library(simpr)Quite often, errors will arise in the course of simulating or fitting models. These errors can be tricky to debug because they may happen within a simulation function and only in certain cases.
The primary place where errors occur in the simulation is in generating the data and fitting models. Both generate() and fit() have the same primary error handling options:
.warn_on_error. When TRUE, the default, a warning is given when the simulation returned errors. If you expect errors or have other ways of checking on them, you can make this FALSE..stop_on_error. When TRUE, the simulation stops as soon as an error is encountered. This is useful when running interactively and when errors are unexpected. Default is FALSE.The default behavior is to warn when there are errors, and storing those error messages in a separate column .sim_error. This gives you the flexibility to continue with the simulation or model-fitting process even if one particular data generation or model fit hit an error.
generate()Consider the following example:
buggy_spec = specify(y = ~ rnorm(size)) %>%
define(size = c(-10, 10))We’d expect this to produce an error when n is negative, since that’s not a valid sample size.
What happens when we try to generate data based on the buggy specification?
set.seed(100)
generate_default = buggy_spec %>%
generate(1)
#> Warning in create_sim_results(specs = specs, x = x[c("meta_info", "specify", :
#> Simulation produced errors. See column '.sim_error'.The default is for R to produce a warning, but to still return the object. This lets us know that simpr hit some issues. We can follow the advice given and take a look at the returned object.
generate_default
#> tibble
#> --------------------------
#> # A tibble: 2 × 5
#> .sim_id size rep sim .sim_error
#> <int> <dbl> <int> <list> <chr>
#> 1 1 -10 1 <NULL> "Error in rnorm(size): invalid argument…
#> 2 2 10 1 <tibble [10 × 1]> <NA>The first simulation had an error and thus did not return any simulation data. We can see the error message given directly in the .sim_error column.
We would get the same output without a warning if we set .warn_on_error = FALSE:
set.seed(100)
generate_no_warn = buggy_spec %>%
generate(1, .warn_on_error = FALSE)
generate_no_warn
#> tibble
#> --------------------------
#> # A tibble: 2 × 5
#> .sim_id size rep sim .sim_error
#> <int> <dbl> <int> <list> <chr>
#> 1 1 -10 1 <NULL> "Error in rnorm(size): invalid argument…
#> 2 2 10 1 <tibble [10 × 1]> <NA>Alternatively, we can set .stop_on_error = TRUE to simply stop the simulation and immediately produce the error. This is often useful during initial development of the simulation, when an error often means that something is misspecified:
generate_error = buggy_spec %>%
generate(1, .stop_on_error = TRUE)
#> Error in rnorm(size): invalid argumentsfit()If there is already an error in the simulation, this will usually propagate to any model-fitting as well. Recall the output above:
generate_no_warn
#> tibble
#> --------------------------
#> # A tibble: 2 × 5
#> .sim_id size rep sim .sim_error
#> <int> <dbl> <int> <list> <chr>
#> 1 1 -10 1 <NULL> "Error in rnorm(size): invalid argument…
#> 2 2 10 1 <tibble [10 × 1]> <NA>Since the simulation with size = -10 has NULL for the generated data, any model-fitting will usually produce errors as well.
fit_propagate = generate_no_warn %>%
fit(t_test = ~ t.test(y))
#> Warning in fit.simpr_tibble(., t_test = ~t.test(y)): fit() produced errors. See
#> '.fit_error_*' column(s).fit_propagate
#> tibble
#> --------------------------
#> # A tibble: 2 × 7
#> .sim_id size rep sim .sim_error t_test .fit_error_t_te…
#> <int> <dbl> <int> <list> <chr> <list> <chr>
#> 1 1 -10 1 <NULL> "Error in rnor… <NULL> "Error in t.tes…
#> 2 2 10 1 <tibble [10 × 1]> <NA> <htest> <NA>
#>
#> t_test[[1]]
#> --------------------------
#> NULLNow, there are new columns, one for errors on each fit attempted. We can see a situation where we have multiple errors:
fit_multi_error = generate_no_warn %>%
fit(t_test = ~ t.test(y),
chisq = ~ chisq.test(y))
#> Warning in fit.simpr_tibble(., t_test = ~t.test(y), chisq = ~chisq.test(y)):
#> fit() produced errors. See '.fit_error_*' column(s).The first fit t_test failed on just the first row, with size = -10, but the second fit chisq was nonsensical either way and so two .fit_error columns are produced.
