From a3e058f8bceca903e7952e66abb4744f66115921 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Nov 2020 09:18:58 +0100 Subject: Some work on example code, pkgdown update --- docs/dev/reference/Rplot003.png | Bin 15451 -> 52903 bytes docs/dev/reference/Rplot004.png | Bin 13203 -> 49175 bytes docs/dev/reference/saem-1.png | Bin 0 -> 48512 bytes docs/dev/reference/saem-2.png | Bin 0 -> 48630 bytes docs/dev/reference/saem-3.png | Bin 0 -> 82018 bytes docs/dev/reference/saem-4.png | Bin 0 -> 128571 bytes docs/dev/reference/saem.html | 180 +++++++++---- docs/dev/reference/summary.saem.mmkin-1.png | Bin 0 -> 7742 bytes docs/dev/reference/summary.saem.mmkin.html | 385 ++++++++++++++++++---------- 9 files changed, 388 insertions(+), 177 deletions(-) create mode 100644 docs/dev/reference/saem-1.png create mode 100644 docs/dev/reference/saem-2.png create mode 100644 docs/dev/reference/saem-3.png create mode 100644 docs/dev/reference/saem-4.png create mode 100644 docs/dev/reference/summary.saem.mmkin-1.png (limited to 'docs/dev/reference') diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png index dd7e24f3..7514f1a4 100644 Binary files a/docs/dev/reference/Rplot003.png and b/docs/dev/reference/Rplot003.png differ diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png index 2057f883..2a90c6ee 100644 Binary files a/docs/dev/reference/Rplot004.png and b/docs/dev/reference/Rplot004.png differ diff --git a/docs/dev/reference/saem-1.png b/docs/dev/reference/saem-1.png new file mode 100644 index 00000000..9c3421bd Binary files /dev/null and b/docs/dev/reference/saem-1.png differ diff --git a/docs/dev/reference/saem-2.png b/docs/dev/reference/saem-2.png new file mode 100644 index 00000000..bc975b79 Binary files /dev/null and b/docs/dev/reference/saem-2.png differ diff --git a/docs/dev/reference/saem-3.png b/docs/dev/reference/saem-3.png new file mode 100644 index 00000000..5744b722 Binary files /dev/null and b/docs/dev/reference/saem-3.png differ diff --git a/docs/dev/reference/saem-4.png b/docs/dev/reference/saem-4.png new file mode 100644 index 00000000..b020dbbc Binary files /dev/null and b/docs/dev/reference/saem-4.png differ diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 25608fc8..26f4c3e3 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -229,27 +229,27 @@ using mmkin.

state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE) f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:09 2020" +#> [1] "Mon Nov 9 09:03:11 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:11 2020"
+#> [1] "Mon Nov 9 09:03:13 2020"
f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:12 2020" +#> [1] "Mon Nov 9 09:03:14 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:13 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Mon Nov 9 09:03:16 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:14 2020" +#> [1] "Mon Nov 9 09:03:16 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:16 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Mon Nov 9 09:03:18 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:16 2020" +#> [1] "Mon Nov 9 09:03:19 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:19 2020"
+#> [1] "Mon Nov 9 09:03:22 2020"
# The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) @@ -258,14 +258,47 @@ using mmkin.

#> Likelihoods computed by importance sampling
#> AIC BIC #> 1 624.2428 622.2900 #> 2 467.7644 465.0305 -#> 3 491.3541 487.8391
+#> 3 491.3541 487.8391
plot(f_saem_fomc$so, plot.type = "convergence") +
#> Plotting convergence plots
plot(f_saem_fomc$so, plot.type = "individual.fit") +
#> Plotting individual fits
plot(f_saem_fomc$so, plot.type = "npde") +
#> Simulating data using nsim = 1000 simulated datasets +#> Computing WRES and npde . +#> Plotting npde
#> --------------------------------------------- +#> Distribution of npde: +#> mean= -0.01736 (SE= 0.098 ) +#> variance= 0.8562 (SE= 0.13 ) +#> skewness= 0.513 +#> kurtosis= 1.202 +#> --------------------------------------------- +#> +#> Statistical tests +#> Wilcoxon signed rank test : 0.652 +#> Fisher variance test : 0.338 +#> SW test of normality : 0.0757 . +#> Global adjusted p-value : 0.227 +#> --- +#> Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 +#> ---------------------------------------------
plot(f_saem_fomc$so, plot.type = "vpc") +
#> Performing simulations under the model. +#> Plotting VPC +#> Method used for VPC: binning by quantiles on X , dividing into the following intervals +#> Interval Centered.On +#> 1 (-1,3] 1.3 +#> 2 (3,8] 7.4 +#> 3 (8,14] 13.2 +#> 4 (14,21] 20.5 +#> 5 (21,37.7] 29.5 +#> 6 (37.7,60] 50.4 +#> 7 (60,90] 76.6 +#> 8 (90,120] 109.0 +#> 9 (120,180] 156.0
f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:21 2020" +#> [1] "Mon Nov 9 09:03:24 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:26 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +#> [1] "Mon Nov 9 09:03:29 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
#> Likelihoods computed by importance sampling
#> AIC BIC #> 1 467.7644 465.0305 #> 2 469.4862 466.3617
@@ -285,46 +318,105 @@ using mmkin.

