Check if geolink_mach() functions are working?

[ifeanyi588]

@dasalm20,

Here are some tasks for you:

• Please check to see if functions in geolink_mach() functions are working. Leave me an issue if you are getting errors.
• We need to check that parallelization for zonal statistics estimation is working. Please check the parallel_zonalstats() function (https://github.com/SSA-Statistical-Team-Projects/GeoLink/blob/master/R/zonalstats_plugin.R).
• Finally, the code currently depends on the user inputting NULL for arguments which will not be called in order to work. We need to change the if statements to either match arguments (match()) or use work based on whether or not the argument is left blank.

Best regards, Ify

[dasalm20]

Hi Ify,

I tried to run a simple test to geolink_chirps() function using BDI shapefile. The download seems to be fine, but I am getting the error. I believe in the processing part, specifically, when reading the shapefile. For some reason, it is expecting a path rather than using the shapefile already in the environment.

Here is a copy of the error with a traceback :

Error in if (nchar(dsn) < 1) stop("dsn must point to a source, not an empty string.", : the condition has length > 1 7. st_read.character(dsn, layer, ...) 6. st_read.default(..., quiet = quiet, stringsAsFactors = stringsAsFactors, as_tibble = as_tibble) 5. st_read(..., quiet = quiet, stringsAsFactors = stringsAsFactors, as_tibble = as_tibble) 4. sf::read_sf(shp_dt) at zonalstats_plugin.R#165 3. zonalstats_prepshp(shp_dt = shp_dt, shp_fn = shp_fn, grid_size = grid_size) at zonalstats_plugin.R#290 2. postdownload_processor(shp_dt = shp_dt, raster_objs = raster_objs, shp_fn = shp_dt, grid_size = grid_size, survey_dt = survey_dt, survey_fn = survey_fn, survey_lat = survey_lat, survey_lon = survey_lon, extract_fun = extract_fun, buffer_size = buffer_size, survey_crs = survey_crs, ... at geolink_mach.R#119 1. geolink_chirps(time_unit = "month", start_date = "2019-01-01", end_date = "2019-02-01", shp_dt = bdi_sf, grid_size = 1000, extract_fun = "mean")

[ifeanyi588]

Dear Daylan,

Can you take a look at this? Please let know where the error is coming from. I think I have an idea but it’s essential for you to learn how the system works.

Best regards, Ify

On Tue, Nov 7, 2023 at 9:27 PM dasalm20 @.***> wrote:

Hi Ify,

I tried to run a simple test to geolink_chirps() function using BDI shapefile. The download seems to be fine, but I am getting the error. I believe in the processing part, specifically, when reading the shapefile. For some reason, it is expecting a path rather than using the shapefile already in the environment.

Here is a copy of the error with a traceback :

Error in if (nchar(dsn) < 1) stop("dsn must point to a source, not an empty string.", : the condition has length > 1 7. st_read.character(dsn, layer, ...) 6. st_read.default(..., quiet = quiet, stringsAsFactors = stringsAsFactors, as_tibble = as_tibble) 5. st_read(..., quiet = quiet, stringsAsFactors = stringsAsFactors, as_tibble = as_tibble) 4. sf::read_sf(shp_dt) at zonalstats_plugin.R#165 3. zonalstats_prepshp(shp_dt = shp_dt, shp_fn = shp_fn, grid_size = grid_size) at zonalstats_plugin.R#290 2. postdownload_processor(shp_dt = shp_dt, raster_objs = raster_objs, shp_fn = shp_dt, grid_size = grid_size, survey_dt = survey_dt, survey_fn = survey_fn, survey_lat = survey_lat, survey_lon = survey_lon, extract_fun = extract_fun, buffer_size = buffer_size, survey_crs = survey_crs, ... at geolink_mach.R#119 1. geolink_chirps(time_unit = "month", start_date = "2019-01-01", end_date = "2019-02-01", shp_dt = bdi_sf, grid_size = 1000, extract_fun = "mean")

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[dasalm20]

Hi Ify,

I see where the problem was. In line 165 of the zonalstats_pluin.R it was trying to do an st_read() if the shp_fun was null. All i did was instead of an st_read() I just put an st_to_sf() function and it worked. However, it broke when the survey_dt argument was not written in the parameters. I put it as NULL and it worked completely. I will move forward checking how to deal with the issue of having to specify a parameter as NULL instead of not writing it at all.

[Chaser263]

When running the latest version of the code for geolink_chirps() I also got the "nchar(dsn) < 1) stop("dsn must point to a source, not an empty string issue"

I was able to isolate the issue to the following section of code (geolink_machr 117 to 119):

dt <- postdownload_processor(shp_dt = shp_dt,
                               raster_objs = raster_objs,
                               shp_fn = shp_dt, 

shp_fn is set to equal shp_dt. This leads to geolink_chirps running the shp_fn section of the code when it should be null.

This should be:

 dt <- postdownload_processor(shp_dt = shp_dt,
                               raster_objs = raster_objs,
                               shp_fn = shp_fn

After that fix, I am getting the error for "no applicable method for 'st_transform' applied to an object of class "c('data.table', 'data.frame')" I assume Daylan's st_to_sf() fix should work for that one