Subclinical Phase

Calculate subclinical phase duration from incubation and latent phases from other analyses

Calculate Subclinical

Study-wide rates. These estimates are the results from the Incubation and Latent analyses.

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# from other analysis
incubation_samples <- readRDS(here("assets/incubation_samples.rds"))
latent_samples <- readRDS(here("assets/latent_samples.rds"))
median_incubation <- readRDS(here("assets/incubation_median.rds"))
median_latent <- readRDS(here("assets/latent_median.rds")) 
 
median_subclinical <- Map(function(x, y) x - y, median_incubation, median_latent)

medians_df <- as.data.frame(
  rbind(
    Incubation = as.data.frame(median_incubation),
    Subclinical = as.data.frame(median_subclinical),
    Latent = as.data.frame(median_latent)
  )
)

medians_df

	quant0.025	quant0.25	quant0.5	quant0.75	quant0.975
Incubation	1.501	2.301	2.901	3.601	5.901
Subclinical	1.000	1.400	1.700	2.100	3.400
Latent	0.501	0.901	1.201	1.501	2.501

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medians_df$Name <- rownames(medians_df)
medians_df$Name <- ordered(factor(medians_df$Name), c("Latent", "Subclinical", "Incubation"))

Subclinical by group. These estimates are the results from the Incubation and Latent analyses.

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incubation_aft <- readRDS(here("assets/incubation_aft_median.rds"))
latent_aft <- readRDS(here("assets/latent_aft_median.rds"))  

incu_grps <- incubation_aft 
latent_grps <- latent_aft[,3:8]

subclin_grps <- incu_grps %>%
  inner_join(latent_grps, by = "Group", suffix = c("_incu", "_latent")) %>%
  mutate(
    Q_0.025 = Q_0.025_incu - Q_0.025_latent,
    Q_0.25  = Q_0.25_incu - Q_0.25_latent,
    Q_0.5   = Q_0.5_incu - Q_0.5_latent,
    Q_0.75  = Q_0.75_incu - Q_0.75_latent,
    Q_0.975 = Q_0.975_incu - Q_0.975_latent,
    Phase = "Subclinical"
  ) %>%
  select(Phase, Group, Q_0.025, Q_0.25, Q_0.5, Q_0.75, Q_0.975)

subclin_grps

Phase	Group	Q_0.025	Q_0.25	Q_0.5	Q_0.75	Q_0.975
Subclinical	study	1.3635400	1.7093057	1.9020377	2.116677	2.648249
Subclinical	donor	1.6419888	2.1329785	2.4793733	2.785928	3.459646
Subclinical	Group 2	2.4473436	3.1525713	3.5842509	4.013332	5.051369
Subclinical	Group 3	0.6910402	0.8361282	0.9309622	1.098180	1.452167
Subclinical	Group 4	0.9921016	1.2109766	1.3450047	1.553879	2.018282

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incu_grps$Phase <- "Incubation" 
latent_grps$Phase <- "Latent"
  
all_grps_w <- rbind(latent_grps, incu_grps, subclin_grps)

Plot study-wide median phases

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plot_median_phases(medians_df)

Plot subclinical curve based on study-wide rates.

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plot_compare_marginals(incubation_samples, latent_samples)

Plot treatment-specific subclinical estimates from AFT models.

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plot_group_phases(all_grps_w)

save subclinical estimates

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saveRDS(all_grps_w, here("assets/subclinical_w.rds"))