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authorJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:24:04 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:24:04 +0100
commit22c11d5dbc118881f9cfd7c9c2ac9711295a0f16 (patch)
treea2c88069b82633027047c60bf656e53c4b561182 /R/drcfit.R
parentb05f8438729e8070f4e0cbbf628bbbcbbe3f1a7a (diff)
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
Diffstat (limited to 'R/drcfit.R')
-rw-r--r--R/drcfit.R31
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"]
}
}

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