Bioequivalence and Bioavailability Forum

roman_max ☆ Russia, 2019-04-23 18:01 (2054 d 20:09 ago) Posting: # 20210 Views: 16,260	Graphing Mean PK profile [🇷 for BE/BA] Post reply
	Dear R-users, recently I received a request from Sponsor to represent mean PK profile in a box-and-whiskers fashion with application of a mean connection line in one graph. Guess, ggplot2 can do this job, but unfortunately I`m not so familiar with such sofisticated plot-making for PK profile. Can anyone share idea (R-code?) how to do it? How a data-set can be organized for this graph?

Shuanghe
★★

Spain,
2019-04-23 20:31
(2054 d 17:40 ago)

@ roman_max
Posting: # 20213
Views: 15,115

Graphing Mean PK profile

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Dear roman_max,

❝ Can anyone share idea (R-code?) how to do it? How a data-set can be organized for this graph?

Assuming that your data file of individual concentration dat_ind contain at least the following variables: subj, treat, time, conc, you can get mean profile data with

library(dplyr)

dat_mean <- dat_ind %>% 

  group_by(treat, time) %>%

  summarise(conc = mean(conc))

Obviously, time here should be the planned nominal time, not the actual sampling time. With ggplot you can have more or less what you asked for:

library(ggplot2)

p1 <- ggplot(data = dat_ind, aes(x = time, y = conc, color = treat)) +

  geom_point(aes(group = interaction(treat, time)), alpha = 0.5, shape = 1,

             position = position_jitter(width = 0.1, height = 0)) +

  geom_boxplot(aes(fill = treat, group = interaction(treat, time)), alpha = 0.3) +

  geom_line(data = dat_mean, size = 1.3)

The main idea is the group = interaction(treat, time). Feel free to modify the rest to better suit your needs (size/shape of the points etc). position_jitter() helps to avoid point overlapping (you have to specify height = 0 otherwise the data points will not reflect the true concentration value since some randomness will be introduced along y-axis by default) and the last line will add mean profiles with slightly bold lines.

—
All the best,
Shuanghe

roman_max ☆ Russia, 2019-04-24 14:29 (2053 d 23:42 ago) @ Shuanghe Posting: # 20221 Views: 15,134	Graphing Mean PK profile Post reply
	Dear Shuanghe, Today is a beautiful day Thank you very much for your help. I`ve reproduced the code and get what I wanted to see. Hope, Sponsor will be in the best feelings

Helmut
★★★

Vienna, Austria,
2019-04-24 00:23
(2054 d 13:48 ago)

@ roman_max
Posting: # 20214
Views: 15,175

Graphing Mean PK profile

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Hi roman_max,

❝ recently I received a request from Sponsor to represent mean PK profile in a box-and-whiskers fashion with application of a mean connection line in one graph.

The sponsor should re-consider this idea. Box-plots are nonparametric. For log-normal distributed data (which we likely have) the median is an estimate of the geometric mean. If we want to go this way, the arithmetic mean is not a good idea.

❝ Can anyone share idea (R-code?) how to do it? How a data-set can be organized for this graph?

An idea, yes. I borrowed mittyri’s simulation code. With real data work with the second data.frame.

C <- function(F=1, D, Vd, ka, ke, t) {

  C <- F*D/Vd*(ka/(ka - ke))*(exp(-ke*t) - exp(-ka*t))

  return(C)

}

Nsub     <- 24

D        <- 400

ka       <- 1.39

ka.omega <- 0.1

Vd       <- 1

Vd.omega <- 0.2

CL       <- 0.347

CL.omega <- 0.15

t        <- c(seq(0, 1, 0.25), seq(2,6,1), 8,10,12,16,24)

ke       <- CL/Vd

tmax     <- log((ka/ke)/(ka - ke))

Cmax     <- C(D=D, Vd=Vd, ka=ka, ke=ke, t=tmax)

