Suppress error messages in dr(c)fit, maintenance

- Checking examples fails if error messages in dr(c)fit stemming from
failed fits are printed
- Delete trailing whitespace
- Update packaging

1 files changed, 18 insertions, 13 deletions

diff --git a/R/drcfit.R b/R/drcfit.R
index 8c52f6d..0d27c1c 100644
--- a/R/drcfit.R
+++ b/R/drcfit.R
@@ -14,7 +14,7 @@ drcfit <- function(data, chooseone=TRUE,
                                     # model result was appended
     rsubstance <- array()           # the substance names in the results
     rndl <- vector()                # number of dose levels
-    rn <- vector()                  # mean number of replicates 
+    rn <- vector()                  # mean number of replicates
                                     # in each dose level
     runit <- vector()               # vector of units for each result row
     rlhd <- rlld <- vector()        # highest and lowest doses tested
@@ -69,7 +69,8 @@ drcfit <- function(data, chooseone=TRUE,
                     active <- FALSE
                     if (linlogit)
                     {
-                        m <- try(drm(response ~ dose, data = tmp, fct = BC.4(fixed = c(NA, 1, NA, NA))))
+                        m <- try(drm(response ~ dose, data = tmp, fct = BC.4(fixed = c(NA, 1, NA, NA))),
+                                 silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -90,10 +91,11 @@ drcfit <- function(data, chooseone=TRUE,
                                 a[[ri]] <- coef(m)[[2]]
                                 b[[ri]] <- coef(m)[[1]]
                                 c[[ri]] <- coef(m)[[3]]
-                                ED50 <- try(ED(m, 50, interval = "delta", 
+                                ED50 <- try(ED(m, 50, interval = "delta",
                                                lower = lowestdose / 10,
                                                upper = highestdose * 10,
-                                               display = FALSE))
+                                               display = FALSE),
+                                               silent = TRUE)
                                 if (!inherits(ED50, "try-error")) {
                                     logED50[[ri]] <- log10(ED50["1:50", "Estimate"])
                                     logED50low[[ri]] <- log10(ED50["1:50", "Lower"])
@@ -101,14 +103,14 @@ drcfit <- function(data, chooseone=TRUE,
                                     if (logED50[[ri]] > rlhd[[ri]]) {
                                         mtype[[ri]] <- "no fit"
                                     }
-                                } 
+                                }
                             }
                         }
                     }
                     if (probit)
                     {
-                        m <- try(drm(response ~ dose, data = tmp, 
-                                     fct = LN.2()))
+                        m <- try(drm(response ~ dose, data = tmp,
+                                     fct = LN.2()), silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -142,7 +144,8 @@ drcfit <- function(data, chooseone=TRUE,
                     }
                     if (logit)
                     {
-                        m <- try(drm(response ~ dose, data = tmp, fct = LL.2()))
+                        m <- try(drm(response ~ dose, data = tmp, fct = LL.2()),
+                                 silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -179,7 +182,8 @@ drcfit <- function(data, chooseone=TRUE,
                     }
                     if (weibull)
                     {
-                        m <- try(drm(response ~ dose, data = tmp, fct = W1.2()))
+                        m <- try(drm(response ~ dose, data = tmp, fct = W1.2()),
+                                 silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -252,7 +256,7 @@ drcfit <- function(data, chooseone=TRUE,
         }
     }
 
-    results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, 
+    results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype,
         logED50, logED50low, logED50high, runit, sigma, a, b)
     lower_level_percent = paste(100 * (1 - level)/2, "%", sep = "")
     upper_level_percent = paste(100 * (1 + level)/2, "%", sep = "")
@@ -275,12 +279,13 @@ drcfit <- function(data, chooseone=TRUE,
             mtype <- as.character(results[row.i, "mtype"])
             if (mtype %in% c("probit", "logit", "weibull", "linlogit")) {
                 for (EDi in EDx) {
-                    EDx.drc = try(ED(m, EDi, interval = "delta", display = FALSE, level = level))
+                    EDx.drc = try(ED(m, EDi, interval = "delta", display = FALSE, level = level),
+                                  silent = TRUE)
                     if (!inherits(EDx.drc, "try-error")) {
                         results[row.i, paste0("EDx", EDi)] <- EDx.drc[paste0("1:", EDi), "Estimate"]
-                        results[row.i, paste0("EDx", EDi, " ", lower_level_percent)] <- EDx.drc[paste0("1:", EDi), 
+                        results[row.i, paste0("EDx", EDi, " ", lower_level_percent)] <- EDx.drc[paste0("1:", EDi),
                                                                                                 "Lower"]
-                        results[row.i, paste0("EDx", EDi, " ", upper_level_percent)] <- EDx.drc[paste0("1:", EDi), 
+                        results[row.i, paste0("EDx", EDi, " ", upper_level_percent)] <- EDx.drc[paste0("1:", EDi),
                                                                                                 "Upper"]
                     }
                 }