Open mtorchiano opened 3 years ago
Possible MWE
library(lmPerm)
# f = cut(rnorm(100),3,c("A","B","C"))
f = c("B", "B", "B", "B", "B", "B", "C", "C", "B", "C", "C", "B",
"A", "B", "B", "C", "C", "C", "B", "B", "B", "C", "B", "C", "B",
"B", "B", "B", "C", "B", "B", "B", "B", "B", "B", "B", "C", "B",
"B", "B", "B", "B", "C", "B", "B", "B", "C", "A", "B", "B", "B",
"C", "B", "C", "C", "C", "C", "B", "B", "B", "C", "B", "B", "B",
"B", "A", "A", "C", "B", "C", "B", "B", "A", "C", "B", "B", "C",
"C", "B", "B", "C", "C", "B", "C", "C", "B", "C", "C", "B", "B",
"C", "A", "B", "B", "B", "B", "C", "B", "C", "B")
#y = rnorm(100)+as.numeric(factor(f))+10
y = c(12.256065413759, 10.2338690690724, 12.7342274344284, 12.9188818361194,
11.2425645720792, 11.9191845873998, 13.4621700228714, 13.0280296698856,
11.5701046428484, 13.6354826581922, 13.4803913180852, 13.8555835211227,
10.0397561235053, 10.4557730038743, 12.6669319488538, 14.2971956572883,
13.8104686954262, 13.2160674005093, 13.6428077904016, 10.5912079616502,
11.335366008502, 11.9816214335981, 10.606625131425, 10.9083906068353,
10.6571749383987, 12.1377338717305, 10.0989543617672, 11.9654884400516,
12.9869458943188, 11.8411350225723, 11.7889021775581, 10.6235102833348,
12.4227771489572, 12.9425350520532, 11.845440836176, 12.926300807778,
12.6844282127005, 12.6840023540173, 12.2222128585972, 13.0224324226194,
10.9950045205357, 11.317472679311, 14.0893239318522, 11.0031393138157,
12.6120461723261, 11.6373970060832, 13.8067617775476, 10.0986571048258,
10.2697366004439, 11.2442277288498, 11.6356936364825, 13.0613175776661,
12.8016154914051, 13.3038144647712, 11.7808520680228, 14.5061825851365,
13.7854692387179, 12.1645436170462, 12.4507728265225, 10.9405173566993,
14.4545789023988, 12.866918957798, 10.3498418896696, 12.3013283988246,
9.57332217420656, 11.3331405673985, 11.4496638391074, 13.6839878501498,
11.5518141714801, 12.2701031757756, 10.1929479316683, 11.5796756486091,
10.2088585268213, 11.6666759982722, 13.3943982286299, 11.3526453211655,
13.6792439062291, 12.1832351415481, 10.7320906121624, 11.4806682174883,
12.0755897805694, 12.0025970240562, 10.3304369076126, 13.8170431953706,
11.3944912844128, 12.0743252805281, 12.5481848110357, 11.9872187712327,
11.0795021866822, 12.2286602012202, 13.6946529193845, 10.7843432460277,
12.8727044894008, 11.4879130174715, 11.8748751397884, 12.1748751329611,
13.138613540319, 12.993092576695, 11.4344002539369, 12.1081407650721
)
mdl = lmp(y ~ f)
s = summary(mdl)
s ## gives p <2e-16 *** for factor f1
s$coefficients["f1",3] == 0 ## TRUE, coefficient is stored as 0
MWE from original reporter:
### LIBRARIES
library("tidyverse")
library("lmPerm")
library("car")
######################################################
### DATAFRAME
pces <- read.csv("pces.csv", header=TRUE, na.strings = ".")
######################################################
### MODEL
### All predictor and response variables are continuous.
set.seed(1)
m3 <- lmPerm::lmp(trait.value ~ temp.warmest.qt + precip.warmest.qt, data=pces, perm="Prob", center=FALSE, seqs=FALSE)
######################################################
summary(m3)
### Prints output (as expected).
######################################################
summary(m3)$coefficients
### Prints coefficients, but p-values are rounded to 0.
######################################################
summary(m3)$coefficients %>% data.frame()
### Prints coefficients and converts them to object/data frame, but p-values are still rounded to 0.
### Rounding of p-values to 0 thus seems unrelated to print or format in summary().
######################################################
anova(m3)
### Prints anova table (as expected).
######################################################
anova(m3) %>% data.frame()
### Prints anova table, but cannot convert it to object/data frame (see last line).
######################################################
car::Anova(m3, type=3)
### I have not seen any documentation where car::Anova() is used on lmp object.
### Can car::Anova() be used on an lmp object? I do want unique SS (e.g. seqs=FALSE).
### Either way, perhaps this is an interesting point of comparison regarding how the lmp object behaves with different functions.