# solutions written for mkin this took around four minutes f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:28 2020" +#> [1] "Mon Nov 9 09:03:31 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:33 2020"
f_saem_dfop_sfo <- saem(f_mmkin["SFO-SFO", ]) +#> [1] "Mon Nov 9 09:03:36 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:33 2020" +#> [1] "Mon Nov 9 09:03:37 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:39 2020"
+#> [1] "Mon Nov 9 09:03:46 2020"
summary(f_saem_dfop_sfo, data = FALSE) +
#> saemix version used for fitting: 3.1.9000 +#> mkin version used for pre-fitting: 0.9.50.4 +#> R version used for fitting: 4.0.3 +#> Date of fit: Mon Nov 9 09:03:47 2020 +#> Date of summary: Mon Nov 9 09:03:47 2020 +#> +#> Equations: +#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * +#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) +#> * parent +#> d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) +#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * +#> exp(-k2 * time))) * parent - k_A1 * A1 +#> +#> Data: +#> 170 observations of 2 variable(s) grouped in 5 datasets +#> +#> Model predictions using solution type analytical +#> +#> Fitted in 9.758 s using 300, 100 iterations +#> +#> Variance model: Constant variance +#> +#> Mean of starting values for individual parameters: +#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 +#> 93.8101519 -9.7647455 -0.9711148 -1.8799371 -4.2708142 +#> g_qlogis +#> 0.1356441 +#> +#> Fixed degradation parameter values: +#> None +#> +#> Results: +#> +#> Likelihood computed by importance sampling +#> AIC BIC logLik +#> 841.3208 836.2435 -407.6604 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> est. lower upper +#> parent_0 93.7514328489 91.113651 96.3892150 +#> log_k_A1 -6.1262333211 -8.432492 -3.8199749 +#> f_parent_qlogis -0.9739851652 -1.371984 -0.5759863 +#> log_k1 -2.4818388836 -3.746899 -1.2167788 +#> log_k2 -3.6138616567 -5.294149 -1.9335743 +#> g_qlogis -0.0004613666 -1.063179 1.0622564 +#> +#> Correlation: +#> prnt_0 lg__A1 f_prn_ log_k1 log_k2 +#> log_k_A1 -0.013 +#> f_parent_qlogis -0.025 0.050 +#> log_k1 0.030 0.000 -0.005 +#> log_k2 0.013 0.005 -0.003 0.037 +#> g_qlogis -0.068 -0.016 0.011 -0.181 -0.181 +#> +#> Random effects: +#> est. lower upper +#> SD.parent_0 2.7857084 0.7825105 4.7889063 +#> SD.log_k_A1 2.1412505 0.4425207 3.8399803 +#> SD.f_parent_qlogis 0.4463087 0.1609059 0.7317116 +#> SD.log_k1 1.4097204 0.5240566 2.2953842 +#> SD.log_k2 1.8739067 0.6979362 3.0498773 +#> SD.g_qlogis 0.4559301 -0.8149852 1.7268453 +#> +#> Variance model: +#> est. lower upper +#> a.1 1.882757 1.665681 2.099832 +#> +#> Backtransformed parameters with asymmetric confidence intervals: +#> est. lower upper +#> parent_0 93.751432849 9.111365e+01 96.38921497 +#> k_A1 0.002184795 2.176784e-04 0.02192835 +#> f_parent_to_A1 0.274086887 2.022995e-01 0.35985666 +#> k1 0.083589373 2.359079e-02 0.29618269 +#> k2 0.026947583 5.020885e-03 0.14463032 +#> g 0.499884658 2.567024e-01 0.74312150 +#> +#> Resulting formation fractions: +#> ff +#> parent_A1 0.2741 +#> parent_sink 0.7259 +#> +#> Estimated disappearance times: +#> DT50 DT90 DT50back DT50_k1 DT50_k2 +#> parent 13.91 60.89 18.33 8.292 25.72 +#> A1 317.26 1053.91 NA NA NA
# Using a single core, the following takes about 6 minutes, using 10 cores # it is slower instead of faster -f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1) -
#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:39 2020" -#> DLSODA- At current T (=R1), MXSTEP (=I1) steps -#> taken on this call before reaching TOUT -#> In above message, I1 = 5000 -#> -#> In above message, R1 = 0.00156238 -#> -#> DLSODA- At T (=R1) and step size H (=R2), the -#> corrector convergence failed repeatedly -#> or with ABS(H) = HMIN -#> In above message, R1 = 0, R2 = 1.1373e-10 -#> -#> DLSODA- At current T (=R1), MXSTEP (=I1) steps -#> taken on this call before reaching TOUT -#> In above message, I1 = 5000 -#> -#> In above message, R1 = 2.24752e-06 -#> -#> DLSODA- At current T (=R1), MXSTEP (=I1) steps -#> taken on this call before reaching TOUT -#> In above message, I1 = 5000 -#> -#> In above message, R1 = 0.000585935 -#> -#> .... -#> Minimisation finished -#> [1] "Mon Nov 9 07:11:24 2020"
#> Warning: Creating predictions from the saemix model failed
# } +#f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1) +# } 
# S3 method for saem.mmkin
-summary(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...)
+summary(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...)
 
