Geospatial Spatialcovariate files will be not read correctly

[OJWatson]

The geospatial covariates csv files that you can download from the DHS website do not have support yet for being read in. Need to add a better catch and stop/warning message for these.

---

However, currently you should not be able to download these, as I do not place geospatial covariate files into the available datasets function. So @nickbrazeau could you attach the output of get_available_datasets() as an .rds that would be great and i can figure out how they got there :)

[nickbrazeau]

Hey OJ,

Here is the code chunk I used to produce the issue above.

rdhs::set_rdhs_config(email = "nbrazeau@med.unc.edu",
                      project = "Malaria Spatiotemporal Analysis",
                      config_path = "rdhs.json",
                      global = FALSE,
                      cache_path = "/Users/NFB/Documents/GitHub/VivID_Epi")

survs <- rdhs::dhs_surveys(countryIds = c("CD"),
                     surveyYearStart = 2013)


datasets <- rdhs::dhs_datasets(surveyIds = survs$SurveyId,
                         fileFormat = "flat")

# debug
availdatasets <- rdhs::get_available_datasets()
readr::write_rds(x=availdatasets, path = "~/Google_Drive/PhD_Work/sandbox/avail_datasets_dhs.rds")


# download all DHS datsets 
downloads <- rdhs::get_datasets(datasets$FileName) 

I've hosted the .rds here which includes other geospatial covariates (interestingly).

Here is my rdhs client file/json:

{
"email": "nbrazeau@med.unc.edu",
"project": "Malaria Spatiotemporal Analysis",
"password": ****",
"cache_path": "/Users/NFB/Documents/GitHub/VivID_Epi",
"config_path": "rdhs.json",
"global": false,
"verbose_download": false,
"verbose_setup": true,
"timeout": 30,
"data_frame": null,
"project_choice": null
}

And here is my session info:

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin17.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.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] rdhs_0.6.0      forcats_0.3.0   stringr_1.3.1   dplyr_0.7.7     purrr_0.2.5     readr_1.2.1     tidyr_0.8.2     tibble_1.4.2    ggplot2_3.1.0   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] storr_1.2.1      tidyselect_0.2.5 haven_2.0.0      lattice_0.20-35  colorspace_1.3-2 yaml_2.2.0       rlang_0.3.0.1    pillar_1.3.0     glue_1.3.0      
[10] withr_2.1.2      rappdirs_0.3.1   sp_1.3-1         modelr_0.1.2     readxl_1.1.0     bindrcpp_0.2.2   bindr_0.1.1      plyr_1.8.4       munsell_0.5.0   
[19] gtable_0.2.0     cellranger_1.1.0 rvest_0.3.2      devtools_1.13.6  memoise_1.1.0    qdapRegex_0.7.2  curl_3.2         broom_0.5.0      Rcpp_1.0.0      
[28] scales_1.0.0     backports_1.1.2  jsonlite_1.5     hms_0.4.2        digest_0.6.18    stringi_1.2.4    getPass_0.2-2    grid_3.5.1       rgdal_1.3-6     
[37] cli_1.0.1        tools_3.5.1      magrittr_1.5     lazyeval_0.2.1   crayon_1.3.4     pkgconfig_2.0.2  xml2_1.2.0       lubridate_1.7.4  assertthat_0.2.0
[46] httr_1.3.1       rstudioapi_0.7   R6_2.3.0         nlme_3.1-137     compiler_3.5.1   git2r_0.21.0 

[OJWatson]

Tracked it down - if you request SPA datasets from the DHS this will cause Geospatial covariates to be included. Have addressed in 973dced

[OJWatson]

@nickbrazeau - if you fancy checking that this now works for you (it's in the master branch) that would be good, but no rush, i'll have a check once the DHS approves my reqest for the SPA datasets as well.

[OJWatson]

Not fully fixed - just noticed a bug in this.