lintr cleanup for 0.7.1

lanl · Dec 29, 2024 · 6cd46c7 · 6cd46c7
1 parent d898349
commit 6cd46c7
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Showing 15 changed files with 76 additions and 272 deletions.
diff --git a/R/calibrate_ambient_carbon_gainoffset.R b/R/calibrate_ambient_carbon_gainoffset.R
@@ -1,5 +1,5 @@
 calibrate_ambient_carbon_Bowling2003 <- function(...) {
-  lifecycle::deprecate_soft("0.7.1","calibrate_ambient_carbon_Bowling2003()",
+  lifecycle::deprecate_soft("0.7.1", "calibrate_ambient_carbon_Bowling2003()",
                             "calibrate_ambient_carbon_gainoffset()")
   calibrate_ambient_carbon_gainoffset(...)
 }
@@ -44,13 +44,13 @@ calibrate_ambient_carbon_Bowling2003 <- function(...) {
 #' @importFrom lubridate %within%
 #'
 calibrate_ambient_carbon_gainoffset <- function(amb_data_list,
-                                                 caldf,
-                                                 site,
-                                                 filter_data = TRUE,
-                                                 force_to_end = TRUE,
-                                                 force_to_beginning = TRUE,
-                                                 gap_fill_parameters = FALSE,
-                                                 r2_thres = 0.9) {
+                                                caldf,
+                                                site,
+                                                filter_data = TRUE,
+                                                force_to_end = TRUE,
+                                                force_to_beginning = TRUE,
+                                                gap_fill_parameters = FALSE,
+                                                r2_thres = 0.9) {
 
   #-----------------------------------------------------------
   # should be able to get a calGainsOffsets object from the H5 file.
@@ -108,7 +108,7 @@ calibrate_ambient_carbon_gainoffset <- function(amb_data_list,
       # print notice that we're gap filling
       print("Gap filling calibrations...")
       # 12CO2 calibration parameters.
-      if (!is.na(caldf$r2_12C[i]) & caldf$r2_12C[i] < r2_thres) {
+      if (!is.na(caldf$r2_12C[i]) && caldf$r2_12C[i] < r2_thres) {
         # if we're in calibration period 2 or later, carry previous
         # calibration period forward. else if the first calibration period
         # is bad, find the first good calibration period at index n,
@@ -126,7 +126,7 @@ calibrate_ambient_carbon_gainoffset <- function(amb_data_list,
       }
 
       # 13CO2 calibration parameters - equivalent logic to 12Co2.
-      if (!is.na(caldf$r2_13C[i]) & caldf$r2_13C[i] < r2_thres) {
+      if (!is.na(caldf$r2_13C[i]) && caldf$r2_13C[i] < r2_thres) {
         if (i > 1) {
           caldf$gain13C[i] <- caldf$gain13C[i - 1]
           caldf$offset13C[i] <- caldf$offset13C[i - 1]

diff --git a/R/calibrate_ambient_carbon_linreg.R b/R/calibrate_ambient_carbon_linreg.R
@@ -71,7 +71,7 @@ calibrate_ambient_carbon_linreg <- function(amb_data_list,
   # determine which cal period each ambient data belongs to.
   var_inds_in_calperiod <- list()
 
-  for (i in 1:nrow(caldf)) {
+  for (i in seq_len(nrow(caldf))) {
     int <- lubridate::interval(caldf$timeBgn[i], caldf$timeEnd[i])
     var_inds_in_calperiod[[i]] <- which(amb_end_times %within% int)
 
@@ -80,7 +80,7 @@ calibrate_ambient_carbon_linreg <- function(amb_data_list,
       # print notice that we're gap filling
       print("Gap filling calibrations...")
 
-      if (!is.na(caldf$d13C_r2[i]) & caldf$d13C_r2[i] < r2_thres) {
+      if (!is.na(caldf$d13C_r2[i]) && caldf$d13C_r2[i] < r2_thres) {
         # if we're in calibration period 2 or later, carry previous
         # calibration period forward. else if the first calibration period
         # is bad, find the first good calibration period at index n,
@@ -98,7 +98,7 @@ calibrate_ambient_carbon_linreg <- function(amb_data_list,
       }
 
       # apply same logic to CO2 calibration.
-      if (!is.na(caldf$co2_r2[i]) & caldf$co2_r2[i] < r2_thres) {
+      if (!is.na(caldf$co2_r2[i]) && caldf$co2_r2[i] < r2_thres) {
         if (i > 1) {
           caldf$co2_slope[i] <- caldf$co2_slope[i - 1]
           caldf$co2_intercept[i] <- caldf$co2_intercept[i - 1]
@@ -128,7 +128,7 @@ calibrate_ambient_carbon_linreg <- function(amb_data_list,
   co2_ambdf$cv5rmse  <- rep(NA, length(co2_ambdf$mean))
   co2_ambdf$cv5mae   <- rep(NA, length(co2_ambdf$mean))
 