 # S3 method for summary.saem.mmkin
 print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)
@@ -220,25 +220,34 @@ The print method is called for its side effect, i.e. printing the summary. saemix authors for the parts inherited from saemix.

Examples

- 
# Generate five datasets following SFO kinetics
+    
# Generate five datasets following DFOP-SFO kinetics
 sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-dt50_sfo_in_pop <- 50
-k_in_pop <- log(2) / dt50_sfo_in_pop
+dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"),
+ m1 = mkinsub("SFO"), quiet = TRUE)
 set.seed(1234)
-k_in <- rlnorm(5, log(k_in_pop), 0.5)
-SFO <- mkinmod(parent = mkinsub("SFO"))
-
-pred_sfo <- function(k) {
-  mkinpredict(SFO,
-    c(k_parent = k),
-    c(parent = 100),
+k1_in <- rlnorm(5, log(0.1), 0.3)
+k2_in <- rlnorm(5, log(0.02), 0.3)
+g_in <- plogis(rnorm(5, qlogis(0.5), 0.3))
+f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3))
+k_m1_in <- rlnorm(5, log(0.02), 0.3)
+
+pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) {
+  mkinpredict(dfop_sfo,
+    c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1),
+    c(parent = 100, m1 = 0),
     sampling_times)
 }
 
-ds_sfo_mean <- lapply(k_in, pred_sfo)
-names(ds_sfo_mean) <- paste("ds", 1:5)
+ds_mean_dfop_sfo <- lapply(1:5, function(i) {
+  mkinpredict(dfop_sfo,
+    c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i],
+      f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]),
+    c(parent = 100, m1 = 0),
+    sampling_times)
+})
+names(ds_mean_dfop_sfo) <- paste("ds", 1:5)
 
-ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) {
+ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) {
   add_err(ds,
     sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),
     n = 1)[[1]]
@@ -246,34 +255,41 @@ saemix authors for the parts inherited from saemix.

 
 # \dontrun{
 # Evaluate using mmkin and saem
-f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
-f_saem <- saem(f_mmkin)
+f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, quiet = TRUE, error_model = "tc", cores = 5)
+f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
 
#> Running main SAEM algorithm
-#> [1] "Sun Nov  8 02:58:03 2020"
+#> [1] "Mon Nov  9 09:11:04 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sun Nov  8 02:58:07 2020"
summary(f_saem, data = TRUE)
+#> [1] "Mon Nov  9 09:11:16 2020"
summary(f_saem_dfop_sfo, data = TRUE)
 
#> saemix version used for fitting:      3.1.9000 
 #> mkin version used for pre-fitting:  0.9.50.4 
 #> R version used for fitting:         4.0.3 
-#> Date of fit:     Sun Nov  8 02:58:07 2020 
-#> Date of summary: Sun Nov  8 02:58:07 2020 
+#> Date of fit:     Mon Nov  9 09:11:17 2020 
+#> Date of summary: Mon Nov  9 09:11:17 2020 
 #> 
 #> Equations:
-#> d_parent/dt = - k_parent * parent
+#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+#>            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+#>            * parent
+#> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
+#>            * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
+#>            exp(-k2 * time))) * parent - k_m1 * m1
 #> 
 #> Data:
-#> 90 observations of 1 variable(s) grouped in 5 datasets
+#> 171 observations of 2 variable(s) grouped in 5 datasets
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted in 4.175 s using 300, 100 iterations
+#> Fitted in 13.497 s using 300, 100 iterations
 #> 
 #> Variance model: Two-component variance function 
 #> 
 #> Mean of starting values for individual parameters:
-#>     parent_0 log_k_parent 
-#>    97.849556    -4.455036 
+#>        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
+#>    101.65644697     -4.05368181     -0.94310703     -2.35943247     -4.07006293 
+#>        g_qlogis 
+#>     -0.01132621 
 #> 
 #> Fixed degradation parameter values:
 #> None
@@ -281,129 +297,232 @@ saemix authors for the parts inherited from saemix.