### Also note how the p-values are different here compared to above.
######################################################
car::Anova(m3, type=3) %>% data.frame()
### Prints anova table and converts it to object/data frame.
######################################################
data for the example pces.csv
"country","pop","line","trait.value","temp.warmest.qt","precip.warmest.qt"
"USA","ALA","ALA01",25,20.1,341
"USA","ALA","ALA03",21,20.1,341
"USA","ALA","ALA04",21,20.1,341
"USA","ALA","ALA05",20,20.1,341
"USA","ALA","ALA06",21,20.1,341
"USA","ALA","ALA07",22,20.1,341
"USA","ALA","ALA08",22,20.1,341
"USA","ALA","ALA09",21,20.1,341
"USA","ALA","ALA11",23,20.1,341
"USA","ALA","ALA12",27,20.1,341
"USA","ALA","ALA14",20,20.1,341
"USA","ALA","ALA15",28,20.1,341
"USA","ALA","ALA16",22,20.1,341
"USA","ALA","ALA17",21,20.1,341
"USA","ALA","ALA18",21,20.1,341
"USA","ALA","ALA20",21,20.1,341
"USA","ALA","ALA21",22,20.1,341
"USA","ALA","ALA22",21,20.1,341
"USA","ALA","ALA23",22,20.1,341
"USA","ALA","ALA24",22,20.1,341
"USA","ARM","ARM01",20,19.9,297
"USA","ARM","ARM03",21,19.9,297
"USA","ARM","ARM04",20,19.9,297
"USA","ARM","ARM05",22,19.9,297
"USA","ARM","ARM08",19,19.9,297
"USA","ARM","ARM11",19,19.9,297
"USA","ARM","ARM13",19,19.9,297
"USA","ARM","ARM14",18,19.9,297
"USA","ARM","ARM15",21,19.9,297
"USA","ARM","ARM16",21,19.9,297
"USA","ARM","ARM19",31,19.9,297
"USA","ARM","ARM21",27,19.9,297
"USA","ARM","ARM22",22,19.9,297
"USA","ARM","ARM23",25,19.9,297
"USA","ARM","ARM25",21,19.9,297
"USA","ARM","ARM27",20,19.9,297
"USA","ARM","ARM29",19,19.9,297
"USA","ARM","ARM34",21,19.9,297
"USA","ARM","ARM35",21,19.9,297
"USA","AST","AST01",22,19.1,263
"USA","AST","AST03",23,19.1,263
"USA","AST","AST04",23,19.1,263
"USA","AST","AST05",25,19.1,263
"USA","AST","AST06",24,19.1,263
"USA","AST","AST08",25,19.1,263
"USA","AST","AST10",30,19.1,263
"USA","AST","AST11",22,19.1,263
"USA","AST","AST12",38,19.1,263
"USA","AST","AST13",25,19.1,263
"USA","AST","AST16",21,19.1,263
"USA","AST","AST18",34,19.1,263
"USA","AST","AST20",23,19.1,263
"USA","AST","AST21",33,19.1,263
"USA","AST","AST22",24,19.1,263
"USA","AST","AST23",23,19.1,263
"USA","AST","AST24",25,19.1,263
"USA","AST","AST29",20,19.1,263
"USA","AST","AST32",23,19.1,263
"USA","AST","AST33",22,19.1,263
"USA","BRL","BRL02",21,20.2,306
"USA","BRL","BRL03",21,20.2,306
"USA","BRL","BRL07",22,20.2,306
"USA","BRL","BRL09",20,20.2,306
"USA","BRL","BRL14",23,20.2,306
"USA","BRL","BRL16",24,20.2,306
"USA","BRL","BRL17",22,20.2,306
"USA","BRL","BRL19",20,20.2,306
"USA","BRL","BRL20",19,20.2,306
"USA","BRL","BRL22",20,20.2,306
"USA","BRL","BRL23",21,20.2,306
"USA","BRL","BRL25",20,20.2,306
"USA","BRL","BRL26",19,20.2,306
"USA","BRL","BRL33",20,20.2,306
"USA","DUM","DUM01",19,19,300
"USA","DUM","DUM02",19,19,300