LLOQ.pct <- 2 # LLOQ = 2% of theoretical Cmax

LLOQ     <- Cmax*LLOQ.pct/100

df1      <- data.frame(t=t)

for (j in 1:Nsub) {

  ka.sub <- ka * exp(rnorm(1, sd = sqrt(ka.omega)))

  Vd.sub <- Vd * exp(rnorm(1, sd = sqrt(Vd.omega)))

  CL.sub <- CL * exp(rnorm(1, sd = sqrt(CL.omega)))

  df1    <- cbind(df1, C(D=D, Vd=Vd.sub, ka=ka.sub, ke=CL.sub/Vd.sub, t=t))

  df1[which(df1[, j+1] < LLOQ), j+1] <- NA

}

names(df1)[2:(Nsub+1)] <- paste0("S.", 1:Nsub)

df2 <- data.frame(t(df1[-1]))

colnames(df2) <- df1[, 1]


names(df2) <- t

print(signif(df2, 3)) # show what we have

plot(x=t, y=rep(0, length(t)), type="n", log="y", xlim=range(t),

     ylim=range(df2, na.rm=TRUE), xlab="time",

     ylab="concentration", las=1)

for (j in seq_along(t)) {

  bx <- boxplot(df2[, j], plot=FALSE)

  if (bx$n > 0) bxp(bx, log="y", boxwex=0.25, at=t[j], axes=FALSE, add=TRUE)

}

Which gave in one run:

      0  0.25 0.5 0.75   1     2     3      4     5      6      8    10    12    16    24

