diff options
| -rw-r--r-- | R/plot.mkinfit.R | 21 | ||||
| -rw-r--r-- | R/plot.mmkin.R | 18 | ||||
| -rw-r--r-- | man/mmkin.Rd | 15 | ||||
| -rw-r--r-- | man/plot.mkinfit.Rd | 2 | ||||
| -rw-r--r-- | man/plot.mmkin.Rd | 4 |
5 files changed, 49 insertions, 11 deletions
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 317c74a3..58ff88bc 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -103,6 +103,27 @@ plot.mkinfit <- function(x, fit = x, ylim_row = ylim } + if (sep_obs) { + # Margins for top row of plots when we have more than one row + # Reduce bottom margin by 2.1 - hides x axis legend + if (plot_row == 1 & n_plot_rows > 1) { + par(mar = c(3.0, 4.1, 4.1, 2.1)) + } + + # Margins for middle rows of plots, if any + if (plot_row > 1 & plot_row < n_plot_rows) { + # Reduce top margin by 2 after the first plot as we have no main title, + # reduced plot height, therefore we need rel.height.middle in the layout + par(mar = c(3.0, 4.1, 2.1, 2.1)) + } + + # Margins for bottom row of plots when we have more than one row + if (plot_row == n_plot_rows & n_plot_rows > 1) { + # Restore bottom margin for last plot to show x axis legend + par(mar = c(5.1, 4.1, 2.1, 2.1)) + } + } + # Set up the main plot if not to be added to an existing plot if (add == FALSE) { plot(0, type="n", diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R index 7b54be4b..2cbb4a79 100644 --- a/R/plot.mmkin.R +++ b/R/plot.mmkin.R @@ -46,15 +46,29 @@ plot.mmkin <- function(x, main = "auto", legends = 1, errmin_var = "All data", e else rep(1, n.fits) layout(matrix(1:(2 * n.fits), n.fits, 2, byrow = TRUE), heights = rel.heights) - par(mar = c(3.0, 4.1, 4.1, 2.1)) # Reduce bottom margin by 2.1 - hides x axis legend par(cex = cex) for (i.fit in 1:n.fits) { - if (i.fit == 2) { + + # Margins for top row of plots when we have more than one row + # Reduce bottom margin by 2.1 - hides x axis legend + if (i.fit == 1 & n.fits > 1) { + par(mar = c(3.0, 4.1, 4.1, 2.1)) + } + + # Margins for middle rows of plots, if any + if (i.fit > 1 & i.fit < n.fits) { # Reduce top margin by 2 after the first plot as we have no main title, # reduced plot height, therefore we need rel.height.middle in the layout par(mar = c(3.0, 4.1, 2.1, 2.1)) } + + # Margins for bottom row of plots when we have more than one row + if (i.fit == n.fits & n.fits > 1) { + # Restore bottom margin for last plot to show x axis legend + par(mar = c(5.1, 4.1, 2.1, 2.1)) + } + fit <- x[[i.fit]] plot(fit, legend = legends == i.fit, ...) diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 44caf8d2..d088e804 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -45,16 +45,17 @@ mmkin(models, datasets, } \examples{ \dontrun{ -m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), - M1 = list(type = "SFO", to = "M2"), - M2 = list(type = "SFO"), use_of_ff = "max") +m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"), + M1 = mkinsub("SFO", "M2"), + M2 = mkinsub("SFO"), use_of_ff = "max") -m_synth_FOMC_lin <- mkinmod(parent = list(type = "FOMC", to = "M1"), - M1 = list(type = "SFO", to = "M2"), - M2 = list(type = "SFO"), use_of_ff = "max") +m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"), + M1 = mkinsub("SFO", "M2"), + M2 = mkinsub("SFO"), use_of_ff = "max") models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin) datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data) +names(datasets) <- paste("Dataset", 1:3) time_default <- system.time(fits.0 <- mmkin(models, datasets)) time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1)) @@ -66,9 +67,11 @@ endpoints(fits[["SFO_lin", 2]]) # Plot.mkinfit handles rows or columns of mmkin result objects plot(fits.0[1, ]) +plot(fits.0[, 1]) # Double brackets to select a single mkinfit object, which will be # plotted by plot.mkinfit plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE) +plot(fits.0[1, 1]) } } \keyword{ optimize } diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 00b2eca5..bc0b85e8 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -18,7 +18,7 @@ lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add, show_residuals = FALSE, maxabs = "auto", - sep_vars = FALSE, rel.height.middle = 0.9, + sep_obs = FALSE, rel.height.middle = 0.9, lpos = "topright", inset = c(0.05, 0.05), \dots) } \arguments{ diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index ffd83d2f..37d7a25a 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -45,9 +45,9 @@ Johannes Ranke } \examples{ - # Only use one core not to offend CRAN checks + # Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), - cores = 1, quiet = TRUE) + cores = 1, quiet = TRUE, method.modFit = "Marq") plot(fits[, "FOCUS C"]) plot(fits["FOMC", ]) |