 #> Results:
 #> 
 #> Likelihood computed by importance sampling
-#>        AIC      BIC    logLik
-#>   555.6718 553.3284 -271.8359
+#>        AIC     BIC   logLik
+#>   828.8639 823.396 -400.432
 #> 
 #> Optimised, transformed parameters with symmetric confidence intervals:
-#>                   est.     lower      upper
-#> parent_0     97.840291 94.701895 100.978686
-#> log_k_parent -4.464246 -5.001413  -3.927078
+#>                         est.      lower       upper
+#> parent_0        101.35835807 97.8846505 104.8320657
+#> log_k_m1         -4.06644838 -4.1861445  -3.9467523
+#> f_parent_qlogis  -0.94818070 -1.3124706  -0.5838908
+#> log_k1           -2.92096208 -3.7684319  -2.0734922
+#> log_k2           -3.54529352 -4.2532018  -2.8373852
+#> g_qlogis         -0.09254475 -0.9675848   0.7824953
 #> 
 #> Correlation: 
-#>              prnt_0
-#> log_k_parent 0.022 
+#>                 prnt_0 lg_k_1 f_prn_ log_k1 log_k2
+#> log_k_m1        -0.217                            
+#> f_parent_qlogis -0.153  0.203                     
+#> log_k1           0.066 -0.067 -0.035              
+#> log_k2           0.002  0.010  0.001 -0.041       
+#> g_qlogis        -0.014  0.005  0.015 -0.163 -0.106
 #> 
 #> Random effects:
-#>                      est.     lower     upper
-#> SD.parent_0     3.0805465 0.4960170 5.6650760
-#> SD.log_k_parent 0.6109508 0.2301398 0.9917617
+#>                          est.      lower     upper
+#> SD.parent_0        2.70034095 -0.7003441 6.1010260
+#> SD.log_k_m1        0.08269959 -0.0456860 0.2110852
+#> SD.f_parent_qlogis 0.39452161  0.1376650 0.6513782
+#> SD.log_k1          0.90605744  0.2946394 1.5174755
+#> SD.log_k2          0.77604374  0.2646031 1.2874844
+#> SD.g_qlogis        0.37531563 -0.6836568 1.4342881
 #> 
 #> Variance model:
 #>           est.      lower      upper
-#> a.1 1.06249961 0.23012265 1.89487657
-#> b.1 0.04649661 0.03060849 0.06238473
+#> a.1 0.65736042 0.48750246 0.82721839
+#> b.1 0.06424086 0.05011127 0.07837046
 #> 
 #> Backtransformed parameters with asymmetric confidence intervals:
-#>                 est.        lower        upper
-#> parent_0 97.84029088 94.701895315 100.97868644
-#> k_parent  0.01151338  0.006728434   0.01970115
+#>                        est.       lower        upper
+#> parent_0       101.35835807 97.88465048 104.83206565
+#> k_m1             0.01713815  0.01520479   0.01931734
+#> f_parent_to_m1   0.27925085  0.21207372   0.35803781
+#> k1               0.05388182  0.02308824   0.12574588
+#> k2               0.02886015  0.01421864   0.05857864
+#> g                0.47688031  0.27536216   0.68621766
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.2793
+#> parent_sink 0.7207
 #> 
 #> Estimated disappearance times:
-#>        DT50 DT90
-#> parent 60.2  200
+#>         DT50   DT90 DT50back DT50_k1 DT50_k2
+#> parent 17.57  63.28    19.05   12.86   24.02
+#> m1     40.44 134.35       NA      NA      NA
 #> 
 #> Data:
-#>    ds   name time observed predicted   residual standardized
-#>  ds 1 parent    0    103.6    97.303   6.297361     -1.12720
-#>  ds 1 parent    0     95.9    97.303  -1.402639      0.25107
-#>  ds 1 parent    1     95.4    96.599  -1.198705      0.21583
-#>  ds 1 parent    1     95.3    96.599  -1.298705      0.23383
-#>  ds 1 parent    3     91.6    95.206  -3.606076      0.65693
-#>  ds 1 parent    3     94.5    95.206  -0.706076      0.12863
-#>  ds 1 parent    7     88.1    92.481  -4.380761      0.81692
-#>  ds 1 parent    7     89.6    92.481  -2.880761      0.53720
-#>  ds 1 parent   14     90.3    87.898   2.402166     -0.46649
-#>  ds 1 parent   14     96.0    87.898   8.102166     -1.57340
-#>  ds 1 parent   28     80.2    79.402   0.797948     -0.16783
-#>  ds 1 parent   28     77.9    79.402  -1.502052      0.31593
-#>  ds 1 parent   60     59.3    62.940  -3.639829      0.91247
-#>  ds 1 parent   60     59.6    62.940  -3.339829      0.83726
-#>  ds 1 parent   90     59.4    50.620   8.779547     -2.56999