S.1  NA 199.0 304  353 367 295.0 198.0 128.00  82.2  52.60  21.40  8.75    NA    NA    NA

S.2  NA 132.0 218  269 296 278.0 199.0 129.00  79.7  47.90  16.70  5.65    NA    NA    NA

S.3  NA  82.7 121  136 141 126.0 106.0  88.30  73.5  61.30  42.50 29.50 20.50  9.87    NA

S.4  NA 150.0 202  204 184  76.8  24.3   6.91    NA     NA     NA    NA    NA    NA    NA

S.5  NA 102.0 167  206 226 216.0 160.0 110.00  72.6  47.30  19.70  8.16    NA    NA    NA

S.6  NA 132.0 213  260 285 285.0 241.0 197.00 160.0 129.00  84.30 55.10 36.00 15.40    NA

S.7  NA  96.9 157  193 213 216.0 185.0 152.00 124.0 101.00  67.20 44.50 29.50 13.00    NA

S.8  NA  84.1 141  179 203 229.0 213.0 189.00 165.0 143.00 108.00 81.70 61.70 35.20 11.40

S.9  NA 183.0 283  332 349 296.0 211.0 146.00  99.5  67.90  31.50 14.60  6.80    NA    NA

S.10 NA  93.8 150  181 194 166.0 110.0  66.40  38.6  22.10   7.03    NA    NA    NA    NA

S.11 NA 148.0 236  284 304 261.0 176.0 109.00  65.9  39.10  13.60    NA    NA    NA    NA

S.12 NA  95.3 156  193 213 206.0 159.0 114.00  79.8  55.30  26.30 12.50  5.89    NA    NA

S.13 NA  69.3 120  157 182 214.0 197.0 166.00 135.0 108.00  67.40 41.80 25.90  9.91    NA

S.14 NA  73.8 118  144 157 157.0 133.0 109.00  89.2  72.70  48.30 32.10 21.30  9.43    NA

S.15 NA 245.0 383  453 481 419.0 304.0 213.00 147.0 101.00  48.10 22.90 10.90    NA    NA

S.16 NA  97.4 157  192 211 204.0 163.0 124.00  93.4  69.90  39.00 21.80 12.20    NA    NA

S.17 NA  71.9 119  149 167 179.0 160.0 136.00 115.0  96.50  67.90 47.80 33.60 16.60    NA

S.18 NA 133.0 203  232 236 159.0  80.0  35.90  15.1   6.10     NA    NA    NA    NA    NA

S.19 NA 209.0 307  340 338 226.0 127.0  68.00  36.2  19.20   5.39    NA    NA    NA    NA

S.20 NA 156.0 235  266 267 172.0  83.5  36.00  14.6   5.66     NA    NA    NA    NA    NA

S.21 NA 158.0 261  325 360 355.0 274.0 196.00 136.0  92.60  42.50 19.40  8.83    NA    NA

S.22 NA  97.0 163  206 233 248.0 210.0 165.00 127.0  96.30  54.90 31.20 17.70  5.69    NA

S.23 NA 114.0 182  220 240 240.0 208.0 175.00 147.0 123.00  86.70 60.90 42.80 21.20  5.17

S.24 NA 121.0 195  238 261 260.0 216.0 173.00 137.0 109.00  67.90 42.40 26.50 10.40    NA

The bad thing is that you have to use very narrow boxes in order to avoid overlaps (boxwex=0.25).

[image]

In my “bible” that’s called a high ink-to-information ratio* which is bad style. One option would be to draw a thick line instead of the box, a thin line for the whiskers, and smaller points for the outliers, e.g.,

plot(x=t, y=rep(0, length(t)), type="n", log="y", xlim=range(t),

     ylim=range(df2, na.rm=TRUE), xlab="time",

     ylab="concentration", las=1)

for (j in seq_along(t)) {

  bx <- boxplot(df2[, j], plot=FALSE)

  if (bx$n > 0) {

    lines(rep(t[j], 2), c(bx$stats[1, 1], bx$stats[5, 1]))

    lines(rep(t[j], 2), c(bx$stats[2, 1], bx$stats[4, 1]), lwd=3, col="gray50")

    points(t[j], bx$stats[3, 1], pch=3, cex=0.6)

    points(rep(t[j], length(bx$out)), bx$out, pch=1, cex=0.5)

  }

}

Add a line connecting the medians and you are doomed.

Tufte ER. The Visual Display of Quantitative Information. 2nd ed. Cheshire: Graphics Press; 2001.

Edit: Hey, Shuanghe – you were much faster!

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

nobody nothing 2019-04-24 13:23 (2054 d 00:47 ago) @ Helmut Posting: # 20215 Views: 14,945	Graphing Mean PK profile Post reply
	...if you want to plot T and R in one graph I would suggest "stacked" or "pseudo-3D" view, by adding/subtracting a few minutes to the actual time for T/R... — Kindest regards, nobody

Helmut
★★★

Vienna, Austria,
2019-04-24 13:49
(2054 d 00:21 ago)

@ nobody
Posting: # 20217
Views: 15,568

Graphing Mean PK profile

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Hi nobody,

❝ ...if you want to plot T and R in one graph I would suggest "stacked" or "pseudo-3D" view, by adding/subtracting a few minutes to the actual time for T/R...

I make it sometimes upon sponsor’s demand. Personally I think that such a plot is too “crowded”.

[image]

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

nobody nothing 2019-04-24 13:53 (2054 d 00:17 ago) @ Helmut Posting: # 20218 Views: 14,984	Graphing Mean PK profile Post reply
	..add some more minutes and keep the symbols smaller — Kindest regards, nobody

Helmut ★★★ Vienna, Austria, 2019-04-24 14:32 (2053 d 23:38 ago) @ nobody Posting: # 20222 Views: 15,029	Graphing Mean PK profile Post reply
	Hi nobody, ❝ ..add some more minutes and keep the symbols smaller Like this? ±10 instead of ±5 and symbols –40%: — Dif-tor heh smusma 🖖🏼 Довге життя Україна! Helmut Schütz The quality of responses received is directly proportional to the quality of the question asked. 🚮 Science Quotes

nobody nothing 2019-04-24 14:49 (2053 d 23:22 ago) @ Helmut Posting: # 20224 Views: 14,887	Graphing Mean PK profile Post reply
	I would prefer the blue ones on the right side, but otherwise: Yepp... — Kindest regards, nobody

roman_max
☆

Russia,
2019-04-24 14:36
(2053 d 23:35 ago)

@ Helmut
Posting: # 20223
Views: 14,946

Graphing Mean PK profile

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Dear Helmut,

thank you very much for the contribution to my knowledge :-)

Indeed, very useful.

