Update model params. Closes #1. Closes #2.

brews · Jan 3, 2019 · cfbd1a3 · cfbd1a3
1 parent e7c2623
commit cfbd1a3
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Showing 8 changed files with 30,017 additions and 30,021 deletions.
diff --git a/R/predict.R b/R/predict.R
@@ -31,9 +31,8 @@ quantile.prediction <- function(x, ...) {
 #' @param d18osw Numeric or vector of observed seawater d18O (‰ VSMOW). 
 #' @param foram Optional. String or \code{NULL}. String indicating the foram 
 #'species/subspecies to infer for hierarchical models. String must be one of 
-#'"G. bulloides", "G. ruber white", "G. ruber pink", "G. sacculifer", 
-#'"N. incompta", or "N. pachyderma sinistral". \code{NULL} indicates that a 
-#'pooled model is desired.
+#'"G. bulloides", "G. ruber", "T. sacculifer", "N. incompta", or 
+#'"N. pachyderma". \code{NULL} indicates that a pooled model is desired.
 #' @param seasonal_seatemp Optional boolean indicating whether to use the seasonal 
 #'sea-surface temperature calibrations. Default is \code{FALSE}, i.e. using 
 #'annual SST calibrations.
@@ -59,13 +58,13 @@ quantile.prediction <- function(x, ...) {
 #' @seealso \code{\link{predict_seatemp}}, \code{\link{predictplot}}
 #'
 #' @examples
-#' # Infer d18Oc for ruber white core top sample using annual hierarchical model.
+#' # Infer d18Oc for a G. bulloides core top sample using annual hierarchical model.
 #' # The true, d18Oc for this sample is -2.16 (‰ VPDB).
-#' delo_ann <- predict_d18oc(seatemp=28.6, d18osw=0.48, foram="G. ruber white")
+#' delo_ann <- predict_d18oc(seatemp=28.6, d18osw=0.48, foram="G. bulloides")
 #' head(quantile(delo_ann, probs=c(0.159, 0.5, 0.841)))  # ± 1 standard deviation
 #'
 #' # Now using seasonal hierarchical model:
-#' delo_sea <- predict_d18oc(seatemp=28.6, d18osw=0.48, foram="G. ruber white",
+#' delo_sea <- predict_d18oc(seatemp=28.6, d18osw=0.48, foram="G. bulloides",
 #'                           seasonal_seatemp = TRUE)
 #' head(quantile(delo_sea, probs=c(0.159, 0.5, 0.841)))  # ± 1 standard deviation
 #'
@@ -104,9 +103,8 @@ predict_d18oc <- function(seatemp, d18osw, foram=NULL, seasonal_seatemp=FALSE,
 #'temperature (°C).
 #' @param foram Optional. String or \code{NULL}. String indicating the foram 
 #'species/subspecies to infer for hierarchical models. String must be one of 
-#'"G. bulloides", "G. ruber white", "G. ruber pink", "G. sacculifer", 
-#'"N. incompta", or "N. pachyderma sinistral". \code{NULL} indicates that a 
-#'pooled model is desired.
+#'"G. bulloides", "G. ruber", "T. sacculifer", "N. incompta", or 
+#'"N. pachyderma". \code{NULL} indicates that a pooled model is desired.
 #' @param seasonal_seatemp Optional boolean indicating whether to use the seasonal 
 #'sea-surface temperature calibrations. Default is \code{FALSE}, i.e. using 
 #'annual SST calibrations.

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/data-raw/annual_hierarchical_trace.csv b/data-raw/annual_hierarchical_trace.csv
diff --git a/data-raw/annual_pooled_trace.csv b/data-raw/annual_pooled_trace.csv
diff --git a/data-raw/seasonal_hierarchical_trace.csv b/data-raw/seasonal_hierarchical_trace.csv
diff --git a/data-raw/traces.R b/data-raw/traces.R
@@ -5,7 +5,7 @@ require("devtools")
 traces <- list()
 trace_files <- Sys.glob("*_trace.csv")
 for (fl in trace_files) {
-    basename <- unlist(strsplit(fl, '_trace'))[1]
+    basename <- unlist(strsplit(fl, "_trace"))[1]
     df <- read.csv(fl, check.names = FALSE)
     traces[[basename]] <- df
 }

diff --git a/man/predict_d18oc.Rd b/man/predict_d18oc.Rd
diff --git a/man/predict_seatemp.Rd b/man/predict_seatemp.Rd