-#>  ds 1 parent   90     51.0    50.620   0.379547     -0.11110
-#>  ds 1 parent  120     38.8    40.712  -1.912380      0.64706
-#>  ds 1 parent  120     38.9    40.712  -1.812380      0.61323
-#>  ds 2 parent    0    103.2    97.185   6.015158     -1.07774
-#>  ds 2 parent    0     95.1    97.185  -2.084842      0.37354
-#>  ds 2 parent    1     88.3    95.609  -7.309466      1.32706
-#>  ds 2 parent    1    102.4    95.609   6.790534     -1.23285
-#>  ds 2 parent    3     88.4    92.535  -4.134911      0.77071
-#>  ds 2 parent    3     95.2    92.535   2.665089     -0.49675
-#>  ds 2 parent    7     83.5    86.679  -3.179231      0.62426
-#>  ds 2 parent    7     96.4    86.679   9.720769     -1.90873
-#>  ds 2 parent   14     77.3    77.309  -0.009268      0.00199
-#>  ds 2 parent   14     76.0    77.309  -1.309268      0.28113
-#>  ds 2 parent   28     61.7    61.499   0.201491     -0.05137
-#>  ds 2 parent   28     56.5    61.499  -4.998509      1.27449
-#>  ds 2 parent   60     35.1    36.454  -1.353571      0.49087
-#>  ds 2 parent   60     32.2    36.454  -4.253571      1.54256
-#>  ds 2 parent   90     21.2    22.326  -1.125996      0.53604
-#>  ds 2 parent   90     23.3    22.326   0.974004     -0.46368
-#>  ds 2 parent  120     14.1    13.674   0.426440     -0.25110
-#>  ds 2 parent  120     16.9    13.674   3.226440     -1.89983
-#>  ds 3 parent    0     92.4    93.838  -1.437848      0.26501
-#>  ds 3 parent    0     94.0    93.838   0.162152     -0.02989
-#>  ds 3 parent    1     95.7    91.709   3.991384     -0.74932
-#>  ds 3 parent    1     90.8    91.709  -0.908616      0.17058
-#>  ds 3 parent    3     86.7    87.594  -0.893997      0.17409
-#>  ds 3 parent    3     85.8    87.594  -1.793997      0.34934
-#>  ds 3 parent    7     77.1    79.910  -2.810299      0.58817
-#>  ds 3 parent    7     81.5    79.910   1.589701     -0.33271
-#>  ds 3 parent   14     69.1    68.050   1.050102     -0.24845
-#>  ds 3 parent   14     62.4    68.050  -5.649898      1.33675
-#>  ds 3 parent   28     49.1    49.349  -0.248837      0.07412
-#>  ds 3 parent   28     47.2    49.349  -2.148837      0.64010
-#>  ds 3 parent   60     21.9    23.676  -1.775776      0.82085
-#>  ds 3 parent   60     23.6    23.676  -0.075776      0.03503
-#>  ds 3 parent   90     12.4    11.892   0.507660     -0.31425
-#>  ds 3 parent   90     13.8    11.892   1.907660     -1.18088
-#>  ds 3 parent  120      4.9     5.974  -1.073521      0.80099
-#>  ds 3 parent  120      7.5     5.974   1.526479     -1.13895
-#>  ds 4 parent    0     91.8   102.087 -10.287197      1.77084
-#>  ds 4 parent    0    104.6   102.087   2.512803     -0.43256
-#>  ds 4 parent    1    117.5   101.632  15.867689     -2.74145
-#>  ds 4 parent    1     99.3   101.632  -2.332311      0.40295
-#>  ds 4 parent    3     94.0   100.729  -6.728610      1.17100
-#>  ds 4 parent    3     98.7   100.729  -2.028610      0.35304
-#>  ds 4 parent    7    109.2    98.945  10.254756     -1.81080
-#>  ds 4 parent    7     89.2    98.945  -9.745244      1.72083
-#>  ds 4 parent   14    103.3    95.900   7.400009     -1.34021
-#>  ds 4 parent   14    103.0    95.900   7.100009     -1.28588
-#>  ds 4 parent   28     90.8    90.088   0.712227     -0.13563
-#>  ds 4 parent   28     88.7    90.088  -1.387773      0.26427
-#>  ds 4 parent   60     74.8    78.091  -3.291273      0.70124
-#>  ds 4 parent   60     75.3    78.091  -2.791273      0.59471
-#>  ds 4 parent   90     71.1    68.300   2.800407     -0.66075
-#>  ds 4 parent   90     78.0    68.300   9.700407     -2.28880
-#>  ds 4 parent  120     59.1    59.736  -0.635668      0.16554
-#>  ds 4 parent  120     53.8    59.736  -5.935668      1.54574
-#>  ds 5 parent    0     94.9    98.353  -3.452694      0.61266
-#>  ds 5 parent    0    101.8    98.353   3.447306     -0.61171
-#>  ds 5 parent    1     96.1    96.722  -0.621996      0.11187
-#>  ds 5 parent    1     97.1    96.722   0.378004     -0.06799
-#>  ds 5 parent    3     93.8    93.541   0.258738     -0.04781