❝ The sponsor should re-consider this idea. Box-plots are nonparametric. For log-normal distributed data (which we likely have) the median is an estimate of the geometric mean. If we want to go this way, the arithmetic mean is not a good idea.

Agree, but if it is easier for Sponsor to view and "understand" data, no problem.

Helmut
★★★

Vienna, Austria,
2019-04-24 15:50
(2053 d 22:21 ago)

@ roman_max
Posting: # 20225
Views: 15,035

Graphing Mean PK profile

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Hi roman_max,

❝ ❝ The sponsor should re-consider this idea. Box-plots are nonparametric. For log-normal distributed data (which we likely have) the median is an estimate of the geometric mean. If we want to go this way, the arithmetic mean is not a good idea.

❝

❝ Agree, but if it is easier for Sponsor to view and "understand" data, no problem.

Any kind of plot is problematic. Given, some guidelines require them (e.g., the Canadian guidance). We should be aware that such a plot gives just an impression and is not related with the assessment of BE.
I once received a deficiency letter asking for a clarification why in plots of geometric mean profiles the highest concentrations and their time points didn’t agree with the reported C_max/t_max. Well, C at any given time point has nothing to do with the individual C_max-values and their geometric mean. Oh, dear!
There’s another obstacle. How to deal with BQLs? If you set them to NA (in R) or keep them as a character-code (Phoenix/WinNonlin) you open Pandora’s box. Let’s have a look at the 16 h time point of my example:

loc.stat <- function(x, type, na.rm) {

  non.numerics    <- which(is.na(suppressWarnings(as.numeric(x))))

  x[non.numerics] <- NA

  x <- as.numeric(x)

  switch(type,

         arith.mean = round(mean(x, na.rm=na.rm), 2),

         median     = round(median(x, na.rm=na.rm), 2),

         geom.mean  = round(exp(mean(log(x), na.rm=na.rm)), 2),

         harm.mean  = round(length(x)/sum(1/x, na.rm=na.rm), 2))

}

C <- c(rep("BQL", 2), 9.87, rep("BQL", 2), 15.4, 13.0, 35.2,

       rep("BQL", 4), 9.91, 9.43, rep("BQL", 2), 16.6, rep("BQL", 4),

       5.69, 21.2, 10.4)

df <- data.frame(statistic=c(rep("arith.mean", 2), rep("median", 2),

                 rep("geom.mean", 2), rep("harm.mean", 2)),

                 na.rm=rep(c(FALSE, TRUE), 4),

                 location=NA, stringsAsFactors=FALSE)

for (j in 1:nrow(df)) {

  df$location[j] <- loc.stat(C, df$statistic[j], df$na.rm[j])

}

print(df, row.names=FALSE)



  statistic na.rm location

 arith.mean FALSE       NA

 arith.mean  TRUE    14.67

     median FALSE       NA

     median  TRUE    11.70

  geom.mean FALSE       NA

  geom.mean  TRUE    12.98

  harm.mean FALSE       NA

  harm.mean  TRUE    27.98 # not meaningful, only for completeness

Some people set all BQLs to zero in order to calculate the arithmetic mean. Others set the first BQL after t_max to LLOQ/2, and, and, and… There will always be a bias.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

nobody
nothing

2019-04-24 16:15
(2053 d 21:55 ago)

@ Helmut
Posting: # 20226
Views: 15,238

Graphing Mean PK profile

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❝ Some people set all BQLs to zero in order to calculate the arithmetic mean. Others set the first BQL after t_max to LLOQ/2, and, and, and… There will always be a bias.

How would you otherwise calculate the geo. mean profile?

