 Bihar IN-BR              0           0          0            0             0               0       NA         NA         NA
 6 2020-03-14 Chan… IN-CH              0           0          0            0             0               0       NA         NA         NA
 7 2020-03-14 Chha… IN-CT              0           0          0            0             0               0       NA         NA         NA
 8 2020-03-14 Dadr… IN-DN              0           0          0            0             0               0       NA         NA         NA
 9 2020-03-14 Dama… IN-DD              0           0          0            0             0               0       NA         NA         NA
10 2020-03-14 Goa   IN-GA              0           0          0            0             0               0       NA         NA         NA
# … with 10,326 more rows, and 1 more variable: tested_total <int>
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=C              LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] covidregionaldata_0.8.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5        rstudioapi_0.13   xml2_1.3.2        magrittr_2.0.1    hms_0.5.3         tidyselect_1.1.0  rvest_0.3.6      
 [8] R6_2.5.0          rlang_0.4.9       fansi_0.4.1       stringr_1.4.0     httr_1.4.2        dplyr_1.0.2       tools_4.0.3      
[15] utf8_1.1.4        cli_2.2.0         ellipsis_0.3.1    assertthat_0.2.1  readxl_1.3.1      digest_0.6.27     tibble_3.0.4     
[22] lifecycle_0.2.0   countrycode_1.2.0 crayon_1.3.4      tidyr_1.1.2       purrr_0.3.4       readr_1.4.0       vctrs_0.3.5      
[29] curl_4.3          memoise_1.1.0     glue_1.4.2        stringi_1.5.3     compiler_4.0.3    pillar_1.4.7      cellranger_1.1.0 
[36] generics_0.1.0    jsonlite_1.7.1    lubridate_1.7.9.2 pkgconfig_2.0.3  

I think this may be an unpatched issue in the CRAN version of covidregionaldata so trying the dev version should hopefully help. I was planning on pushing out another CRAN update today as there are quite a few bug fixes so it would be really good to resolve your issue to prevent it impacting others.

Sam

(snap Kath 😄)

P.S I just had a quick skim of your nbTransmission package and related work. Looks very interesting!

from covidregionaldata.

sarahleavitt avatar sarahleavitt commented on July 19, 2024 1

Installing from GitHub fixed the problem. Thanks for the suggestion!

from covidregionaldata.

kathsherratt avatar kathsherratt commented on July 19, 2024

Hi @sarahleavitt - I'm sorry for the slow response.

I actually don't see this error when I run get_regional_data(country = "India"). When you saw this a while ago it could have been due to a short-term change in the data source that was quickly resolved by the data owners (which we have little insight into).

I'm closing this issue for now, but please do re-open and let me know if you are still seeing an error.

from covidregionaldata.

sarahleavitt avatar sarahleavitt commented on July 19, 2024

I am still getting the error. I am not sure what is different. I reinstalled the package from CRAN and that doesn't fix it. Here is a screen shot with a trace on the error:
image

from covidregionaldata.

kathsherratt avatar kathsherratt commented on July 19, 2024

Thanks for checking this Sarah and sorry you are still seeing this. On re-installing from CRAN I can also see the error.

It looks like this error is now only in the version on CRAN, as we have made some bug fixes since the last release.

Please could you try re-installing from Github with remotes::install_github("epiforecasts/covidregionaldata") ?

This should fix the issue. We are aiming to submit a new CRAN release today, so hopefully this will be resolved for all users downloading from CRAN shortly.

from covidregionaldata.

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