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+    "markdown": "---\ntitle: \"Correlation Matrices of Case Study Data\"\nformat: \n  html:\n    code-fold: true\n    echo: true\neditor: visual\nnumber-sections: true\nexecute:\n  freeze: auto  # re-render only when source changes\ntoc: false\npre-render: \"utils.R\"\nbibliography: \n  - ../ms/references.bib\n  - ../ms/grateful-refs.bib\n---\n\n::: {.cell}\n\n```{.r .cell-code}\nlibrary(tidyverse)\nlibrary(ManyEcoEvo)\nlibrary(GGally)\nset.seed(1234)\nsource(here::here(\"utils.R\"))\n```\n:::\n\n\n\n\nPairwise-correlation plots for the *Eucalyptus* and blue tit case-study data provided to analysts are shown in @fig-ggpairs-eucalyptus and @fig-ggpairs-bt, respectively. Plots were created with R package `GGally` [@GGally].\n\n\n\n\n::: {.cell .fig-column-screen}\n\n```{.r .cell-code}\neuc_data %>%\n  select(where(is_double),\n         -Date, \n         -`Quadrat no`,\n         -Easting, \n         -Northing,\n         -`small*0.25+medium*1.25+large*2.5`,\n         -`average.proportion.of.plots.containing.at.least.one.euc.seedling.of.any.size`) %>%\n  GGally::ggpairs()\n```\n\n::: {.cell-output-display}\n![Pairwise correllation plot for all *Eucalyptus* dataset variables except for `Date`, `Quadrat no`, `Easting`, `Northing`.](SM4_case_study_datasets_files/figure-html/fig-ggpairs-eucalyptus-1.png){#fig-ggpairs-eucalyptus width=1920}\n:::\n:::\n\n::: {.cell .fig-column-screen}\n\n```{.r .cell-code}\nblue_tit_data %>%\n  naniar::replace_with_na_all(condition = ~ .x == \".\") %>% \n  mutate(across(c(contains(\"_ring\"), \n                  rear_nest_trt, \n                  hatch_year, \n                  hatch_nest_breed_ID,\n                  hatch_Area,\n                  hatch_Box,\n                  day14_measurer,\n                  contains(\"hatch_Box\"),\n                  starts_with(\"rear_\"),\n                  starts_with(\"hatch_nest\"),\n                  home_or_away,\n                  -rear_d0_rear_nest_brood_size,\n                  contains(\"manipulation\"),\n                  chick_sex_molec,\n                  Date_of_day14,\n                  `Extra-pair_paternity`,\n                  -rear_Cs_in,\n                  -rear_Cs_out,\n                  chick_survival_to_first_breed_season,\n                  -rear_Cs_at_start_of_rearing), \n                as.factor),\n         across(where(is.character), as.numeric),\n         across(c(rear_Cs_out,\n                  rear_Cs_in,\n                  rear_Cs_at_start_of_rearing),\n                as.integer)) %>% \n  select(where(is.numeric), -`day 14 weight`) %>% \n  GGally::ggpairs() \n```\n\n::: {.cell-output-display}\n![Pairwise correlation plot of all numeric variables in blue tit case study dataset](SM4_case_study_datasets_files/figure-html/fig-ggpairs-bt-1.png){#fig-ggpairs-bt width=1440}\n:::\n:::\n",
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