And AUCtlast is a mess with different tlast for T and R and and and. Statistics is always some kind of abstraction. Do a spaghetti plot for T and R and individual T+R for each subject and you might get completely different "ideas" / insights...

—
Kindest regards, nobody

Helmut
★★★

Vienna, Austria,
2019-04-24 16:41
(2053 d 21:30 ago)

@ nobody
Posting: # 20227
Views: 15,618

Graphing Mean PK profile

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Hi nobody,

❝ ❝ Some people set all BQLs to zero in order to calculate the arithmetic mean. Others set the first BQL after t_max to LLOQ/2, and, and, and… There will always be a bias.

❝

❝ How would you otherwise calculate the geo. mean profile?

Tons of rules. Mine: If at any given time point ≥⅔ of concentrations are ≥LLOQ I calculate the geometric mean of those (i.e., exclude the BQLs). If less, I don’t calculate the geometric mean at all. Luckily in my studies the LLOQ was always lo_w enough. ;-)

Had a look at the Canadian guidance and the example given in the appendix. HC calculates the arithmetic (!) mean whilst treating BQLs as zero (Table A1-B/C, p.23/24). If a mean is <LLOQ, it is not shown in the plot (Figure 1, p.31).

Played a bit with the example (after correcting the typo 3723 → 37.23 which sits happily in the table for 25 years). R-code at the end.

                             method  0 0.33  0.67     1   1.5     2     3     4     6     8   12  16

         arithm.mean (BQL excluded)  0  NaN 60.44 73.28 82.85 70.94 49.62 29.09 17.19 10.38 6.56 NaN

             arithm.mean (BQL => 0)  0  0.0 45.33 73.28 82.85 70.94 49.62 29.09 17.19  6.49 1.64 0.0

arithm.mean (BQL => 0, NA if <LLOQ) NA   NA 45.33 73.28 82.85 70.94 49.62 29.09 17.19  6.49   NA  NA

        arithm.mean (BQL => LLOQ/2)  0  2.5 45.95 73.28 82.85 70.94 49.62 29.09 17.19  7.42 3.52 2.5

           geom.mean (BQL excluded)  0  NaN 39.58 57.55 71.98 61.44 45.24 26.08 14.98  9.74 6.51 NaN

          geom.mean (BQL => LLOQ/2)  0  2.5 19.84 57.55 71.98 61.44 45.24 26.08 14.98  5.85 3.18 2.5

geom.mean (if at least 2/3 >= LLOQ)  0   NA 39.58 57.55 71.98 61.44 45.24 26.08 14.98    NA   NA  NA

              median (BQL excluded)  0   NA 40.97 54.39 67.57 63.05 44.69 26.46 16.86  9.19 6.62  NA

             median (BQL => LLOQ/2)  0  2.5 33.24 54.39 67.57 63.05 44.69 26.46 16.86  6.84 2.50 2.5

Added some jitter to separate the lines.
Now what? I think everything (except arithmetic means) is OK. Coming up with sumfink which is <LLOQ? Hhm. As soon as we have a single value <LLOQ it might be that the estimate is <LLOQ as well (if all others are LLOQ). But how much? No idea.

Will submit a study to HC soon. Will report back how they like my approach. :lookaround:

❝ And AUCtlast is a mess with different tlast for T and R and and and.

Can’t agree more.

❝ Do a spaghetti plot for T and R and individual T+R for each subject and you might get completely different "ideas" / insights...

Yes and yes. Henning Blume always apologized when presenting (arithmetic) mean plots. I’m pissed when I get a report without spaghetti plots.

loc.stat <- function(x, type, na.rm) {

  non.numerics    <- which(is.na(suppressWarnings(as.numeric(x))))

  x[non.numerics] <- NA

  x <- as.numeric(x)

  switch(type,

         arith.mean = round(mean(x, na.rm=na.rm), 2),

         median     = round(median(x, na.rm=na.rm), 2),

         geom.mean  = round(exp(mean(log(x), na.rm=na.rm)), 2))