-#>  ds 5 parent    3     85.8    93.541  -7.741262      1.43043
-#>  ds 5 parent    7     87.6    87.490   0.109848     -0.02141
-#>  ds 5 parent    7     94.0    87.490   6.509848     -1.26885
-#>  ds 5 parent   14     82.5    77.827   4.672679     -0.99818
-#>  ds 5 parent   14     81.7    77.827   3.872679     -0.82728
-#>  ds 5 parent   28     60.0    61.585  -1.585419      0.40382
-#>  ds 5 parent   28     61.0    61.585  -0.585419      0.14911
-#>  ds 5 parent   60     32.5    36.068  -3.568284      1.30251
-#>  ds 5 parent   60     35.5    36.068  -0.568284      0.20744
-#>  ds 5 parent   90     21.8    21.842  -0.042136      0.02028
-#>  ds 5 parent   90     24.4    21.842   2.557864     -1.23088
-#>  ds 5 parent  120     14.1    13.227   0.872898     -0.52035
-#>  ds 5 parent  120     12.1    13.227  -1.127102      0.67189
# }
+#>    ds   name time observed  predicted  residual standardized
+#>  ds 1 parent    0     89.8  9.848e+01  -8.68339     1.243323
+#>  ds 1 parent    0    104.1  9.848e+01   5.61661    -0.804209
+#>  ds 1 parent    1     88.7  9.403e+01  -5.32943     0.795687
+#>  ds 1 parent    1     95.5  9.403e+01   1.47057    -0.219557
+#>  ds 1 parent    3     81.8  8.584e+01  -4.04129     0.654791
+#>  ds 1 parent    3     94.5  8.584e+01   8.65871    -1.402929
+#>  ds 1 parent    7     71.5  7.196e+01  -0.46034     0.087182
+#>  ds 1 parent    7     70.3  7.196e+01  -1.66034     0.314448
+#>  ds 1 parent   14     54.2  5.384e+01   0.36125    -0.087766
+#>  ds 1 parent   14     49.6  5.384e+01  -4.23875     1.029821
+#>  ds 1 parent   28     31.5  3.220e+01  -0.69922     0.256514
+#>  ds 1 parent   28     28.8  3.220e+01  -3.39922     1.247025
+#>  ds 1 parent   60     12.1  1.264e+01  -0.53539     0.364441
+#>  ds 1 parent   60     13.6  1.264e+01   0.96461    -0.656614
+#>  ds 1 parent   90      6.2  6.081e+00   0.11929    -0.113824
+#>  ds 1 parent   90      8.3  6.081e+00   2.21929    -2.117659
+#>  ds 1 parent  120      2.2  3.055e+00  -0.85531     1.001955
+#>  ds 1 parent  120      2.4  3.055e+00  -0.65531     0.767664
+#>  ds 1     m1    1      0.3  1.115e+00  -0.81540     1.118502
+#>  ds 1     m1    1      0.2  1.115e+00  -0.91540     1.255673
+#>  ds 1     m1    3      2.2  3.111e+00  -0.91095     1.062691
+#>  ds 1     m1    3      3.0  3.111e+00  -0.11095     0.129432
+#>  ds 1     m1    7      6.5  6.292e+00   0.20799    -0.195930
+#>  ds 1     m1    7      5.0  6.292e+00  -1.29201     1.217079
+#>  ds 1     m1   14     10.2  9.886e+00   0.31362    -0.242650
+#>  ds 1     m1   14      9.5  9.886e+00  -0.38638     0.298948
+#>  ds 1     m1   28     12.2  1.259e+01  -0.39388     0.268603
+#>  ds 1     m1   28     13.4  1.259e+01   0.80612    -0.549726
+#>  ds 1     m1   60     11.8  1.092e+01   0.87659    -0.644982
+#>  ds 1     m1   60     13.2  1.092e+01   2.27659    -1.675083
+#>  ds 1     m1   90      6.6  7.814e+00  -1.21445     1.047509
+#>  ds 1     m1   90      9.3  7.814e+00   1.48555    -1.281347
+#>  ds 1     m1  120      3.5  5.275e+00  -1.77526     1.781944
+#>  ds 1     m1  120      5.4  5.275e+00   0.12474    -0.125213
+#>  ds 2 parent    0    118.0  1.045e+02  13.54366    -1.838241
+#>  ds 2 parent    0     99.8  1.045e+02  -4.65634     0.631992
+#>  ds 2 parent    1     90.2  9.872e+01  -8.51733     1.216927
+#>  ds 2 parent    1     94.6  9.872e+01  -4.11733     0.588270
+#>  ds 2 parent    3     96.1  8.872e+01   7.38009    -1.160975
+#>  ds 2 parent    3     78.4  8.872e+01 -10.31991     1.623443
+#>  ds 2 parent    7     77.9  7.337e+01   4.52584    -0.842647
+#>  ds 2 parent    7     77.7  7.337e+01   4.32584    -0.805409
+#>  ds 2 parent   14     56.0  5.616e+01  -0.15795     0.037034
+#>  ds 2 parent   14     54.7  5.616e+01  -1.45795     0.341841
+#>  ds 2 parent   28     36.6  3.859e+01  -1.99435     0.635813
+#>  ds 2 parent   28     36.8  3.859e+01  -1.79435     0.572052
+#>  ds 2 parent   60     22.1  2.113e+01   0.97273    -0.482843
+#>  ds 2 parent   60     24.7  2.113e+01   3.57273    -1.773425
