diff options
| -rw-r--r-- | ChangeLog | 13 | ||||
| -rw-r--r-- | R/twa.R | 11 | ||||
| -rw-r--r-- | docs/reference/one_box.html | 2 | ||||
| -rw-r--r-- | docs/reference/plot.one_box-8.png | bin | 13490 -> 13603 bytes | |||
| -rw-r--r-- | docs/reference/plot.one_box.html | 2 | ||||
| -rw-r--r-- | docs/reference/sawtooth-6.png | bin | 13490 -> 13603 bytes | |||
| -rw-r--r-- | docs/reference/sawtooth.html | 6 | ||||
| -rw-r--r-- | man/one_box.Rd | 2 | ||||
| -rw-r--r-- | man/plot.one_box.Rd | 2 | ||||
| -rw-r--r-- | man/sawtooth.Rd | 2 |
10 files changed, 26 insertions, 14 deletions
@@ -1,3 +1,16 @@ +commit dd30f0d0ff1d8d0cc46aaef6e0917c51fe798f52 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2017-01-19 10:36:19 +0100 + + Move mkin::twa to pfm::max_twa.mkinfit + + - Add max_twa.mkinfit() recently introduced to mkin as mkin::twa() but + never released with it + - Add a test to check max_twa.one_box() against analytical solutions in + max_twa.mkinfit(). + - Clean up R CMD check + - Update docs + commit 3ead7acba845b4f2552f555dfb29da889ed0cda8 Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2017-01-19 09:42:21 +0100 @@ -43,7 +43,7 @@ #' # Use a model with more than one observed variable #' m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) #' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) -#' pred_2 <- one_box(fit_2) +#' pred_2 <- one_box(fit_2, ini = "model") #' plot(pred_2) one_box <- function(x, ini, ..., t_end = 100, res = 0.01) @@ -99,11 +99,10 @@ one_box.character <- function(x, ini = 1, parms, ..., #' @export one_box.mkinfit <- function(x, ini = c("model", 1), ..., t_end = 100, res = 0.01) { fit <- x - - ini = match.arg(ini) - if (ini == "model") { + if (ini[1] == "model") { odeini = x$bparms.state } else { + if (ini[1] != 1) stop ("Argument ini can only be 'model' or 1") odeini <- c(1, rep(0, length(fit$mkinmod$spec) - 1)) names(odeini) <- names(fit$mkinmod$spec) } @@ -142,7 +141,7 @@ one_box.mkinfit <- function(x, ini = c("model", 1), ..., t_end = 100, res = 0.01 #' # Use a fitted mkinfit model #' m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) #' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) -#' pred_2 <- one_box(fit_2) +#' pred_2 <- one_box(fit_2, ini = 1) #' pred_2_saw <- sawtooth(pred_2, 2, 7) #' plot(pred_2_saw, max_twa = 21, max_twa_var = "m1") plot.one_box <- function(x, @@ -184,7 +183,7 @@ plot.one_box <- function(x, #' #' m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) #' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) -#' pred_2 <- one_box(fit_2) +#' pred_2 <- one_box(fit_2, ini = 1) #' pred_2_saw <- sawtooth(pred_2, 2, 7) #' plot(pred_2_saw, max_twa = 21, max_twa_var = "m1") #' diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index cb49c02..853f892 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -116,7 +116,7 @@ decline. If x is an mkinfit object, the decline is calculated from this object</ <span class='fu'>plot</span>(<span class='no'>pred_1</span>)</div><img src='one_box-4.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># Use a model with more than one observed variable</span> <span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>) +<span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>) <span class='fu'>plot</span>(<span class='no'>pred_2</span>)</div><img src='one_box-8.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/plot.one_box-8.png b/docs/reference/plot.one_box-8.png Binary files differindex f534444..161ecb4 100644 --- a/docs/reference/plot.one_box-8.png +++ b/docs/reference/plot.one_box-8.png diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index d43c415..d75b465 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -110,7 +110,7 @@ be shown if max_twa is not NULL.</dd> <span class='fu'>plot</span>(<span class='no'>dfop_pred</span>)</div><img src='plot.one_box-2.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><img src='plot.one_box-4.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># Use a fitted mkinfit model</span> <span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>) +<span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) <span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><img src='plot.one_box-8.png' alt='' width='540' height='400' /></pre> </div> diff --git a/docs/reference/sawtooth-6.png b/docs/reference/sawtooth-6.png Binary files differindex f534444..161ecb4 100644 --- a/docs/reference/sawtooth-6.png +++ b/docs/reference/sawtooth-6.png diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index 216f64a..be43745 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -98,12 +98,12 @@ the corresponding amounts applied in the second column.</dd> <span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>) <span class='fu'>plot</span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><img src='sawtooth-2.png' alt='' width='540' height='400' /><div class='input'> <span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>) +<span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) <span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><img src='sawtooth-6.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#> $max -#> parent m1 -#> 66.01096 85.08484 +#> parent m1 +#> 0.6627707 0.8542785 #> #> $window_start #> parent m1 diff --git a/man/one_box.Rd b/man/one_box.Rd index 8132a70..1bdc791 100644 --- a/man/one_box.Rd +++ b/man/one_box.Rd @@ -49,6 +49,6 @@ plot(pred_1) # Use a model with more than one observed variable m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) -pred_2 <- one_box(fit_2) +pred_2 <- one_box(fit_2, ini = "model") plot(pred_2) } diff --git a/man/plot.one_box.Rd b/man/plot.one_box.Rd index 69ee908..8c8a301 100644 --- a/man/plot.one_box.Rd +++ b/man/plot.one_box.Rd @@ -38,7 +38,7 @@ plot(sawtooth(dfop_pred, 3, 7), max_twa = 21) # Use a fitted mkinfit model m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) -pred_2 <- one_box(fit_2) +pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = "m1") } diff --git a/man/sawtooth.Rd b/man/sawtooth.Rd index 8eb8bea..3b1bd3e 100644 --- a/man/sawtooth.Rd +++ b/man/sawtooth.Rd @@ -30,7 +30,7 @@ plot(sawtooth(pred, applications = applications)) m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) -pred_2 <- one_box(fit_2) +pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = "m1") |
