Merge pull request #120 from weecology/reports

Add nest success summaries and SFWMD report table script [minor]

DataCleaningScripts/get_nest_success.R

@@ -73,6 +73,35 @@ unique(success$species[which(!(success$species %in% species$species))])
 success <- success %>% dplyr::arrange(year,colony,species)
 write.table(success, "Nesting/nest_success.csv", row.names = FALSE, na = "", sep = ",", quote = 18)
 
+
+success_summary <- read.csv("Nesting/nest_success_summary.csv")
+success_summary_new <- read.csv("../Desktop/nest_success_summary.csv") %>%
+  dplyr::rename_with(tolower) %>%
+  dplyr::mutate(metric = tolower(metric),
+                metric = gsub(paste(c("[(]", "[)]"), collapse = "|"), "", metric),
+                metric = gsub("overall", "", metric),
+                metric = gsub("success", "", metric),
+                metric = gsub(" ", "", metric),
+                colony = replace(colony, colony=="cuthbert", "cuthbert_lake"),
+                colony = replace(colony, colony=="paurotis", "paurotis_pond")) %>%
+  tidyr::pivot_longer(cols = !c(year,colony,type,metric), 
+                      names_to = "species",
+                      values_to = "value") %>%
+  dplyr::filter(!is.na(value)) %>%
+  dplyr::mutate(variable = paste(type,metric,sep="_")) %>%
+  tidyr::pivot_wider(id_cols = c(year,colony,species), names_from = variable, values_from = value, 
+                     values_fill = NA) %>%
+  dplyr::mutate(year=as.integer(year)) %>% 
+  dplyr::arrange(year,colony,species)
+
+unique(success_summary_new$colony[which(!(success_summary_new$colony %in% colonies$colony))])
+unique(success_summary_new$species[which(!(success_summary_new$species %in% species$species))])
+
+success_summary <- success_summary %>% 
+                   dplyr::bind_rows(success_summary_new) %>%
+                   dplyr::arrange(year,colony,species)
+write.table(success_summary, "Nesting/nest_success_summary.csv", row.names = FALSE, na = "", sep = ",")
+
 # make metadata
 success_metadata <- data.frame(name = as.vector(colnames(success))) %>%
                     dplyr::mutate(class=sapply(success,class),

DataCleaningScripts/old_counts.R

@@ -59,7 +59,7 @@ counts <- counts %>% dplyr::arrange(counts)
 write.csv(counts, "Counts/maxcounts.csv", row.names = FALSE, na = "", quote = 9)
 
 species <- species %>% dplyr::arrange(species)
-write.csv(species, "SiteandMethods/species_list.csv", row.names = FALSE, na = "", quote = 5:25)
+write.csv(species, "SiteandMethods/species_list.csv", row.names = FALSE, na = "", quote = 7:27)
 
 colonies <- colonies %>% dplyr::arrange(colony)
 write.csv(colonies, "SiteandMethods/colonies.csv", row.names = FALSE, na = "", quote = c(7,8))

Nesting/README.md

@@ -3,12 +3,49 @@
 Please see the [methods](../SiteandMethods/methods.md) for details about collection and how to use the data.
 
 ### Nest Checks
+
 year
+
 colony
+
 nest - nest id
+
 species
+
 date
+
 eggs - number of eggs
+
 chicks - number of chicks
+
 stage - nesting stage
-notes
+
+notes
+
+### Nest Success
+
+We use the Mayfield method to calculate nest success. The nest-level metrics required for calculations are stored in this table. See the [metadata](../Nesting/nest_success_metadata.csv) for data details.
+
+### Nest Success Summary
+
+This is colony-level nest success, based on the data from the [nest_success table](../Nesting/nest_success.csv). Success is summarized for the incubation stage, nestling stage, and overall for the whole nesting period.
+
+k - total number of nests
+
+sumy - total number of nests that hatched (s(i))
+
+e - total number of days monitored (n(i))
+
+p - 1-((k-sumy)/e), success
+
+j - incubation or nestling period, in days (constant by species, can be found in the [species table](../SiteandMethods/species.csv))
+
+pj - p\^j, hatch success
+
+varp - (p\*(1-p))/e, variation of p
+
+varpj - varp\*((j\*(p\^(j-1)))\^2), variation of pj
+
+sdp - standard deviation of p
+
+sdpj - standard deviation of pj