chi_calc validation & address devtools::check

DESCRIPTION

@@ -27,6 +27,7 @@ Imports:
     glue (>= 1.6.1),
     odbc (>= 1.2.2),
     progressr,
+    qs,
     rads (>= 1.3.4), 
     rads.data,
     stats,

R/chi_calc.R

@@ -80,6 +80,19 @@ chi_calc <- function(ph.data = NULL,
     if (nrow(ph.instructions) == 0) stop("\n\U1F6D1 ph.instructions is empty")
     if (!is.data.table(ph.instructions)) setDT(ph.instructions)
 
+    # Validate year range in ph.instructions
+    if (nrow(ph.instructions[end > max(ph.data[['chi_year']], na.rm = T), ]) > 0){
+      warning("\u26A0\ufe0f There are rows in ph.instructions where the end year is > the maximum chi_year in ph.data.\n",
+              "These rows have been dropped from your instructions.", immediate. = TRUE)
+      ph.instructions <- ph.instructions[!(end > max(ph.data[['chi_year']], na.rm = T)),]
+    }
+
+    if (nrow(ph.instructions[start < min(ph.data[['chi_year']], na.rm = T), ]) > 0){
+      warning("\u26A0\ufe0f There are rows in ph.instructions where the start year is < the minimum chi_year in ph.data.\n",
+              "These rows have been dropped from your instructions.", immediate. = TRUE)
+      ph.instructions <- ph.instructions[!(start < min(ph.data[['chi_year']], na.rm = T)),]
+    }
+
     # Validate ci parameter
     if (!is.numeric(ci)) stop("\n\U1F6D1 ci must be numeric")
     if (ci <= 0 || ci >= 1) stop("\n\U1F6D1 ci must be between 0 and 1")

R/chi_get_proper_pop.R

@@ -187,8 +187,8 @@ chi_get_proper_pop <- function(pop.template = NULL,
       # Use a non-equi join to match all_population_data rows with pop.template rows
       # based on batched_id and proper year range
       population_subsets <- all_population_data[
-        pop.template[, .(batched_id, start, stop, row_index)],
-        on = .(batched_id == batched_id, year >= start, year <= stop),
+        pop.template[, list(batched_id, start, stop, row_index)],
+        on = list(batched_id == batched_id, year >= start, year <= stop),
         nomatch = 0  # Drop rows that don't match
       ]