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Mayfield corrections [no version bump]
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@gmyenni
gmyenni committed May 28, 2024
1 parent 4864cb7 commit d0c80f1
Showing 1 changed file with 31 additions and 16 deletions.
47 changes: 31 additions & 16 deletions DataCleaningScripts/mayfield.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ species <- read.csv("SiteandMethods/species_list.csv")
#'
nests <- read.csv("Nesting/nest_checks.csv", na.strings = "") %>%
dplyr::filter(year>=2017) %>%
dplyr::mutate(species = replace(species, species %in% c("unkn", "anhi", "coga", "rsha", "grhe"), "smhe")) %>%
plyr::join(species[,c(1,5,6)], by = "species") %>%
dplyr::mutate(date = lubridate::as_date(date),
eggs = as.integer(eggs),
Expand All @@ -15,20 +16,20 @@ nests <- read.csv("Nesting/nest_checks.csv", na.strings = "") %>%
(is.na(stage) & chicks %in% c(1:10)) ~ "nestling",
(is.na(stage) & !(eggs %in% c(1:10)) & !(chicks %in% c(1:10))) ~ "empty",
TRUE ~ stage)) %>%
dplyr::mutate(start_date = dplyr::case_when(stage == "incubating" ~ date-1,
stage == "pipping" ~ date - incubation_j,
stage == "hatching" ~ date - incubation_j,
stage == "wet_chick" ~ date - incubation_j,
stage == "chick_dry" ~ date - incubation_j - 1,
stage == "nestling" ~ date - incubation_j - 2,
dplyr::mutate(start_date = dplyr::case_when(stage == "incubating" ~ date - eggs - 1,
stage == "pipping" ~ date - eggs - incubation_j - 1,
stage == "hatching" ~ date - eggs - incubation_j - 1,
stage == "wet_chick" ~ date - chicks - incubation_j - 1,
stage == "chick_dry" ~ date - chicks - incubation_j - 2,
stage == "nestling" ~ date - chicks - incubation_j - 3,
TRUE ~ NA),
incubation_end = dplyr::case_when(stage == "pipping" ~ date,
stage == "hatching" ~ date,
stage == "wet_chick" ~ date,
stage == "chick_dry" ~ date-1,
stage == "nestling" ~ date-2,
stage == "fledged" ~ date-nestling_j,
stage == "branchling" ~ date-nestling_j-2,
stage == "chick_dry" ~ date - 1,
stage == "nestling" ~ date - 2,
stage == "fledged" ~ date - nestling_j,
stage == "branchling" ~ date - nestling_j - 2,
TRUE ~ NA))
nest_success <- nests %>%
dplyr::rename(nest_number = nest) %>%
Expand All @@ -44,7 +45,7 @@ nest_success <- nests %>%
young_lost = clutch - fledged,
start_date = min(start_date, na.rm=TRUE),
incubation_end = max(incubation_end, na.rm=TRUE),
end_date = max(date, na.rm=TRUE),
end_date = dplyr::last(date[!(stage %in% c("empty", "missed", "collapsed", "pulled", "unknown"))]),
start_date = dplyr::case_when(!is.finite(start_date) ~ NA,
TRUE ~ start_date),
incubation_end = dplyr::case_when(!is.finite(incubation_end) ~ NA,
Expand All @@ -57,7 +58,19 @@ nest_success <- nests %>%
fledged %in% c(1:10) ~ 1,
TRUE ~ 0),
nestling_success = dplyr::case_when(fledged %in% c(1:10) ~ 1,
TRUE ~ 0))
any(stage %in% c("fledged","branchling")) ~ 1,
TRUE ~ 0)) %>%
plyr::join(species[,c(1,5,6)], by = "species") %>%
dplyr::mutate(n_days_incubation = dplyr::case_when(is.na(incubation_end) ~ as.numeric(end_date-start_date),
TRUE ~ n_days_incubation),
n_days_nestling = dplyr::case_when(n_days_incubation > incubation_j ~ n_days_nestling + n_days_incubation - incubation_j,
n_days_nestling > nestling_j ~ nestling_j,
is.na(n_days_nestling) & nestling_success==1 ~ nestling_j,
is.na(n_days_nestling) ~ 0,
TRUE ~ n_days_nestling),
n_days_incubation = dplyr::case_when(n_days_incubation > incubation_j ~ incubation_j,
is.na(n_days_incubation) ~ 0,
TRUE ~ n_days_incubation))

#' Do summary calculations
#'
Expand All @@ -66,7 +79,7 @@ nest_success_manual <- read.csv("Nesting/nest_success.csv")

success <- nest_success %>%
dplyr::filter(year>=2017) %>%
plyr::join(species[,c(1,5,6)], by = "species") %>%

# make consistent use of success columns
dplyr::mutate(incubation_success = dplyr::case_when(is.na(incubation_success) & brood %in% c(1:10) ~ 1,
is.na(incubation_success) & fledged %in% c(1:10) ~ 1,
Expand Down Expand Up @@ -94,7 +107,9 @@ success <- nest_success %>%
nestling_sdpj = sqrt(nestling_varpj),
overall_p = (incubation_p^incubation_j)*(nestling_p^nestling_j),
overall_varp = ((incubation_pj^2)*nestling_varpj)+((nestling_pj^2)*incubation_varpj)+(incubation_varpj*nestling_varpj),
overall_sd = sqrt(overall_varp))
overall_sd = sqrt(overall_varp)) %>%
dplyr::mutate_if(is.double, list(~dplyr::na_if(., Inf))) %>%
dplyr::mutate_if(is.double, list(~dplyr::na_if(., -Inf)))

compare <- dplyr::left_join(success,success_summary, by=dplyr::join_by(year, colony, species)) %>%
dplyr::filter(species %in% c("bcnh","gbhe","glib","greg","rosp","smhe","sneg","whib","wost"))
Expand Down Expand Up @@ -157,7 +172,7 @@ f <- ggplot(compare, aes(x=nestling_e.x, y=nestling_e.y)) +
theme_minimal()

g <- ggplot(compare, aes(x=incubation_j.x, y=incubation_j.y)) +
geom_jitter(aes(color=species)) +
geom_point(aes(color=species)) +
geom_abline(slope = 1, intercept = 0) +
annotate(geom="text", x=22, y=28, color="red",
label=paste("Missing:",sum(is.na(compare$incubation_j.y)))) +
Expand All @@ -166,7 +181,7 @@ g <- ggplot(compare, aes(x=incubation_j.x, y=incubation_j.y)) +
theme_minimal()

h <- ggplot(compare, aes(x=nestling_j.x, y=nestling_j.y)) +
geom_jitter(aes(color=species)) +
geom_point(aes(color=species)) +
geom_abline(slope = 1, intercept = 0) +
annotate(geom="text", x=20, y=50, color="red",
label=paste("Missing:",sum(is.na(compare$nestling_j.y)))) +
Expand Down

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