}

t <- c(0, 0.33, 0.67, 1, 1.5, 2, 3, 4, 6, 8, 12, 16)

LLOQ <- 5

df <- data.frame(ID=c("A", "B", "C", "E", "F", "G", "H", "I",

                      "K", "L", "M", "N", "O", "P", "Q", "R"),

                 t.1=rep(0, 16), t.2=rep("BQL", 16),

                 t.3=c(116.40,  88.45,  "BQL",  37.23,  29.25,   6.89, 113.50, 181.90,

                        42.71,  14.29,   8.21,  47.20,  "BQL",  39.23,  "BQL",  "BQL"),

                 t.4=c(124.60, 121.40,  95.57,  37.26,  62.88,  50.04, 218.70, 135.80,

                        58.75,  21.32,  48.87,  34.90,  20.35,  86.29,  30.86,  24.84),

                 t.5=c(126.20, 206.90, 122.80,  35.90,  64.26,  55.27, 125.80,  96.51,

                        59.68,  24.32,  57.05,  34.90,  70.88,  97.46,  88.38,  59.27),

                 t.6=c(107.60, 179.00, 103.20,  28.87,  84.67,  51.68,  69.77,  90.50,

                        54.37,  25.56,  56.32,  24.19,  70.60,  52.26,  37.67,  98.82),

                 t.7=c( 45.65,  84.53, 101.70,  28.48,  45.21,  38.58,  45.03,  62.58,

                        44.35,  25.51,  42.08,  20.11,  70.38,  40.53,  29.28,  69.98),

                 t.8=c( 33.22,  40.02,  57.65,  25.10,  25.05,  26.19,  32.78,  30.43,

                        22.94,  10.49,  24.79,   8.08,  40.51,  26.74,  14.99,  46.50),

                 t.9=c( 16.11,  38.01,  23.85,  24.91,  17.18,   7.79,  18.55,  18.50,

                        11.58,   5.49,  16.54,   7.27,  26.93,  12.54,   6.38,  23.46),

                t.10=c( 12.60,  15.12,  14.59,   6.72,   8.47,  "BQL",   5.42,  "BQL",

                         6.95,  "BQL",  15.81,  "BQL",   8.20,  "BQL",  "BQL",   9.91),

                t.11=c( "BQL",   5.39,   6.29,  "BQL",  "BQL",  "BQL",  "BQL",  "BQL",

                        "BQL",  "BQL",   7.60,  "BQL",  "BQL",  "BQL",  "BQL",   6.96),

                t.12=rep("BQL", 16), stringsAsFactors=FALSE)

loc <- data.frame(method=c("arithm.mean (BQL excluded)",

                           "arithm.mean (BQL => 0)",

                           "arithm.mean (BQL => 0, NA if <LLOQ)",

                           "arithm.mean (BQL => LLOQ/2)",

                           "geom.mean (BQL excluded)",

                           "geom.mean (BQL => LLOQ/2)",

                           "geom.mean (if at least 2/3 >= LLOQ)",

                           "median (BQL excluded)",

                           "median (BQL => LLOQ/2)"),

                  t.1=NA, t.2=NA, t.3=NA, t.4=NA, t.5=NA, t.6=NA,

                  t.7=NA, t.8=NA, t.9=NA, t.10=NA, t.11=NA, t.12=NA,

                  stringsAsFactors=FALSE)

names(df)[2:13] <- names(loc)[2:13] <- t

for (j in 2:ncol(df)) {

   x <- df[, j]


   loc[1, j] <- loc.stat(x, "arith.mean", TRUE)

   y <- x

   y[which(x == "BQL")] <- 0

   loc[2, j] <- loc.stat(y, "arith.mean", FALSE)

   ifelse(loc[2, j] >= LLOQ, loc[3, j] <- loc[2, j], loc[3, j] <- NA)

   y <- x

   y[which(x == "BQL")] <- LLOQ/2

   loc[4, j] <- loc.stat(y, "arith.mean", FALSE)

   loc[5, j] <- loc.stat(x, "geom.mean", TRUE)

   loc[6, j] <- loc.stat(y, "geom.mean", FALSE)

   if (length(which(x != "BQL")) >= nrow(df)*2/3) {

      loc[7, j] <- loc[4, j]


