raw

Author: smasongarrison

data-raw/1000_gps.png

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+# devtools::install_github("R-Computing-Lab/BGmisc")
+library(tidyverse)
+library(usethis)
+library(readr)
+
+#  https://doi.org/10.6084/m9.figshare.31513204.v2
+ped <- read_delim("data-raw/Pedigree4G.csv",
+  delim = ";", escape_double = FALSE,
+  trim_ws = TRUE
+) %>%
+  janitor::clean_names() %>%
+  rename(
+    ID = id,
+    dadID = sire,
+    momID = dam
+  )
+
+
+pheno <- read_delim("data-raw/FenotiposPesos90.csv",
+  col_types = cols(p0 = col_character()),
+  delim = ";", escape_double = FALSE, trim_ws = TRUE
+) %>%
+  janitor::clean_names() %>%
+  rename(
+    ID = id,
+    dadID = sire_id,
+    momID = dam_id
+  )
+
+# check the distribution of p0
+pheno %>%
+  pull(p0) %>%
+  table()
+
+
+pheno <- pheno %>%
+  mutate(
+    p0 = as.double(case_when(
+      p0 == "ABORTO" ~ NA_character_,
+      TRUE ~ p0
+    ))
+  )
+
+
+
+ped_pheno <- ped %>%
+  full_join(pheno, by = c("ID", "dadID", "momID"))
+
+# find the duplicated IDs in ped_pheno
+dup_id <- ped_pheno %>%
+  group_by(ID) %>%
+  summarise(n = n()) %>%
+  filter(n > 1) %>%
+  pull(ID)
+
+dup_id_df <- ped_pheno %>%
+  filter(ID %in% dup_id) %>%
+  arrange(ID)
+
+
+ped_growth <- ped_pheno %>%
+  filter(!is.na(p0)) %>%
+  select(
+    ID, Sexo, dadID, momID,
+    p0, p15, p30, p45, p60, p90
+  ) %>%
+  pivot_longer(
+    cols = starts_with("p"), names_to = "day",
+    values_to = "weight"
+  ) %>%
+  mutate(day = as.numeric(str_remove(day, "p")))
+
+# growth graph over time p0, p15, p30, p45, p60, p90, where 0 is day 0, 15 is day 15, etc.
+
+
+
+library(ggplot2)
+if (FALSE) {
+  pl <- ggplot(
+    ped_growth %>% filter(ID %in% sample(unique(ped_growth$ID), 1000)),
+    aes(x = day, y = weight, group = ID)
+  ) +
+    geom_line(alpha = 0.1) +
+    geom_jitter(alpha = 0.05, width = 1, height = 0) +
+    geom_smooth(method = "loess", se = TRUE, color = "blue", group = 1) +
+    labs(
+      title = "Growth Trajectories of Individuals Over Time",
+      x = "Day",
+      y = "Weight"
+    ) +
+    theme_minimal()
+  ##
+  pl
+}
+# data processing
+
+write.csv(ped_pheno, "data-raw/ped_pheno.csv", row.names = FALSE)
+usethis::use_data(ped_pheno, overwrite = TRUE, compress = "xz")