"USA","DUM","DUM04",21,19,300
"USA","DUM","DUM05",21,19,300
"USA","DUM","DUM07",21,19,300
"USA","DUM","DUM08",20,19,300
"USA","DUM","DUM11",19,19,300
"USA","DUM","DUM12",18,19,300
"USA","DUM","DUM13",18,19,300
"USA","DUM","DUM14",19,19,300
"USA","DUM","DUM15",21,19,300
"USA","DUM","DUM16",19,19,300
"USA","DUM","DUM17",20,19,300
"USA","DUM","DUM19",20,19,300
"USA","DUM","DUM20",21,19,300
"USA","DUM","DUM21",19,19,300
"USA","DUM","DUM22",20,19,300
"USA","DUM","DUM24",20,19,300
"USA","DUM","DUM25",18,19,300
"USA","DUM","DUM26",20,19,300
"USA","DUM","DUM29",21,19,300
"USA","ELK","ELK01",69,22.8,311
"USA","ELK","ELK03",60,22.8,311
"USA","ELK","ELK04",65,22.8,311
"USA","ELK","ELK05",64,22.8,311
"USA","ELK","ELK06",61,22.8,311
"USA","ELK","ELK08",65,22.8,311
"USA","ELK","ELK09",65,22.8,311
"USA","ELK","ELK10",64,22.8,311
"USA","ELK","ELK11",61,22.8,311
"USA","ELK","ELK14",67,22.8,311
"USA","ELK","ELK15",67,22.8,311
"USA","ELK","ELK16",65,22.8,311
"USA","ELK","ELK17",57,22.8,311
"USA","ELK","ELK20",68,22.8,311
"USA","ELK","ELK21",67,22.8,311
"USA","ELK","ELK22",59,22.8,311
"USA","ELK","ELK23",65,22.8,311
"USA","ELK","ELK24",66,22.8,311
"USA","ELK","ELK26",66,22.8,311
"USA","ELK","ELK30",67,22.8,311
"USA","FOS","FOS06",22,20.9,342
"USA","FOS","FOS08",22,20.9,342
"USA","FOS","FOS09",21,20.9,342
"USA","FOS","FOS10",22,20.9,342
"USA","FOS","FOS13",22,20.9,342
"USA","FOS","FOS14",21,20.9,342
"USA","FOS","FOS16",21,20.9,342
"USA","FOS","FOS18",23,20.9,342
"USA","FOS","FOS24",19,20.9,342
"USA","FOS","FOS25",19,20.9,342
"USA","FOS","FOS26",21,20.9,342
"USA","FOS","FOS28",20,20.9,342
"USA","FOS","FOS30",21,20.9,342
"USA","FOS","FOS32",21,20.9,342
"USA","FOS","FOS33",21,20.9,342
"USA","FOS","FOS35",19,20.9,342
"USA","FOS","FOS40",22,20.9,342
"USA","FOS","FOS42",26,20.9,342
"USA","FOS","FOS43",21,20.9,342
"USA","FRE.R","FRE.R02",32,21.7,315
"USA","FRE.R","FRE.R03",33,21.7,315
"USA","FRE.R","FRE.R04",33,21.7,315
"USA","FRE.R","FRE.R06",32,21.7,315
"USA","FRE.R","FRE.R07",86,21.7,315
"USA","FRE.R","FRE.R08",94,21.7,315
"USA","FRE.R","FRE.R12",82,21.7,315
"USA","FRE.R","FRE.R13",84,21.7,315
"USA","FRE.R","FRE.R14",93,21.7,315
"USA","FRE.R","FRE.R16",98,21.7,315
"USA","FRE.R","FRE.R19",57,21.7,315
"USA","FRE.R","FRE.R20",86,21.7,315
"USA","FRE.R","FRE.R21",35,21.7,315
"USA","FRE.R","FRE.R23",31,21.7,315
"USA","FRE.R","FRE.R30",76,21.7,315
"USA","FRE.R","FRE.R31",24,21.7,315
"USA","FRE.R","FRE.R33",82,21.7,315
"USA","FRE.R","FRE.R34",32,21.7,315
"USA","FRE.R","FRE.R37",92,21.7,315
"USA","FRE.R","FRE.R38",20,21.7,315
"USA","GRT","GRT01",58,23.6,280
"USA","GRT","GRT02",79,23.6,280
"USA","GRT","GRT03",71,23.6,280
"USA","GRT","GRT05",81,23.6,280
"USA","GRT","GRT08",68,23.6,280
"USA","GRT","GRT09",107,23.6,280
"USA","GRT","GRT10",58,23.6,280