   } else {

      loc[7, j] <- NA

   }

   loc[8, j] <- loc.stat(x, "median", TRUE)

   loc[9, j] <- loc.stat(y, "median", FALSE)

}

clr <- c("black", "blue", "pink", "red", "darkgreen",

         "gray50", "magenta", "orange", "gold")

print(df, row.names=FALSE);print(loc, row.names=FALSE)

plot(t, loc[1, 2:ncol(df)], type="l", las=1, col=clr[1], lwd=2,

     ylim=c(0, max(loc[, 2:ncol(df)], na.rm=TRUE)),

     xlab="time", ylab="concentration")

abline(h=LLOQ, lty=2)

grid(); rug(t)

for (j in 2:9) {

  lines(jitter(t, factor=1.5), loc[j, 2:ncol(df)], col=clr[j], lwd=2)

}

legend("topright", bg="white", inset=0.02, title="method",

       legend=loc[, 1], lwd=2, col=clr, cex=0.9)

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

Ohlbe ★★★ France, 2019-04-25 14:47 (2052 d 23:24 ago) @ Helmut Posting: # 20228 Views: 15,089	Pasta Post reply
	Dear Helmut, ❝ I’m pissed when I get a report without spaghetti plots. And you complain that overlaying two plots of means is too crowded I find spaghetti plots rather difficult to read with more than 30 subjects, or even less depending on what they look like... — Regards Ohlbe

nobody nothing 2019-04-25 16:36 (2052 d 21:35 ago) @ Ohlbe Posting: # 20230 Views: 14,767	Pasta Post reply
	I don't read 'em, I have a quick look, "see" the variability/"outliers" and job done. Totally correct that more than 36 is hard to see anything, but if all profiles are pretty close that's in important info, too, imho. ' — Kindest regards, nobody

Helmut
★★★

Vienna, Austria,
2019-04-25 16:39
(2052 d 21:32 ago)

@ Ohlbe
Posting: # 20231
Views: 15,179

Spaghetti Viennese

Post reply

Dear Ohlbe,

❝ ❝ I’m pissed when I get a report without spaghetti plots.

❝

❝ And you complain that overlaying two plots of means is too crowded ;-)

Nope. Overlaying two plots ±SD. I’m fine with one plot of both T and R plus two showing the treatments separately (geom. mean ±SD).

❝ I find spaghetti plots rather difficult to read with more than 30 subjects, or even less depending on what they look like...

You get used to it. ;-)

Our brains are great in pattern-recognition. Two examples (amoxicillin 1 g tablets, different tests but same reference in both studies) of Blume/Mutschler*

Study metric 90% CI ──────────────────────── 1 AUC 92 – 111% Cmax 87 – 109% 2 AUC 82 – 99% Cmax 75 – 99%

Both studies passed (limits for AUC 80–125% and for C_max 70–143%).
@ Mittyri: Good ol’ days! :waving:

I would say:

Higher concentrations in the second study don’t bother me. Different subjects. The analytical method in the second one was 5times more sensitive and slightly more precise. The former explains why in the first study profiles in some subjects could not be measured up to the last sampling time.
In the second study both treatments were absorbed slightly faster than in the first one.
Now it gets interesting. In the mean curves we see that in the second study the profiles close to C_max are more flat (independent from the formulation). However, individual profiles (yep, the pasta) of the reference in both studies were similar whereas the ones of the tests not. I prefer the second test.

