ipeagit / aopdata Goto Github PK

It could be a good idea to include a function that loads the data dictionary into a data.frame or an htlm page.

Include

• box plot by income
• palma ratio
• cleveland plot

I'm trying to install the package from GitHub, but the following message appears:

> devtools::install_github("ipeaGIT/aopdata")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo ipeaGIT/aopdata@HEAD
Error: Failed to install 'aopdata' from GitHub:
  Does not appear to be an R package (no DESCRIPTION)

Add peak as a Logical parameter to the read_access() function. Defaults to TRUE. This parameter is only relevant when mode = public_transport.

for the same reason as geobr.

Vignettes are throwing this error on both macOS-latest (oldrel) and ubuntu-20.04 (release).

• creating vignettes ... ERROR
  Error: --- re-building ‘access_inequality.Rmd’ using rmarkdown
  Quitting from lines 26-31 (access_inequality.Rmd)
  Error: Error: processing vignette 'access_inequality.Rmd' failed with diagnostics:
  package or namespace load failed for 'sf' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
  there is no package called 'units'
  --- failed re-building ‘access_inequality.Rmd’

--- re-building ‘access_maps.Rmd’ using rmarkdown
Quitting from lines 27-31 (access_maps.Rmd)
Error: Error: processing vignette 'access_maps.Rmd' failed with diagnostics:
package or namespace load failed for 'sf' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'units'
--- failed re-building ‘access_maps.Rmd’

I just got this from the CRAN team:

Dear maintainer,

Please see the problems shown on
https://cran.r-project.org/web/checks/check_results_aopdata.html.

Please correct before 2021-04-12 to safely retain your package on CRAN.

It seems we need to remind you of the CRAN policy:

'Packages which use Internet resources should fail gracefully with an informative message
if the resource is not available or has changed (and not give a check warning nor error).'

This needs correction whether or not the resource recovers.

The CRAN Team

and a secont message from them:

I have seen several different failures in the last few days:

--- re-building ‘access_maps.Rmd’ using rmarkdown
Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 6.3.2
Quitting from lines 36-43 (access_maps.Rmd)
Error: processing vignette 'access_maps.Rmd' failed with diagnostics:
object 'type' not found
--- failed re-building ‘access_maps.Rmd’

--- re-building ‘landuse_maps.Rmd’ using rmarkdown
Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 6.3.2
Quitting from lines 35-42 (landuse_maps.Rmd)
Error: processing vignette 'landuse_maps.Rmd' failed with diagnostics:
Cannot open "/tmp/RtmprkkzTh/working_dir/RtmpKy82ey/hex_grid_for.gpkg";
The source could be corrupt or not supported. See st_drivers() for a
list of supported formats.
--- failed re-building ‘landuse_maps.Rmd’

--- re-building ‘access_maps.Rmd’ using rmarkdown
Linking to GEOS 3.9.0, GDAL 3.2.1, PROJ 6.3.2
Using year 2019
Using mode public_transport
Quitting from lines 36-43 (access_maps.Rmd)
Error: processing vignette 'access_maps.Rmd' failed with diagnostics:
Timeout was reached: [www.ipea.gov.br] Connection timed out after 10013
milliseconds
--- failed re-building ‘access_maps.Rmd’

And that website currently also has

Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: unable to re-encode 'utils.R' line 334

(checking in Latin-1) and

 --- re-building ‘landuse_maps.Rmd’ using rmarkdown
 Linking to GEOS 3.9.0, GDAL 3.2.1, PROJ 7.2.1
 Quitting from lines 35-42 (landuse_maps.Rmd)
 Error: processing vignette 'landuse_maps.Rmd' failed with diagnostics:
 some columns are not in the data.table:

abbrev_muni,name_muni,code_muni,id_hex
--- failed re-building ‘landuse_maps.Rmd’

--- re-building ‘landuse_maps.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling
back to R Markdown v1.
Linking to GEOS 3.6.4, GDAL 2.2.4, PROJ 5.2.0
Quitting from lines 35-42 (landuse_maps.Rmd)
Error: processing vignette 'landuse_maps.Rmd' failed with diagnostics:
Timeout was reached: [www.ipea.gov.br] Operation timed out after
10140 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘landuse_maps.Rmd’

--
Brian D. Ripley,

This again:

'Packages which use Internet resources should fail gracefully with an informative message
if the resource is not available or has changed (and not give a check warning nor error).'

@dhersz , could you pleave have a look into this? No hurry.

The function rm_accent() currently throws this WARNING with CMD Check:

checking R files for non-ASCII characters ... WARNING
Found the following file with non-ASCII characters:
utils.R
Portable packages must use only ASCII characters in their R code,
except perhaps in comments.
Use \uxxxx escapes for other characters.

