replace dist_spec() with Gamma() in ebola challenge

[avallecam]

After epiforecasts/EpiNow2#504

replace challenge in

tutorials-early/episodes/delays-functions.Rmd

Lines 518 to 537 in 4bf44d1

	```{r,message=FALSE,warning=FALSE,eval=TRUE}
	# subset one distribution
	ebola_serial <- epidist_db(
	disease = "ebola",
	epi_dist = "serial",
	single_epidist = TRUE
	)
	# adapt epiparameter to epinow2
	ebola_serial_discrete <- discretise(ebola_serial)
	ebola_serial_discrete_max <- quantile(ebola_serial_discrete, p = 0.999)
	serial_interval_ebola <-
	dist_spec(
	mean = ebola_serial$summary_stats$mean,
	sd = ebola_serial$summary_stats$sd,
	max = ebola_serial_discrete_max,
	distribution = "gamma" # don't forget! it's a must!
	)

library(epiparameter)
library(EpiNow2)
#> Warning: package 'EpiNow2' was built under R version 4.2.3

ebola_serial <- epidist_db(
  disease = "ebola",
  epi_dist = "serial",
  single_epidist = TRUE
)
#> Using WHO Ebola Response Team, Agua-Agum J, Ariyarajah A, Aylward B, Blake I,
#> Brennan R, Cori A, Donnelly C, Dorigatti I, Dye C, Eckmanns T, Ferguson
#> N, Formenty P, Fraser C, Garcia E, Garske T, Hinsley W, Holmes D,
#> Hugonnet S, Iyengar S, Jombart T, Krishnan R, Meijers S, Mills H,
#> Mohamed Y, Nedjati-Gilani G, Newton E, Nouvellet P, Pelletier L,
#> Perkins D, Riley S, Sagrado M, Schnitzler J, Schumacher D, Shah A, Van
#> Kerkhove M, Varsaneux O, Kannangarage N (2015). "West African Ebola
#> Epidemic after One Year — Slowing but Not Yet under Control." _The New
#> England Journal of Medicine_. doi:10.1056/NEJMc1414992
#> <https://doi.org/10.1056/NEJMc1414992>.. 
#> To retrieve the short citation use the 'get_citation' function

# adapt epiparameter to epinow2
ebola_serial_discrete <- discretise(ebola_serial)

ebola_serial_discrete_max <- quantile(ebola_serial_discrete, p = 0.999)

serial_interval_ebola <-
  dist_spec(
    mean = ebola_serial$summary_stats$mean,
    sd = ebola_serial$summary_stats$sd,
    max = ebola_serial_discrete_max,
    distribution = "gamma" # don't forget! it's a must!
  )
#> Warning: The meaning of the 'max' argument has changed compared to previous versions. It now indicates the maximum of a distribution rather than the length of the probability mass function (including 0) that it represented previously. To replicate previous behaviour reduce max by 1.
#> This warning is displayed once every 8 hours.

serial_interval_ebola
#> 
#>   Fixed distribution with PMF [0.0063 0.02 0.031 0.039 0.045 0.05 0.052 0.053 0.052 0.051 0.049 0.047 0.045 0.042 0.039 0.036 0.034 0.031 0.028 0.026 0.023 0.021 0.019 0.017 0.016 0.014 0.013 0.011 0.01 0.009 0.0081 0.0072 0.0064 0.0057 0.005 0.0045 0.004 0.0035 0.0031 0.0027 0.0024 0.0021 0.0019 0.0017 0.0015 0.0013 0.0011 0.00099 0.00087 0.00077 0.00067 0.00059 0.00052 0.00045 4e-04 0.00035 0.00031 0.00027 0.00023 2e-04 0.00018 0.00016 0.00014]

^{Created on 2024-02-26 with reprex v2.0.2}

by

library(epiparameter)
library(EpiNow2)
#> 
#> Attaching package: 'EpiNow2'
#> The following object is masked from 'package:epiparameter':
#> 
#>     discretise
#> The following object is masked from 'package:stats':
#> 
#>     Gamma

ebola_serial <- epidist_db(
  disease = "ebola",
  epi_dist = "serial",
  single_epidist = TRUE
)
#> Using WHO Ebola Response Team, Agua-Agum J, Ariyarajah A, Aylward B, Blake I,
#> Brennan R, Cori A, Donnelly C, Dorigatti I, Dye C, Eckmanns T, Ferguson
#> N, Formenty P, Fraser C, Garcia E, Garske T, Hinsley W, Holmes D,
#> Hugonnet S, Iyengar S, Jombart T, Krishnan R, Meijers S, Mills H,
#> Mohamed Y, Nedjati-Gilani G, Newton E, Nouvellet P, Pelletier L,
#> Perkins D, Riley S, Sagrado M, Schnitzler J, Schumacher D, Shah A, Van
#> Kerkhove M, Varsaneux O, Kannangarage N (2015). "West African Ebola
#> Epidemic after One Year — Slowing but Not Yet under Control." _The New
#> England Journal of Medicine_. doi:10.1056/NEJMc1414992
#> <https://doi.org/10.1056/NEJMc1414992>.. 
#> To retrieve the short citation use the 'get_citation' function

# adapt epiparameter to epinow2
ebola_serial_discrete <- epiparameter::discretise(ebola_serial)

ebola_serial_discrete_max <- quantile(ebola_serial_discrete, p = 0.999)

serial_interval_ebola <-
  Gamma(
    mean = ebola_serial$summary_stats$mean,
    sd = ebola_serial$summary_stats$sd,
    max = ebola_serial_discrete_max
  )

serial_interval_ebola
#> - gamma distribution (max: 62):
#>   shape:
#>     2.2
#>   rate:
#>     0.15

^{Created on 2024-02-26 with reprex v2.1.0}

UPDATE:

• added reprex to this issue

[avallecam]

fixed in #80