updates to case study 2

case-study-2-butterfly/code/spAbundance-code/main-spAbundance.R

@@ -28,11 +28,8 @@ str(data.list)
 #          (6): week.cov: indicator for week of sampling.
 #          (7): site.cov: site id. 
 #          (8): county.cov: county id.
-#          (9): survey.cov: the total number of surveys performed for the 
-#                           given combination of year, week, spatial location. Note
-#                           this is actually equal to number of surveys - 1, such 
-#                           that a value of 0 corresponds to surveys with one 
-#                           survey (aka the intercept is expected count for one survey).
+#          (9): survey.cov: the log of the total number of surveys performed for the 
+#                           given combination of year, week, spatial location. 
 # Note that the object on GitHub has an identical format, except there is 
 # no column for oh.ind (since the Ohio data is not included). 
 

case-study-2-butterfly/code/spAbundance-code/summary-spAbundance.R

@@ -83,7 +83,8 @@ data.df <- data.frame(counts = c(t(data.list$y)),
 		      covs.df)
 data.df %>%
   group_by(sp, data.set) %>%
-  summarize(average = mean(counts, na.rm = TRUE)) %>%
+  summarize(average = mean(counts, na.rm = TRUE), 
+	    sd = sd(counts, na.rm = TRUE)) %>%
   arrange(sp, data.set) %>%
   print(n = nrow(.))
 

case-study-2-butterfly/code/stan-code/main-stan.R

@@ -26,11 +26,8 @@ str(data.list)
 #          (6): week.cov: indicator for week of sampling.
 #          (7): site.cov: site id. 
 #          (8): county.cov: county id.
-#          (9): survey.cov: the total number of surveys performed for the 
-#                           given combination of year, week, spatial location. Note
-#                           this is actually equal to number of surveys - 1, such 
-#                           that a value of 0 corresponds to surveys with one 
-#                           survey (aka the intercept is expected count for one survey).
+#          (9): survey.cov: the log of the total number of surveys performed for the 
+#                           given combination of year, week, spatial location. 
 
 # Format data in list for stan --------------------------------------------
 sp.names <- dimnames(data.list$y)[[1]]

case-study-2-butterfly/data/README.md

@@ -4,4 +4,5 @@ Contains some of the data used for the butterfly case study. Note this directory
 
 1. `BflyNames.csv`: contains information on butterfly common names, latin names, and codes.
 2. `DayWeek.csv`: contains information for linking different days of the year to specific weeks of the year.
-3. `spAbundance-data-github.csv`: contains the butterfly counts and covariate data for three of the five data sources used in the analysis: Illinois Butterfly Monitoring Network, Iowa Butterfly Survey Network, and Michigan Butterfly Network. These data are formatted for use when fitting the model in `spAbundance`. 
+3. `spAbundance-data-github.rda`: contains the butterfly counts and covariate data for three of the five data sources used in the analysis: Illinois Butterfly Monitoring Network, Iowa Butterfly Survey Network, and Michigan Butterfly Network. These data are formatted for use when fitting the model in `spAbundance`. 
+4. `butterfly-data-github.csv`: contains the same data as `spAbundance-data-github.rda`, but in CSV format.