Right now, the behavior when trying to download accessibility by public transport for all cities returns an error:

# download data
aop_data <- aopdata::read_access(city = "all", mode = "public_transport", year = 2019, geometry = TRUE)

`Using mode public_transport
Downloading accessibility data for the year 2019
  |======================================================================================================| 100%
Error in aopdata::read_access(city = "all", mode = "public_transport",  : 
  One of the selected cities does not have public transport data for that year.`

I think it would be nice to pre-filter only cities with public transport for that year and return the accessibility estimates for them, instead of returning an error.
A message indicating the cities would be nice as well.

The landuse database (from read_landuse) is coming duplicated when the chosen year is 2017 or 2018:

> landuse_2017 <- aopdata::read_landuse(city = c("for"), 
                                       year = 2017,
                                       geometry = FALSE)

> table(landuse_2017$year)

2017 2019 
2562 2562 

Also, all the population observations from 2017 or 2018 are NA for that year:

> a <- landuse_2017[year == 2017]
> summary(a$P001)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
     NA      NA      NA     NaN      NA      NA    2562 

The issue may be here, where the year column from the aop_population dataset is always equal to 2019. When merging the two datasets with all = TRUE and year = 2017|2018 from the landuse, the two datasets are rbinded.

The spatial grid downloaded by the function aopdata::read_grid currently contains duplicates of some hexagons. All cities seem to have this issue at the moment.

Two issues raised by CRAM:

1. Also, 'Writing R Extensions' asks you not to use progress bars in non-interactive use such as R CMD check.

2. 'Packages which use Internet resources should fail gracefully with an informative message if the resource is not available or has changed (and not give a check warning nor error).'

We got the following message from CRAN:

Version: 0.2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: unable to re-encode 'utils.R' line 382
Flavor: r-devel-linux-x86_64-debian-clang

I'm replacing the rm_accent() function with a simple base::iconv(city, to="ASCII//TRANSLIT")

The reason for this is beacause they como from different years.

• Land use data is annual data from 2017 onwards.
• Current population data is from the 2010 census. We will eventually add population data from the next census (2021? 2022?)

I've been downloading the data through the read_access function and I saw three enhancements that could be made.

1. The first is the need to mention the cities code in the read_access, read_population, read_grid, and read_landuse documentation. I could only find the codes when I downloaded using city = all.

2. Also, the function could be implemented to accept a vector of cities' names, instead of a single city. By doing this the user doesn't need to use any lapply() command to extract the desired files.

3. When we use mode = 'public_transport' with city = 'all', we get this error:

> a <- aopdata::read_access(city = 'all', mode = 'public_transport', 
peak = TRUE, year = 2019, geometry = TRUE)
Using mode public_transport
Downloading accessibility data from year 2019
  |=====================================================| 100%
Error in aopdata::read_access(city = "all", mode = "public_transport",  : 
  One of the selected cities does not have public transport data for that year.

There could be a condition that uses c("for", "rec", "bho","rio", "spo", "cur", "poa") when the commands (mode = 'public_transport' with city = 'all') are used together.

If you guys agree with these suggestions, I can go forward and open a PR.

updata data dictionary in the documentation of each function to reflect the new data set

Guys, I need some help here. This is the message I got today:

Dear maintainer,

package aopdata_0.2.2.tar.gz has been auto-processed.
The auto-check found additional issues for the last version released on CRAN:
M1mac https://www.stats.ox.ac.uk/pub/bdr/M1mac/aopdata.out
CRAN incoming checks do not test for these additional issues and you will need an appropriately instrumented build of R to reproduce these.
Hence please reply-all and explain: Have these been fixed?

Log dir: https://win-builder.r-project.org/incoming_pretest/aopdata_0.2.2_20210423_192923/
The files will be removed after roughly 7 days.
Installation time in seconds: 5
Check time in seconds: 98
R version 4.1.0 alpha (2021-04-22 r80209)

Pretests results:
Windows: https://win-builder.r-project.org/incoming_pretest/aopdata_0.2.2_20210423_192923/Windows/00check.log
Status: OK
Debian: https://win-builder.r-project.org/incoming_pretest/aopdata_0.2.2_20210423_192923/Debian/00check.log
Status: OK

Last released version's CRAN status: ERROR: 3, WARN: 2, OK: 8
See: https://CRAN.R-project.org/web/checks/check_results_aopdata.html

Last released version's additional issues:
M1mac https://www.stats.ox.ac.uk/pub/bdr/M1mac/aopdata.out

CRAN Web: https://cran.r-project.org/package=aopdata

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
Maintainer: 'Rafael H. M. Pereira [email protected]'

It seems the access data stored in the server only includes off-peak.

Error message could be more specific about the availability of access estimates by car

df_car <- read_access(
  city='Curitiba',
  mode='car',
  year=2018,
  peak = F,
  geometry = TRUE,
  showProgress = FALSE
)

Error in select_mode_input(temp_meta, mode = m) :
Error: This 'mode' is not available for this 'city' & 'year.' It must be one of the following: bicycle public_transport walk

It doesn't make sense to default to any city, IMO.