SYC 2016-2020 Sparse grid cells

[QLLZ]

List of countries with error type "Error in (function (cl, name, valueClass)":

1. SYC 2016-01-01:2020-12-31 Error in (function (cl, name, valueClass) : assignment of an object of class “numeric” is not valid for @‘Dim’ in an object of class “lsTMatrix”; is(value, "integer") is not TRUE Collapse

[QLLZ]

New updates: sparse grid cells issue has been fixed. But new issues come when running the stan model:

[1] "Running STAN" Init values were only set for a subset of parameters. Missing init values for the following parameters:

• chain 1: rho, log_std_dev_w, eta_tilde, sigma_eta_tilde
• chain 2: rho, log_std_dev_w, eta_tilde, sigma_eta_tilde
• chain 3: rho, log_std_dev_w, eta_tilde, sigma_eta_tilde
• chain 4: rho, log_std_dev_w, eta_tilde, sigma_eta_tilde

Running MCMC with 4 parallel chains...

Chain 1 Exception: dagar_seasonal_flexible_model_namespace::dagar_seasonal_flexible_model: N_edges is 0, but must be greater than or equal to 1.000000 (in '/tmp/Rtmpf1qDV1/model-50e59100e83.stan', line 10, column 2 to column 24) Chain 2 Exception: dagar_seasonal_flexible_model_namespace::dagar_seasonal_flexible_model: N_edges is 0, but must be greater than or equal to 1.000000 (in '/tmp/Rtmpf1qDV1/model-50e59100e83.stan', line 10, column 2 to column 24) Chain 3 Exception: dagar_seasonal_flexible_model_namespace::dagar_seasonal_flexible_model: N_edges is 0, but must be greater than or equal to 1.000000 (in '/tmp/Rtmpf1qDV1/model-50e59100e83.stan', line 10, column 2 to column 24) Chain 4 Exception: dagar_seasonal_flexible_model_namespace::dagar_seasonal_flexible_model: N_edges is 0, but must be greater than or equal to 1.000000 (in '/tmp/Rtmpf1qDV1/model-50e59100e83.stan', line 10, column 2 to column 24) Warning: Chain 1 finished unexpectedly!

Warning: Chain 2 finished unexpectedly!

Warning: Chain 3 finished unexpectedly!

Warning: Chain 4 finished unexpectedly!

Warning: All chains finished unexpectedly! Use the $output(chain_id) method for more information.

Warning: Use read_cmdstan_csv() to read the results of the failed chains. Warning: No chains finished successfully. Unable to retrieve the fit. Error: No chains finished successfully. Unable to retrieve the draws.

[NedaJalali-codes]

I do not get these errors but I get:

Error in if (nrow(.x) <= 1) { : argument is of length zero

Enter a frame number, or 0 to exit

 1: source("Analysis/R/execute_pipeline.R")
 2: withVisible(eval(ei, envir))
 3: eval(ei, envir)
 4: eval(ei, envir)
 5: execute_pipeline.R#436: taxdat::aggregate_case_data(temporally_linked_obser
 6: case_data %>% dplyr::filter(!!rlang::sym(cases_column) > 0) %>% dplyr::grou
 7: dplyr::ungroup(.)
 8: dplyr::group_modify(., function(.x, .y) {
    if (nrow(.x) <= 1) {

 9: group_modify.grouped_df(., function(.x, .y) {
    if (nrow(.x) <= 1) {

10: group_map(.data, fun, .keep = .keep)
11: group_map.data.frame(.data, fun, .keep = .keep)
12: structure(list(), ptype = .f(attr(chunks, "ptype"), keys[integer(0), ], ...
13: .f(attr(chunks, "ptype"), keys[integer(0), ], ...)
14: .f(.x, .y, ...)