fit_multi_error
#> tibble
#> --------------------------
#> # A tibble: 2 × 9
#> .sim_id size rep sim .sim_error t_test .fit_error_t_te… chisq
#> <int> <dbl> <int> <list> <chr> <list> <chr> <list>
#> 1 1 -10 1 <NULL> "Error in rnorm(… <NULL> "Error in t.tes… <NULL>
#> 2 2 10 1 <tibble> <NA> <htest> <NA> <NULL>
#> # … with 1 more variable: .fit_error_chisq <chr>
#>
#> t_test[[1]]
#> --------------------------
#> NULL
#>
#> chisq[[1]]
#> --------------------------
#> NULLEven in this degenerate case, tidy_fits still gathers together whatever valid fits it can find, and reproduces the errors when there is not a valid fit:
fit_multi_error %>%
tidy_fits
#> # A tibble: 4 × 14
#> .sim_id size rep .sim_error Source .fit_error estimate statistic p.value
#> <int> <dbl> <int> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 1 -10 1 "Error in rn… t_test "Error in… NA NA NA
#> 2 1 -10 1 "Error in rn… chisq "Error in… NA NA NA
#> 3 2 10 1 <NA> t_test <NA> 0.172 0.826 0.430
#> 4 2 10 1 <NA> chisq "Error in… NA NA NA
#> # … with 5 more variables: parameter <dbl>, conf.low <dbl>, conf.high <dbl>,
#> # method <chr>, alternative <chr>Sometimes it is difficult to tell what went wrong in a simulation just from the error message. In this case it is useful to use R’s powerful debugging features. See ?browser and the debugging chapter from Advanced R for general information on using R’s debugger.
Both generate() and fit() allow you to set .debug = TRUE to look interactively at what is coming in to R. This allows you to see how the data is coming in and to figure out what is causing the error.
Let’s use the same example as above:
specify(y = ~ rnorm(size)) %>%
define(size = c(-10, 10)) %>%
generate(1, .debug = TRUE)If we run this in Rstudio, we’ll see this in the .debugger view:
function (..., .x = ..1, .y = ..2, . = ..1)
rnorm(size)This is a behind-the-scenes function created by simpr based on the specification of y, but we can see the rnorm(n) that was originally in the specification.
And this in the console:
Browse[2]> What’s nice is that we can see what the incoming data look like, so we can for instance type n at the console to see what’s coming in:
Browse[2]> size
[1] -10We can type "Q" to exit debugging or "n" to move to the next debug step. (If we have a variable called n, we would need to use print(n) to see its value.)
If you aren’t seeing any output when you type commands in the debugger, try running the command sink(), which seems to allow the output to show up in some cases.
This same mechanism is used by fit():
set.seed(100)
specify(y1 = ~ rnorm(10),
y2 = ~ rnorm(10)) %>%
generate(2) %>%
fit(t_test = ~ t.test(y1, y2),
.debug = TRUE)The function displays a bit differently:
function (..., .x = ..1, .y = ..2, . = ..1)
with(data = ., expr = t.test(y1, y2))Our input, t.test(y) is still present, but it is within the call for with. The input simulation data is stored in the special variable .:
Browse[2]> .
# A tibble: 10 × 2
y1 y2
<dbl> <dbl>
1 0.922 -0.559
2 0.0958 0.827
3 -0.866 0.486
4 0.922 -0.717
5 1.15 -0.375
6 1.71 -0.0771
7 1.44 0.508
8 -0.244 -1.59
9 0.153 0.386
10 -0.294 1.18 We can perform whatever test calculations on this sample data to diagnose issues that are coming up.
We can type n to move to the next simulation, which has different data:
Browse[2]> n
exiting from: ...furrr_fn(...)
debugging in: ...furrr_fn(...)
debug: with(data = ., expr = t.test(y1, y2))
Browse[2]> .
# A tibble: 10 × 2
y1 y2
<dbl> <dbl>
1 -0.335 0.212
2 1.23 -0.834
3 -0.821 -0.668
4 -0.0373 0.246
5 0.436 -0.0761
6 -1.83 -0.704
7 0.765 0.507
8 0.825 1.07
9 -2.49 2.61
10 1.13 0.261