"USA","GRT","GRT11",77,23.6,280
"USA","GRT","GRT12",99,23.6,280
"USA","GRT","GRT13",76,23.6,280
"USA","GRT","GRT14",84,23.6,280
"USA","GRT","GRT17",75,23.6,280
"USA","GRT","GRT18",82,23.6,280
"USA","GRT","GRT19",73,23.6,280
"USA","GRT","GRT20",78,23.6,280
"USA","GRT","GRT22",100,23.6,280
"USA","GRT","GRT23",84,23.6,280
"USA","GRT","GRT25",103,23.6,280
"USA","GRT","GRT27",103,23.6,280
"USA","GRT","GRT29",82,23.6,280
"USA","JAM","JAM01",21,19.7,298
"USA","JAM","JAM02",21,19.7,298
"USA","JAM","JAM03",20,19.7,298
"USA","JAM","JAM04",20,19.7,298
"USA","JAM","JAM05",20,19.7,298
"USA","JAM","JAM07",21,19.7,298
"USA","JAM","JAM08",20,19.7,298
"USA","JAM","JAM09",22,19.7,298
"USA","JAM","JAM13",21,19.7,298
"USA","JAM","JAM14",20,19.7,298
"USA","JAM","JAM16",20,19.7,298
"USA","JAM","JAM18",21,19.7,298
"USA","JAM","JAM19",22,19.7,298
"USA","JAM","JAM20",20,19.7,298
"USA","JAM","JAM22",21,19.7,298
"USA","JAM","JAM31",21,19.7,298
"USA","JAM","JAM34",21,19.7,298
"USA","JOK","JOK04",21,20.6,346
"USA","JOK","JOK08",22,20.6,346
"USA","JOK","JOK09",22,20.6,346
"USA","JOK","JOK11",34,20.6,346
"USA","JOK","JOK12",19,20.6,346
"USA","JOK","JOK16",21,20.6,346
"USA","JOK","JOK18",20,20.6,346
"USA","JOK","JOK19",20,20.6,346
"USA","JOK","JOK21",23,20.6,346
"USA","JOK","JOK23",19,20.6,346
"USA","JOK","JOK25",20,20.6,346
"USA","JOK","JOK30",20,20.6,346
"USA","JOK","JOK32",21,20.6,346
"USA","JOK","JOK33",21,20.6,346
"USA","JOK","JOK34",20,20.6,346
"USA","JOK","JOK37",21,20.6,346
"USA","JOK","JOK38",20,20.6,346
"USA","JOK","JOK39",20,20.6,346
"USA","JOK","JOK42",19,20.6,346
"USA","JOK","JOK49",21,20.6,346
"USA","SUS","SUS01",60,22.8,317
"USA","SUS","SUS07",65,22.8,317
"USA","SUS","SUS08",67,22.8,317
"USA","SUS","SUS10",59,22.8,317
"USA","SUS","SUS11",76,22.8,317
"USA","SUS","SUS13",75,22.8,317
"USA","SUS","SUS15",66,22.8,317
"USA","SUS","SUS17",63,22.8,317
"USA","SUS","SUS21",67,22.8,317
"USA","SUS","SUS23",69,22.8,317
"USA","SUS","SUS26",66,22.8,317
"USA","SUS","SUS27",67,22.8,317
"USA","SUS","SUS29",60,22.8,317
"USA","SUS","SUS32",67,22.8,317
"USA","SUS","SUS34",64,22.8,317
"USA","SUS","SUS37",67,22.8,317
"USA","SUS","SUS41",72,22.8,317
"USA","SUS","SUS43",57,22.8,317
"USA","SUS","SUS47",74,22.8,317
"USA","SUS","SUS50",67,22.8,317
"USA","TRO","TRO03",29,21.6,331
"USA","TRO","TRO04",24,21.6,331
"USA","TRO","TRO09",33,21.6,331
"USA","TRO","TRO12",31,21.6,331
"USA","TRO","TRO14",29,21.6,331
"USA","TRO","TRO18",22,21.6,331
"USA","TRO","TRO19",20,21.6,331
"USA","TRO","TRO20",32,21.6,331
"USA","TRO","TRO21",31,21.6,331
"USA","TRO","TRO24",31,21.6,331
"USA","TRO","TRO25",22,21.6,331
"USA","TRO","TRO30",30,21.6,331
"USA","TRO","TRO31",33,21.6,331
"USA","TRO","TRO32",31,21.6,331
"USA","TRO","TRO33",30,21.6,331
"USA","TRO","TRO36",32,21.6,331