+#>  ds 2 parent   90     12.4  1.258e+01  -0.17909     0.122205
+#>  ds 2 parent   90     10.8  1.258e+01  -1.77909     1.214019
+#>  ds 2 parent  120      6.8  7.509e+00  -0.70864     0.621767
+#>  ds 2 parent  120      7.9  7.509e+00   0.39136    -0.343380
+#>  ds 2     m1    1      1.3  1.466e+00  -0.16566     0.220431
+#>  ds 2     m1    3      3.7  3.947e+00  -0.24719     0.271357
+#>  ds 2     m1    3      4.7  3.947e+00   0.75281    -0.826421
+#>  ds 2     m1    7      8.1  7.501e+00   0.59910    -0.525881
+#>  ds 2     m1    7      7.9  7.501e+00   0.39910    -0.350323
+#>  ds 2     m1   14     10.1  1.082e+01  -0.71564     0.529253
+#>  ds 2     m1   14     10.3  1.082e+01  -0.51564     0.381342
+#>  ds 2     m1   28     10.7  1.248e+01  -1.78322     1.221977
+#>  ds 2     m1   28     12.2  1.248e+01  -0.28322     0.194082
+#>  ds 2     m1   60     10.7  1.058e+01   0.12295    -0.091967
+#>  ds 2     m1   60     12.5  1.058e+01   1.92295    -1.438427
+#>  ds 2     m1   90      9.1  8.029e+00   1.07074    -0.912688
+#>  ds 2     m1   90      7.4  8.029e+00  -0.62926     0.536381
+#>  ds 2     m1  120      6.1  5.816e+00   0.28391    -0.275375
+#>  ds 2     m1  120      4.5  5.816e+00  -1.31609     1.276529
+#>  ds 3 parent    0    106.2  1.048e+02   1.43237    -0.193885
+#>  ds 3 parent    0    106.9  1.048e+02   2.13237    -0.288636
+#>  ds 3 parent    1    107.4  9.616e+01  11.23530    -1.643774
+#>  ds 3 parent    1     96.1  9.616e+01  -0.06470     0.009466
+#>  ds 3 parent    3     79.4  8.238e+01  -2.97800     0.500554
+#>  ds 3 parent    3     82.6  8.238e+01   0.22200    -0.037315
+#>  ds 3 parent    7     63.9  6.427e+01  -0.36601     0.076477
+#>  ds 3 parent    7     62.4  6.427e+01  -1.86601     0.389900
+#>  ds 3 parent   14     51.0  4.825e+01   2.74941    -0.731807
+#>  ds 3 parent   14     47.1  4.825e+01  -1.15059     0.306250
+#>  ds 3 parent   28     36.1  3.501e+01   1.09474    -0.376700
+#>  ds 3 parent   28     36.6  3.501e+01   1.59474    -0.548750
+#>  ds 3 parent   60     20.1  2.050e+01  -0.40214     0.203675
+#>  ds 3 parent   60     19.8  2.050e+01  -0.70214     0.355617
+#>  ds 3 parent   90     11.3  1.257e+01  -1.27210     0.868328
+#>  ds 3 parent   90     10.7  1.257e+01  -1.87210     1.277883
+#>  ds 3 parent  120      8.2  7.710e+00   0.48984    -0.424960
+#>  ds 3 parent  120      7.3  7.710e+00  -0.41016     0.355837
+#>  ds 3     m1    0      0.8 -1.421e-13   0.80000    -1.216988
+#>  ds 3     m1    1      1.8  1.928e+00  -0.12842     0.164382
+#>  ds 3     m1    1      2.3  1.928e+00   0.37158    -0.475623
+#>  ds 3     m1    3      4.2  4.925e+00  -0.72511     0.744654
+#>  ds 3     m1    3      4.1  4.925e+00  -0.82511     0.847349
+#>  ds 3     m1    7      6.8  8.542e+00  -1.74215     1.444429
+#>  ds 3     m1    7     10.1  8.542e+00   1.55785    -1.291627
+#>  ds 3     m1   14     11.4  1.096e+01   0.44492    -0.326877
+#>  ds 3     m1   14     12.8  1.096e+01   1.84492    -1.355438
+#>  ds 3     m1   28     11.5  1.122e+01   0.27920    -0.202587
+#>  ds 3     m1   28     10.6  1.122e+01  -0.62080     0.450442
+#>  ds 3     m1   60      7.5  8.912e+00  -1.41171     1.147867
+#>  ds 3     m1   60      8.6  8.912e+00  -0.31171     0.253453
+#>  ds 3     m1   90      7.3  6.683e+00   0.61657    -0.567369
+#>  ds 3     m1   90      8.1  6.683e+00   1.41657    -1.303536
+#>  ds 3     m1  120      5.3  4.825e+00   0.47527    -0.491339
+#>  ds 3     m1  120      3.8  4.825e+00  -1.02473     1.059361
+#>  ds 4 parent    0    104.7  9.956e+01   5.14415    -0.729366
+#>  ds 4 parent    0     88.3  9.956e+01 -11.25585     1.595915
+#>  ds 4 parent    1     94.2  9.639e+01  -2.19462     0.320391
+#>  ds 4 parent    1     94.6  9.639e+01  -1.79462     0.261995
+#>  ds 4 parent    3     78.1  9.044e+01 -12.34368     1.908558
+#>  ds 4 parent    3     96.5  9.044e+01   6.05632    -0.936418
+#>  ds 4 parent    7     76.2  7.988e+01  -3.67799     0.635364
+#>  ds 4 parent    7     77.8  7.988e+01  -2.07799     0.358968
