Suggested improvements to package

IvanWilli / DemoKin

DemoKin estimates kinship distribution by type and age

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Suggested improvements to package #6

Closed alburezg closed 1 year ago

alburezg commented 2 years ago

[x] The logical parameter "stable" will be replaced by "time-invariant".
[x] We will change parameters "focal_year" and "focal_cohort" by "output_period" and "output_cohort": those arguments would only apply for selecting which data wants the user as output in the "time-variant" case.
[x] Both previous parameters would only apply for the "time-variant" case, and would not be "heard" in other case.
[x] When no pi or N is supplied as an argument in the "time-variant" case, we would use the stable distribution for mothers´s age and return a message like this "The stable assumption was used for the age distribution of mothers in each input year".

IvanWilli commented 2 years ago

Adding a few more:

[ ] test against Caswell´s papers
[x] No P_b argument. f matrix will imply "effective" births until end of time interval. Include a paragraph in the "using" vignette to show this option.
[x] Make reference to the concept of age-class in documentation, refering to truncated/exact age and its state notion.
[x] Deploy and test the package.
[x] Finish Multi-stage application.

alburezg commented 2 years ago

[x] use igraph to improve network visualisation

alburezg commented 2 years ago

A few more things, ahead of the new release:

[x] DemoKin::rename_kin()'s argument consolidate_kin breaks with update because it needs 'count' column (Diego).
[x] Remove ‘importFrom(DiagrammeR,mermaid)’ from NAMESPACE
[x] Remove library(igraph) from plot_diagram.R (and add igraph to NAMESPACE?)
[x] rename column death in kin_full to dead
[x] rename column count_cum_death in kin_summary to count_dead
[x] The following script returns an error (I think it should work without calling library(tidyverse)?):

library(DemoKin)
swe_surv_2015 <- swe_px[,"2015"]
swe_asfr_2015 <- swe_asfr[,"2015"]
swe_2015 <- kin(U = swe_surv_2015, f = swe_asfr_2015, time_invariant = TRUE)
Error in kin_time_invariant(U = U, f = f, output_kin = output_kin, birth_female = birth_female) %>%  : 
  could not find function "%>%"

IvanWilli commented 2 years ago

The last error was because "%>%" needs a library to load it. use_this has a great solution. Now solved

IvanWilli commented 1 year ago

@alburezg Do we close this? For final testing against Caswell's paper (mostly first) we would need more than visual inspection. Maybe is better to add it in a new list, together with final changes pre CRAN submision, and close this issue.

alburezg commented 1 year ago

Agreed, let's close this!