-  for (i in 1:length(var_inds_in_calperiod)) {
+  for (i in seq_along(var_inds_in_calperiod)) {
 
     d13c_ambdf$mean_cal[var_inds_in_calperiod[[i]]] <- caldf$d13C_intercept[i] +
       d13c_ambdf$mean[var_inds_in_calperiod[[i]]] * caldf$d13C_slope[i]

diff --git a/R/calibrate_ambient_water_isotopes.R b/R/calibrate_ambient_water_isotopes.R
@@ -77,8 +77,8 @@ calibrate_ambient_water_linreg <- function(amb_data_list,
   oxydf$max_cal  <- oxydf$max
   oxydf$min_cal  <- oxydf$min
 
-  for (i in 1:length(var_inds_in_calperiod)) {
-    if (!is.na(caldf$r2_18O[i]) & caldf$r2_18O[i] > r2_thres) {
+  for (i in seq_along(var_inds_in_calperiod)) {
+    if (!is.na(caldf$r2_18O[i]) && caldf$r2_18O[i] > r2_thres) {
 
       oxydf$mean_cal[var_inds_in_calperiod[[i]]] <- caldf$intercept18O[i] +
         oxydf$mean[var_inds_in_calperiod[[i]]] * caldf$slope18O[i]
@@ -129,7 +129,7 @@ calibrate_ambient_water_linreg <- function(amb_data_list,
   # determine which cal period each ambient data belongs to.
   var_inds_in_calperiod <- list()
 
-  for (i in 1:nrow(caldf)) {
+  for (i in seq_len(nrow(caldf))) {
     int <- lubridate::interval(caldf$timeBgn[i], caldf$timeEnd[i])
     var_inds_in_calperiod[[i]] <- which(amb_end_times %within% int)
   }
@@ -138,9 +138,9 @@ calibrate_ambient_water_linreg <- function(amb_data_list,
   hyddf$max_cal  <- hyddf$max
   hyddf$min_cal  <- hyddf$min
 
-  for (i in 1:length(var_inds_in_calperiod)) {
+  for (i in seq_along(var_inds_in_calperiod)) {
 
-    if (!is.na(caldf$r2_2H[i]) & caldf$r2_2H[i] > r2_thres) {
+    if (!is.na(caldf$r2_2H[i]) && caldf$r2_2H[i] > r2_thres) {
 
       hyddf$mean_cal[var_inds_in_calperiod[[i]]] <- caldf$intercept2H[i] +
         hyddf$mean[var_inds_in_calperiod[[i]]] * caldf$slope2H[i]

diff --git a/R/calibrate_carbon.R b/R/calibrate_carbon.R
@@ -147,9 +147,10 @@ calibrate_carbon         <- function(inname,
       inname <- inname[!grepl("2019-07", inname)]
     }
   }
-  
+
   if (method == "Bowling_2003") {
-    lifecycle::deprecate_warn("0.7.1","calibrate_carbon(method = 'Bowling_2003')",
+    lifecycle::deprecate_warn("0.7.1",
+                              "calibrate_carbon(method = 'Bowling_2003')",
                               "calibrate_carbon(method = 'gainoffset')")
   }
 

diff --git a/R/excised.R b/R/excised.R
diff --git a/R/isotope_conversions.R b/R/isotope_conversions.R
@@ -3,11 +3,11 @@
 # of isotope ratios and delta values.
 #------------------------------------------------------
 #' Return heavy-to-light isotope ratio of primary standard.
-#' 
+#'
 #' Returns the heavy-to-light isotope ratio of the dominant
 #' standard for that element. Vienna Standard Mean Ocean Water
 #' (VSMOW) for oxygen and hydrogen isotopes, Vienna Pee Dee
-#' Belemnite (VPDB) for carbon stable isotopes. 
+#' Belemnite (VPDB) for carbon stable isotopes.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'
@@ -36,8 +36,8 @@ get_Rstd <- function(element) {
 }
 
 #' Convert heavy-to-light isotope ratio to delta values.
-#' 
-#' Converts a heavy-to-light stable isotope ratio to 
+#'
+#' Converts a heavy-to-light stable isotope ratio to
 #' a corresponding delta value, in per mil values.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
@@ -64,7 +64,7 @@ R_to_delta <- function(R_values, element) {
 }
 
 #' Converts delta value to heavy-to-light isotope ratio
-#' 
+#'
 #' Converts a delta value (in per mil) to the heavy-to-light
 #' isotope ratio.
 #'
@@ -92,7 +92,7 @@ delta_to_R <- function(delta_values, element) {
 }
 
 #' Calculate 12C-CO2 Mole Fractions
-#' 
+#'
 #' This function calculates mole fractions of 12CO2 based on the total CO2 mole
 #' fraction, the delta13C value of the mixture, and the assumed fraction of CO2
 #' that does not correspond to 12CO2 or 13CO2 (assumed fixed at 0.00474, e.g.,
@@ -127,7 +127,7 @@ calculate_12CO2 <- function(total_co2, delta13c, f = 0.00474) {
 }
 
 #' Calculate 13C-CO2 Mole Fractions
-#' 
+#'
 #' This function calculates mole fractions of 13CO2 based on the total CO2 mole
 #' fraction, the delta13C value of the mixture, and the assumed fraction of CO2
 #' that does not correspond to 12CO2 or 13CO2 (assumed fixed at 0.00474, e.g.,