+#>  ds 4 parent   14     70.8  6.492e+01   5.88059    -1.218059
+#>  ds 4 parent   14     67.3  6.492e+01   2.38059    -0.493097
+#>  ds 4 parent   28     43.1  4.442e+01  -1.32411     0.377111
+#>  ds 4 parent   28     45.1  4.442e+01   0.67589    -0.192494
+#>  ds 4 parent   60     21.3  2.136e+01  -0.06143     0.030267
+#>  ds 4 parent   60     23.5  2.136e+01   2.13857    -1.053671
+#>  ds 4 parent   90     11.8  1.187e+01  -0.06548     0.046122
+#>  ds 4 parent   90     12.1  1.187e+01   0.23452    -0.165204
+#>  ds 4 parent  120      7.0  6.864e+00   0.13645    -0.124240
+#>  ds 4 parent  120      6.2  6.864e+00  -0.66355     0.604171
+#>  ds 4     m1    0      1.6  8.811e-13   1.60000    -2.433977
+#>  ds 4     m1    1      0.9  6.943e-01   0.20568    -0.293006
+#>  ds 4     m1    3      3.7  1.964e+00   1.73568    -2.215152
+#>  ds 4     m1    3      2.0  1.964e+00   0.03568    -0.045539
+#>  ds 4     m1    7      3.6  4.082e+00  -0.48184     0.523977
+#>  ds 4     m1    7      3.8  4.082e+00  -0.28184     0.306486
+#>  ds 4     m1   14      7.1  6.694e+00   0.40571    -0.373099
+#>  ds 4     m1   14      6.6  6.694e+00  -0.09429     0.086710
+#>  ds 4     m1   28      9.5  9.147e+00   0.35343    -0.283895
+#>  ds 4     m1   28      9.3  9.147e+00   0.15343    -0.123245
+#>  ds 4     m1   60      8.3  8.788e+00  -0.48803     0.399399
+#>  ds 4     m1   60      9.0  8.788e+00   0.21197    -0.173474
+#>  ds 4     m1   90      6.6  6.644e+00  -0.04431     0.040866
+#>  ds 4     m1   90      7.7  6.644e+00   1.05569    -0.973711
+#>  ds 4     m1  120      3.7  4.667e+00  -0.96735     1.010605
+#>  ds 4     m1  120      3.5  4.667e+00  -1.16735     1.219548
+#>  ds 5 parent    0    110.4  1.020e+02   8.37855    -1.161863
+#>  ds 5 parent    0    112.1  1.020e+02  10.07855    -1.397604
+#>  ds 5 parent    1     93.5  9.494e+01  -1.43722     0.212725
+#>  ds 5 parent    1     91.0  9.494e+01  -3.93722     0.582755
+#>  ds 5 parent    3     71.0  8.280e+01 -11.80256     1.974773
+#>  ds 5 parent    3     89.7  8.280e+01   6.89744    -1.154061
+#>  ds 5 parent    7     60.4  6.485e+01  -4.45291     0.923157
+#>  ds 5 parent    7     59.1  6.485e+01  -5.75291     1.192667
+#>  ds 5 parent   14     56.5  4.626e+01  10.24038    -2.821727
+#>  ds 5 parent   14     47.0  4.626e+01   0.74038    -0.204011
+#>  ds 5 parent   28     30.2  3.034e+01  -0.13506     0.051824
+#>  ds 5 parent   28     23.9  3.034e+01  -6.43506     2.469220
+#>  ds 5 parent   60     17.0  1.795e+01  -0.95206     0.525822
+#>  ds 5 parent   60     18.7  1.795e+01   0.74794    -0.413085
+#>  ds 5 parent   90     11.3  1.186e+01  -0.56163     0.395692
+#>  ds 5 parent   90     11.9  1.186e+01   0.03837    -0.027033
+#>  ds 5 parent  120      9.0  7.866e+00   1.13427    -0.975579
+#>  ds 5 parent  120      8.1  7.866e+00   0.23427    -0.201493
+#>  ds 5     m1    0      0.7 -4.263e-14   0.70000    -1.064865
+#>  ds 5     m1    1      3.0  3.169e+00  -0.16908     0.196384
+#>  ds 5     m1    1      2.6  3.169e+00  -0.56908     0.660990
+#>  ds 5     m1    3      5.1  8.455e+00  -3.35479     2.794486
+#>  ds 5     m1    3      7.5  8.455e+00  -0.95479     0.795325
+#>  ds 5     m1    7     16.5  1.577e+01   0.73235    -0.438460
+#>  ds 5     m1    7     19.0  1.577e+01   3.23235    -1.935208
+#>  ds 5     m1   14     22.9  2.202e+01   0.88393    -0.426673
+#>  ds 5     m1   14     23.2  2.202e+01   1.18393    -0.571482
+#>  ds 5     m1   28     22.2  2.399e+01  -1.79091     0.814583
+#>  ds 5     m1   28     24.4  2.399e+01   0.40909    -0.186073
+#>  ds 5     m1   60     15.5  1.872e+01  -3.21988     1.731175
+#>  ds 5     m1   60     19.8  1.872e+01   1.08012    -0.580725
+#>  ds 5     m1   90     14.9  1.383e+01   1.06749    -0.690500
+#>  ds 5     m1   90     14.2  1.383e+01   0.36749    -0.237710
+#>  ds 5     m1  120     10.9  1.004e+01   0.85568    -0.656897
+#>  ds 5     m1  120     10.4  1.004e+01   0.35568    -0.273054
# }
 
 

   

-- 
cgit v1.2.1