From b9844e66c2eb1e99ee7b0fb16ce3aa7f67de8d45 Mon Sep 17 00:00:00 2001
From: fawda123 <mbafs2012@gmail.com>
Date: Sun, 11 Aug 2024 14:27:30 -0400
Subject: [PATCH] anlz_fibmatrix returns warning if some insufficient stations,
 error if no sufficient stations

---
 R/anlz_fibmatrix.R                   | 14 ++++++++++----
 tests/testthat/test-anlz_fibmatrix.R |  9 +++++++--
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/R/anlz_fibmatrix.R b/R/anlz_fibmatrix.R
index b871bc3e..858452af 100644
--- a/R/anlz_fibmatrix.R
+++ b/R/anlz_fibmatrix.R
@@ -123,15 +123,21 @@ anlz_fibmatrix <- function(fibdata,
   if(any(!chk))
     stop('Station(s) not found in fibdata: ', paste(stas[!chk], collapse = ', '))
 
-  # check stations include enough years
   chk <- !stas %in% stasval
-  if(any(chk))
-    stop('Stations with insufficient data for lagyr: ', paste(stas[chk], collapse = ', '))
+
+  # check if some stations valid for lagyr
+  if(sum(chk) > 0 & sum(chk) < length(chk))
+    warning('Stations with insufficient data for lagyr: ', paste(stas[chk], collapse = ', '))
+
+  # check if all stations invalid for lagyr
+  if(sum(chk) == length(chk)){
+    stop('No stations with sufficient data for lagyr')
+  }
 
   # get geomean, proportion of sites > 400 cfu / 100mL, and prob of exceedence
   # handles lagged calculations
   dat <- fibdata %>%
-    dplyr::filter(station %in% stas) %>%
+    dplyr::filter(station %in% stasval) %>%
     dplyr::filter(yr >= (yrrng[1] - (lagyr - 1)) & yr <= yrrng[2]) %>%
     dplyr::filter(!is.na(indic) | indic < 0) %>%
     summarise(
diff --git a/tests/testthat/test-anlz_fibmatrix.R b/tests/testthat/test-anlz_fibmatrix.R
index c52ac244..76ca1e4e 100644
--- a/tests/testthat/test-anlz_fibmatrix.R
+++ b/tests/testthat/test-anlz_fibmatrix.R
@@ -8,11 +8,16 @@ test_that("Checking anlz_fibmatrix station error", {
                fixed = T)
 })
 
-test_that("Checking anlz_fibmatrix station error insufficient data", {
-  expect_error(anlz_fibmatrix(fibdata, indic = 'fcolif', stas = '616'), regexp = 'Stations with insufficient data for lagyr: 616',
+test_that("Checking anlz_fibmatrix station warning some insufficient data", {
+  expect_warning(anlz_fibmatrix(fibdata, indic = 'fcolif', stas = c('115', '616')), regexp = 'Stations with insufficient data for lagyr: 616',
                fixed = T)
 })
 
+test_that("Checking anlz_fibmatrix station error all insufficient data", {
+  expect_warning(anlz_fibmatrix(fibdata, indic = 'fcolif', stas = '616'), regexp = 'No stations with sufficient data for lagyr',
+                 fixed = T)
+})
+
 # Example data
 fibdata <- data.frame(
   yr = rep(2000:2005, each = 3),