"USA","TRO","TRO39",32,21.6,331
"USA","TRO","TRO40",31,21.6,331
"USA","TRO","TRO43",24,21.6,331
"USA","TRO","TRO45",30,21.6,331
"USA","TYL","TYL02",31,22.6,327
"USA","TYL","TYL04",32,22.6,327
"USA","TYL","TYL08",33,22.6,327
"USA","TYL","TYL11",32,22.6,327
"USA","TYL","TYL12",33,22.6,327
"USA","TYL","TYL15",33,22.6,327
"USA","TYL","TYL16",31,22.6,327
"USA","TYL","TYL18",32,22.6,327
"USA","TYL","TYL20",30,22.6,327
"USA","TYL","TYL23",36,22.6,327
"USA","TYL","TYL24",29,22.6,327
"USA","TYL","TYL26",68,22.6,327
"USA","TYL","TYL28",31,22.6,327
"USA","TYL","TYL33",82,22.6,327
"USA","TYL","TYL38",21,22.6,327
"USA","TYL","TYL40",75,22.6,327
"USA","TYL","TYL41",22,22.6,327
"USA","TYL","TYL42",21,22.6,327
"USA","TYL","TYL43",81,22.6,327
"USA","TYL","TYL45",32,22.6,327
"USA","WAD","WAD01",21,21.2,290
"USA","WAD","WAD02",21,21.2,290
"USA","WAD","WAD03",20,21.2,290
"USA","WAD","WAD10",21,21.2,290
"USA","WAD","WAD11",19,21.2,290
"USA","WAD","WAD17",20,21.2,290
"USA","WAD","WAD19",22,21.2,290
"USA","WAD","WAD23",20,21.2,290
"USA","WAD","WAD24",22,21.2,290
"USA","WAD","WAD25",20,21.2,290
"USA","WAD","WAD26",20,21.2,290
"USA","WAD","WAD27",21,21.2,290
"USA","WAD","WAD28",21,21.2,290
"USA","WAD","WAD29",21,21.2,290
"USA","WAD","WAD32",27,21.2,290
"USA","WAD","WAD34",21,21.2,290
"USA","WIL","WIL01",32,23.7,279
"USA","WIL","WIL02",31,23.7,279
"USA","WIL","WIL03",32,23.7,279
"USA","WIL","WIL04",34,23.7,279
"USA","WIL","WIL05",31,23.7,279
"USA","WIL","WIL06",89,23.7,279
"USA","WIL","WIL07",104,23.7,279
"USA","WIL","WIL08",32,23.7,279
"USA","WIL","WIL09",31,23.7,279
"USA","WIL","WIL10",102,23.7,279
"USA","WIL","WIL11",103,23.7,279
"USA","WIL","WIL13",31,23.7,279
"USA","WIL","WIL14",91,23.7,279
"USA","WIL","WIL15",93,23.7,279
"USA","WIL","WIL16",106,23.7,279
"USA","WIL","WIL17",93,23.7,279
"USA","WIL","WIL19",33,23.7,279
"USA","WIL","WIL20",31,23.7,279
"USA","WIL","WIL21",107,23.7,279
"USA","WIL","WIL22",107,23.7,279
"USA","WTE","WTE02",31,22.8,307
"USA","WTE","WTE03",31,22.8,307
"USA","WTE","WTE04",37,22.8,307
"USA","WTE","WTE07",38,22.8,307
"USA","WTE","WTE09",90,22.8,307
"USA","WTE","WTE10",33,22.8,307
"USA","WTE","WTE11",30,22.8,307
"USA","WTE","WTE12",31,22.8,307
"USA","WTE","WTE13",37,22.8,307
"USA","WTE","WTE18",25,22.8,307
"USA","WTE","WTE20",31,22.8,307
"USA","WTE","WTE21",31,22.8,307
"USA","WTE","WTE22",27,22.8,307
"USA","WTE","WTE25",22,22.8,307
"USA","WTE","WTE26",24,22.8,307
"USA","WTE","WTE27",25,22.8,307
"USA","WTE","WTE29",32,22.8,307
"USA","WTE","WTE33",33,22.8,307
"USA","WTE","WTE36",21,22.8,307
Issue report from email.
I am using anova() and summary() functions on an lmp object. These functions work; output is generated. The problem is that I cannot save the output (as a data frame) where small p-values are not rounded to 0.