This loose leaf edition (~2,000 pages in 4 volumes, 1989–1996) was prepared for the ABDA („Bundesvereinigung Deutscher Apotherverbände” – Federal Union of German Associations of Pharmacists) to provide pharmacists a means to decide which generic to chose. Already in 1992 ⅓ of all German pharmacists completed a training on BE provided by the ZL (“Zentrallaboratorium Deutscher Apotheker” – Central Laboratory of German Pharmacists). Compare that to the FDA’s Orange Book…

Blume H, Mutschler E, editors. Bioäquivalenz. Qualitätsbewertung wirkstoffgleicher Fertigarzneimittel. Frankurt/Main: Govi-Verlag; 6. Ergänzungslieferung 1996.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

nobody nothing 2019-04-25 17:08 (2052 d 21:03 ago) @ Helmut Posting: # 20232 Views: 14,794	Spaghetti Viennese Post reply
	❝ Blume H, Mutschler E, editors. Bioäquivalenz. Qualitätsbewertung wirkstoffgleicher Fertigarzneimittel. Frankurt/Main: Govi-Verlag; 6. Ergänzungslieferung 1996. WOW, somebody bought that! — Kindest regards, nobody

Helmut
★★★

Vienna, Austria,
2019-04-25 17:32
(2052 d 20:39 ago)

@ nobody
Posting: # 20233
Views: 14,822

OT: Blume/Mutschler

Post reply

Hi nobody,

❝ WOW, somebody bought that! :-D

Though I don’t use it any more I still like the idea behind. At a conference in Toronto 1992 I showed the first file to guys (no gals at that time) of the FDA and told the story that ⅓ of German pharmacists are already trained on BE. Jaws dropped.

As an ol’ salt you know it but for the others: The ZL sent polite letters to manufacturers asking for information (the original evaluation which lead to the approval as well as study data allowing recalculation). Observations:

Some companies refused. Consequently in the collection there was an empty page stating just the name of the product and that the company didn’t provide any information. Very bad idea.
Comparing different products you could see that the same study was used numerous times. Hey, the file was sold.
Sometimes you see a lot of rotten pasta and the one “perfect” study. At that time was what is now.
Sometimes the reported CI didn’t match the calculation of the ZL.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

nobody
nothing

2019-04-25 17:43
(2052 d 20:28 ago)

@ Helmut
Posting: # 20234
Views: 14,757

OT: Blume/Mutschler

Post reply

Yepp, I know the story around that in detail ;-)

It was a move to couple science with politics (health care, pharmacists positioning as the "medicines expert"). Unfortunately this didn't work out, nowadays the health insurance buys the cheapest and decides which generic the patient gets. It's a shame...

RE: Replies from manufacturers. Not that different from today. In EU you still have only patchy Ass Reps from EMA, compared to the data released by FDA on products after MA granted.

Selling BE-studies+product was a fine business model for some time, some guys got rich and big with that. Quality of data has been an issue as long as there is any data around.... ;-)

—
Kindest regards, nobody

d_labes
★★★

Berlin, Germany,
2019-04-25 21:59
(2052 d 16:12 ago)

@ Helmut
Posting: # 20236
Views: 14,786

A lie is a lie is a lie ...

Post reply

Dear All,
especially the contributors to this thread.

I have a simple opinion about that mean PK profile graphs:
Whatever sophisticated group statistics underlying such mean profile you choose, whatever sophistic rules regarding missings and / or values below LLOQ, whatever sophistic graphical effects
you choose - you end with a statistical lie.
A lie
is a lie
is a lie ...

Thus my recommendation: Don't invest too many Gehirnschmalz (brain power).
Try to go without them.
And since that unfortunately doesn't function in many cases, as I know of course, choose a simple effortless solution and go with that. The Blume/Mutschler graphs shown in Helmuts post point in the correct direction.
I only had some seldom requests from some smart alecs to change the graphs. If this happens it is early enough to invest some grey matter.

—
Regards,

Detlew

Graphing Mean PK profile [🇷 for BE/BA]

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Graphing Mean PK profile

Pasta

Pasta

Spaghetti Viennese

Spaghetti Viennese

OT: Blume/Mutschler

OT: Blume/Mutschler

A lie is a lie is a lie ...